Morgan Stanley Institutional Fund Trust NCSR Certified annual shareholder report (management investment company)

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM N-CSR

CERTIFIED SHAREHOLDER REPORT OF REGISTERED
MANAGEMENT INVESTMENT COMPANIES

Investment Company Act file number			811-03980

Morgan Stanley Institutional Fund Trust
(Exact name of registrant as specified in charter)

522 Fifth Avenue, New York, New York					10036
(Address of principal executive offices)					(Zip code)

John H. Gernon 522 Fifth Avenue, New York, New York 10036
(Name and address of agent for service)

Registrant’s telephone number, including area code:				212-296-0289

Date of fiscal year end:	September 30,

Date of reporting period:		September 30, 2016

Item 1 - Report to Shareholders

INVESTMENT MANAGEMENT

Morgan Stanley Institutional Fund Trust

Core Plus Fixed Income Portfolio

Annual Report

September 30, 2016

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Table of Contents

Shareholders' Letter					2
Expense Example					3
Investment Overview					4
Portfolio of Investments					7
Statement of Assets and Liabilities					17
Statement of Operations					19
Statements of Changes in Net Assets					20
Financial Highlights					21
Notes to Financial Statements					25
Report of Independent Registered Public Accounting Firm					36
Investment Advisory Agreement Approval					37
Privacy Notice					39
Trustee and Officer Information					42

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable Portfolio of Morgan Stanley Institutional Fund Trust. To receive a prospectus and/or statement of additional information (SAI), which contains more complete information such as investment objectives, charges, expenses, policies for voting proxies, risk considerations, and describes in detail each of the Portfolio's investment policies to the prospective investor, please call toll free 1 (800) 548-7786. Please read the prospectuses carefully before you invest or send money.

Additionally, you can access information about the Portfolio, including performance, characteristics, and investment team commentary, through Morgan Stanley Investment Management's website: www.morganstanley.com/im.

Market forecasts provided in this report may not necessarily come to pass. There is no guarantee that any sectors mentioned will continue to perform as discussed herein or that securities in such sectors will be held by the Portfolio in the future. There is no assurance that a Portfolio will achieve its investment objective. Portfolios are subject to market risk, which is the possibility that market values of securities owned by the Portfolio will decline and, therefore, the value of the Portfolio's shares may be less than what you paid for them. Accordingly, you can lose money investing in this Portfolio. Please see the prospectus for more complete information on investment risks.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Shareholders' Letter (unaudited)

Dear Shareholders,

We are pleased to provide this Annual report, in which you will learn how your investment in Core Plus Fixed Income Portfolio (the "Portfolio") performed during the latest twelve-month period.

Morgan Stanley Investment Management is a client-centric, investor-led organization. Our global presence, intellectual capital, and breadth of products and services enable us to partner with investors to meet the evolving challenges of today's financial markets. We aim to deliver superior investment service and to empower our clients to make the informed decisions that help them reach their investment goals.

As always, we thank you for selecting Morgan Stanley Investment Management, and look forward to working with you in the months and years ahead.

Sincerely,

John H. Gernon
President and Principal Executive Officer

October 2016

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Expense Example (unaudited)

Core Plus Fixed Income Portfolio

As a shareholder of the Portfolio, you may incur two types of costs: (1) transactional costs, including sales charge (loads) on purchase payments; and (2) ongoing costs, which may include advisory fees, administration fees, distribution and shareholder services fees; and other Portfolio expenses. This example is intended to help you understand your ongoing costs (in dollars) of investing in the Portfolio and to compare these costs with the ongoing costs of investing in other mutual funds.

This example is based on an investment of $1,000 invested at the beginning of the six-month period ended September 30, 2016 and held for the entire six-month period (unless otherwise noted).

Actual Expenses

The table below provides information about actual account values and actual expenses. You may use the information in this table, together with the amount you invested, to estimate the expenses that you paid over the period. Simply divide your account value by $1,000 (for example, an $8,600 account value divided by $1,000 = 8.6), then multiply the result by the number in the table under the heading entitled "Actual Expenses Paid During Period" to estimate the expenses you paid on your account during this period.

Hypothetical Example for Comparison Purposes

The table below provides information about hypothetical account values and hypothetical expenses based on the Portfolio's actual expense ratio and an assumed rate of return of 5% per year before expenses, which is not the Portfolio's actual return. The hypothetical account values and expenses may not be used to estimate the actual ending account balance or expenses you paid for the period. You may use this information to compare the ongoing costs of investing in the Portfolio and other funds. To do so, compare this 5% hypothetical example with the 5% hypothetical examples that appear in the shareholder reports of the other funds.

Please note that the expenses shown in the table are meant to highlight your ongoing costs only and do not reflect any transactional costs, such as sales charges (loads, if applicable). Therefore, the information for each class in the table is useful in comparing ongoing costs only, and will not help you determine the relative total costs of owning different funds. In addition, if these transactional costs were included, your costs would have been higher.

	Beginning Account Value 4/1/16		Actual Ending Account Value 9/30/16		Hypothetical Ending Account Value		Actual Expenses Paid During Period*		Hypothetical Expenses Paid During Period*		Net Expense Ratio During Period**
Core Plus Fixed Income Portfolio Class I	$	1,000.00	$	1,077.00	$	1,023.00	$	2.08	$	2.02		0.40	%***
Core Plus Fixed Income Portfolio Class A		1,000.00		1,074.40		1,021.25		3.89		3.79		0.75	***
Core Plus Fixed Income Portfolio Class L		1,000.00		1,073.70		1,020.00		5.18		5.05		1.00	***
Core Plus Fixed Income Portfolio Class C		1,000.00		1,071.30		1,017.50		7.77		7.57		1.50	***

* Expenses are calculated using each Portfolio Class' annualized net expense ratio (as disclosed), multiplied by the average account value over the period, and multiplied by 183/366 (to reflect the most recent one-half year period).

** Annualized.

*** Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Overview (unaudited)

Core Plus Fixed Income Portfolio

The Portfolio seeks above-average total return over a market cycle of three to five years.

Performance

For the fiscal year ended September 30, 2016, the Portfolio's Class I shares had a total return based on net asset value and reinvestment of distributions per share of 14.80%, net of fees. The Portfolio's Class I shares outperformed against the Portfolio's benchmark, the Bloomberg Barclays U.S. Aggregate Index (the "Index"), which returned 5.19%.

During calendar year 2016, the Portfolio received monies related to certain nonrecurring litigation settlements. If these monies were not received, any period returns which include these settlement monies would have been lower. For example, the 2016 fiscal year total return would have been 7.08% for Class I Shares as of September 30, 2016. The returns on the other Share Classes would also have been similarly impacted. These were one-time settlements, and as a result, the impact on the net asset value and consequently the performance will not likely be repeated in the future. Please call 1-800-548-7786 for additional information.

Factors Affecting Performance

• The rise in risk premia and increase in correlations across asset classes that began when China devalued its currency in the third quarter of 2015 continued to dominate asset prices over the 12-month period. The devaluation of the Chinese currency and ensuing fall in Chinese equity prices was followed by a substantial move lower in oil prices, which continued through February 2016. Oil prices were at the epicenter of market volatility, with investor concerns about Chinese economic performance and a broader emerging markets slowdown reflected in lower commodity prices. Weaker expectations for oil demand, combined with fears of new supply coming on line, pushed oil prices down to levels not seen in a decade. Volatility in the energy market put pressure on all the major risk markets, and correlations between crude oil prices and equities, credit, inflation expectations and even government bond yields were extremely high. The market has since been calmed by a stabilization in oil prices and continued global central bank policy coordination, which has led to a recovery in risk asset prices and

the start of a rise in global government bond yields, mainly at the back-end (that is, the longer maturity range) of yield curves.

• Global government bond yields fell over the period, boosting prices (as bond yields and prices move in opposite directions). Yields on the 10-year U.S. Treasury fell to as low as 1.36% during the period and returned 5.6% over the full period.⁽¹⁾ Ten-year Japanese government bonds returned 4.9%, German 10-year bunds returned 8.5%, and U.K. 10-year gilts returned 12.4%.⁽¹⁾

• While yield spreads on non-agency residential mortgage-backed securities (RMBS) did widen in early 2016, the sector was relatively resilient and the spread widening was largely a result of a rise in global risk premium rather than increased credit risks in the U.S. housing and mortgage markets. Non-agency RMBS spreads are now at their tightest levels since 2014 for most securities. As of the end of the period, non-agency mortgage-backed securities (MBS) offered spreads of 150 to 225 basis points (bps) above Treasuries for investment grade bonds, and 250 to 300 bps for senior non-investment grade bonds on a loss-adjusted basis.⁽²⁾

• Commercial mortgage-backed securities (CMBS) credit spreads were mixed during the period; widening for the bulk of the period, then recovering in the last few months. Year-to-date through September 30, 2016 CMBS performance has sharply diverged based on position in the capital structure, with AAA-rated CMBS 25 to 30 bps tighter, while BBB-rated issues were 40 to 75 bps wider.⁽³⁾Issuance in 2016 remains lighter than initially anticipated with roughly $47 billion issued through the first nine months of the year. We are on pace for $60-70 billion in issuance in 2016, which would be about 60% of the issuance that was initially anticipated for the year.⁽⁴⁾ Fundamentally, CMBS performance remains on solid ground. While price volatility and supply-demand dynamics for CMBS continue to cause some concerns, the fundamental real estate market conditions underlying CMBS market appear to be stable.

⁽¹⁾ Source: Bloomberg L.P. Data as of September 30, 2016.

⁽²⁾ Source: Morgan Stanley Investment Management. Data as of September 30, 2016.

⁽³⁾ Source: Bloomberg Barclays Capital

⁽⁴⁾ Source: Deutsche Bank

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Overview (unaudited) (cont'd)

Core Plus Fixed Income Portfolio

• Emerging market debt experienced broad-based weakness in the fourth quarter of 2015 and the start of 2016, as the potential for rising U.S. interest rates, the direction of commodity prices, and the uncertain path of Chinese economic growth, currency and monetary policy were risk factors weighing on emerging market asset prices. Emerging market assets have since recovered along with other risk assets.

Management Strategies

• Throughout the period, the Portfolio was positioned with exposure to the investment grade credit sector, primarily focused on financials, and to the high yield credit sector, as we believe valuations relative to fundamentals have been attractive in these segments. These positions added to performance during the period.

• Given the attractive yield advantages, improving fundamentals and shrinking net supply, we remain overweight the non-agency MBS sector. This positioning benefited relative performance.

• Within CMBS, we favor more seasoned issues, which have benefited from recent property price appreciation, over newly originated deals, which may have somewhat inflated property valuations as part of their underwriting. Despite improvement in the sector toward the end of the period, positioning here detracted from performance overall.

• With regard to interest rate strategy, the Portfolio is positioned using futures and interest rate swaps to be underweight duration at the intermediate and long parts of the yield curve. This positioning added to relative performance.

* Minimum Investment

In accordance with SEC regulations, the Portfolio's performance shown assumes that all recurring fees (including management fees) were deducted and all dividends and distributions were reinvested. The performance of Class A, Class L and Class C shares will vary from the performance of Class I shares based upon their different inception dates and will be negatively impacted by additional fees assessed to those classes.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Overview (unaudited) (cont'd)

Core Plus Fixed Income Portfolio

Performance Compared to the Bloomberg Barclays U.S. Aggregate Index⁽¹⁾ and the Lipper Core Plus Bond Funds Index⁽²⁾

	Period Ended September 30, 2016 Total Returns⁽³⁾
				Average Annual
	One Year			Five Years			Ten Years			Since Inception⁽⁸⁾
Portfolio — Class I Shares w/o sales charges⁽⁴⁾		14.80	%		6.64	%		4.43	%		7.47	%
Portfolio — Class A Shares w/o sales charges⁽⁵⁾		14.31			6.29			4.13			5.05
Portfolio — Class A Shares with maximum 4.25% sales charges⁽⁵⁾		9.47			5.37			3.68			4.82
Portfolio — Class L Shares w/o sales charges⁽⁶⁾		14.10			—			—			5.63
Portfolio — Class C Shares w/o sales charges⁽⁷⁾		13.52			—			—			7.78
Portfolio — Class C Shares with maximum 1.00% deferred sales charges⁽⁷⁾		12.52			—			—			7.78
Bloomberg Barclays U.S. Aggregate Index		5.19			3.08			4.79			7.28
Lipper Core Plus Bond Funds Index		6.13			4.23			5.34			—

Performance data quoted represents past performance, which is no guarantee of future results, and current performance may be lower or higher than the figures shown. Performance assumes that all dividends and distributions, if any, were reinvested. For the most recent month-end performance figures, please visit www.morganstanley.com/im. Investment returns and principal value will fluctuate so that Portfolio shares, when redeemed, may be worth more or less than their original cost. Total returns do not reflect the deduction of taxes that a shareholder would pay on Portfolio distributions or the redemption of Portfolio shares. Performance of share classes will vary due to differences in sales charges and expenses.

⁽¹⁾ The Bloomberg Barclays U.S. Aggregate Index tracks the performance of U.S. government agency and Treasury securities, investment-grade corporate debt securities, agency mortgage-backed securities, asset-backed securities and commercial mortgage-backed securities. The Index is unmanaged and its returns do not include any sales charges or fees. Such costs would lower performance. It is not possible to invest directly in an index.

⁽²⁾ The Lipper Core Plus Bond Funds Index is an equally weighted performance index of the largest qualifying funds (based on net assets) in the Lipper Core Plus Bond Funds classification. The Index, which is adjusted for capital gains distributions and income dividends, is unmanaged and should not be considered an investment. There are currently 30 funds represented in this Index. As of the date of this report, the Portfolio was in the Lipper Core Plus Bond Funds classification.

⁽³⁾ Total returns for the Portfolio reflect expenses waived and/or reimbursed, if applicable, by the Adviser. Without such waivers and/or reimbursements, total returns would have been lower.

⁽⁴⁾ Commenced operations on November 14, 1984.

⁽⁵⁾ Commenced operations on November 7, 1996.

⁽⁶⁾ Commenced operations on April 27, 2012.

⁽⁷⁾ Commenced operations on April 30, 2015.

⁽⁸⁾ For comparative purposes, average annual since inception returns listed for the Indexes refer to the inception date of Class I of the Portfolio, not the inception of the Indexes.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments

Core Plus Fixed Income Portfolio

	Face Amount (000)		Value (000)
Fixed Income Securities (92.5%)
Agency Adjustable Rate Mortgage (0.1%)
Federal Home Loan Mortgage Corporation, Conventional Pool:
2.55%, 7/1/45	$	243	$	251
Agency Fixed Rate Mortgages (19.9%)
Federal Home Loan Mortgage Corporation,
Gold Pools:
3.50%, 1/1/44 - 2/1/45		2,409		2,564
4.00%, 6/1/44 - 10/1/44		1,294		1,390
5.41%, 7/1/37 - 8/1/37		33		38
5.44%, 1/1/37 - 6/1/38		122		135
5.46%, 5/1/37 - 4/1/38		127		143
5.48%, 8/1/37 - 10/1/37		74		83
5.50%, 8/1/37 - 4/1/38		134		151
5.52%, 9/1/37 - 1/1/38		29		33
5.62%, 12/1/36 - 12/1/37		92		104
6.00%, 10/1/36 - 8/1/38		299		344
6.50%, 12/1/25 - 8/1/33		187		218
7.00%, 6/1/28 - 11/1/31		56		60
Federal National Mortgage Association,
Conventional Pools:
3.00%, 5/1/30 - 4/1/45		1,723		1,805
3.50%, 4/1/29 - 8/1/45		1,365		1,449
4.00%, 11/1/41 - 1/1/46		5,842		6,308
4.50%, 3/1/41 - 11/1/44		2,486		2,774
5.00%, 3/1/41		359		399
5.50%, 6/1/35 - 1/1/37		112		128
5.62%, 12/1/36		35		37
6.50%, 4/1/24 - 1/1/34		1,535		1,774
7.00%, 11/1/17 - 1/1/34		285		308
9.50%, 4/1/30		211		248
October TBA:
2.50%, 10/1/31 (a)		1,050		1,088
3.00%, 10/1/31 - 10/1/46 (a)		7,258		7,550
3.50%, 10/1/46 (a)		5,899		6,225
4.00%, 10/1/46 (a)		2,870		3,083
Government National Mortgage Association,
Various Pools:
3.50%, 11/20/40 - 7/20/46		4,576		4,876
4.00%, 8/20/41 - 3/20/43		920		991
5.48%, 9/20/37		9		10
				44,316
Asset-Backed Securities (5.5%)
American Homes 4 Rent,
6.07%, 10/17/45 (b)		500		550
Bayview Opportunity Master Fund IIIb Trust,
3.47%, 7/28/18 (b)		526		527
ContiMortgage Home Equity Loan Trust,
8.10%, 8/15/25		25		20
CVS Pass-Through Trust,
6.04%, 12/10/28		397		461

	Face Amount (000)			Value (000)
Green Tree Agency Advance Funding Trust I,
2.38%, 10/15/48 (b)	$	800		$	800
Invitation Homes Trust,
4.53%, 9/17/31 (b)(c)		1,000			1,001
5.28%, 8/17/32 (b)(c)		997			1,010
Mid-State Trust IV,
8.33%, 4/1/30		8			8
Nationstar HECM Loan Trust,
4.36%, 2/25/26 (b)		650			650
5.68%, 8/25/26 (b)		475			478
6.54%, 6/25/26 (b)		450			459
OnDeck Asset Securitization Trust II LLC,
4.21%, 5/17/20 (b)		450			454
PRPM LLC,
4.00%, 9/27/21 (b)		500			501
RMAT LLC,
4.83%, 6/25/35 (b)		657			647
Silver Bay Realty Trust,
4.08%, 9/17/31 (b)(c)		700			683
Skopos Auto Receivables Trust,
3.10%, 12/15/23 (b)		126			126
3.55%, 2/15/20 (b)		108			108
U-Haul S Fleet LLC,
4.90%, 10/25/23 (b)		680			688
VOLT NPL X LLC,
4.75%, 10/26/54 (b)		493			484
VOLT XIX LLC,
3.88%, 4/25/55 (b)		410			412
5.00%, 4/25/55 (b)		300			295
VOLT XXII LLC,
4.25%, 2/25/55 (b)		299			291
VOLT XXX LLC,
4.75%, 10/25/57 (b)		399			391
VOLT XXXI LLC,
4.50%, 2/25/55 (b)		399			390
VOLT XXXIII LLC,
4.25%, 3/25/55 (b)		694			673
					12,107
Collateralized Mortgage Obligations — Agency Collateral Series (2.3%)
Federal Home Loan Mortgage Corporation,
3.72%, 6/25/48 (b)(c)		483			415
4.09%, 10/25/48 (b)(c)		750			649
5.50%, 7/25/23		437			437
5.77%, 7/25/26 (b)(c)		286			289
IO REMIC
5.48%, 11/15/43 (c)		1,774			303
5.53%, 4/15/39 (c)		1,691			166
IO STRIPS
7.50%, 12/1/29		44			12
PAC REMIC
9.50%, 4/15/20		—	@		—	@

The accompanying notes are an integral part of the financial statements.
7

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Core Plus Fixed Income Portfolio

	Face Amount (000)			Value (000)
Collateralized Mortgage Obligations — Agency Collateral Series (cont'd)
Federal National Mortgage Association,
IO
5.86%, 9/25/20 (c)	$	3,721		$	563
IO PAC REMIC
8.00%, 9/18/27		176			40
IO REMIC
6.00%, 7/25/33		113			22
IO STRIPS
6.50%, 9/25/29 - 12/25/29		672			128
8.00%, 4/25/24		167			29
8.50%, 10/25/25		59			14
9.00%, 11/25/26		54			12
REMIC
7.00%, 9/25/32		314			363
61.27%, 9/25/20 (d)		—	@		—	@
Government National Mortgage Association,
IO
3.50%, 5/20/43		1,834			343
5.00%, 2/16/41		384			66
5.52%, 11/16/40 (c)		2,336			419
5.57%, 7/16/33 (c)		2,626			194
5.70%, 3/20/43 (c)		874			132
5.97%, 5/20/40 (c)		1,059			169
IO PAC
5.62%, 10/20/41 (c)		3,129			327
					5,092
Commercial Mortgage-Backed Securities (6.7%)
Citigroup Commercial Mortgage Trust,
3.47%, 9/15/27 (b)(c)		800			733
IO
1.06%, 11/10/48 (c)		2,827			160
1.13%, 9/10/58 (c)		9,829			649
COMM Mortgage Trust,
5.07%, 4/10/47 (b)(c)		883			785
5.21%, 8/10/46 (b)(c)		800			775
IO
0.27%, 7/10/45 (c)		15,205			119
1.14%, 10/10/47 (c)		4,644			215
1.43%, 7/15/47 (c)		4,194			253
Commercial Mortgage Pass-Through Certificates,
4.75%, 2/10/47 (b)(c)		575			514
CSMC Trust,
4.67%, 3/15/17 (b)(c)		200			196
GS Mortgage Securities Trust,
4.93%, 8/10/46 (b)(c)		500			463
IO
1.00%, 9/10/47 (c)		5,883			286
1.29%, 10/10/49 (c)		8,184			738
1.53%, 10/10/48 (c)		5,415			491
HILT Mortgage Trust,
4.27%, 7/15/29 (b)(c)		600			567

	Face Amount (000)		Value (000)
JP Morgan Chase Commercial Mortgage Securities Trust,
4.72%, 7/15/47 (b)(c)	$	1,135	$	907
5.46%, 12/12/43		600		601
IO
0.72%, 4/15/46 (c)		6,956		221
1.29%, 7/15/47 (c)		10,549		536
JPMBB Commercial Mortgage Securities Trust,
4.83%, 4/15/47 (b)(c)		775		676
IO
1.25%, 8/15/47 (c)		4,523		287
LB-UBS Commercial Mortgage Trust,
6.45%, 9/15/45 (c)		550		554
Wells Fargo Commercial Mortgage Trust,
1.81%, 11/15/49		6,981		775
3.94%, 8/15/50 (b)		945		775
4.65%, 9/15/58 (b)(c)		471		378
WF-RBS Commercial Mortgage Trust,
3.80%, 11/15/47 (b)(c)		950		694
3.99%, 5/15/47 (b)		580		445
4.27%, 5/15/45 (b)(c)		425		392
5.15%, 9/15/46 (b)(c)		805		794
				14,979
Corporate Bonds (31.4%)
Finance (13.3%)
ABN Amro Bank N.V.,
4.25%, 2/2/17 (b)		600		606
AerCap Ireland Capital Ltd./AerCap Global Aviation Trust,
3.75%, 5/15/19		380		389
Alexandria Real Estate Equities, Inc.,
3.95%, 1/15/27		175		184
Ally Financial, Inc.,
3.25%, 2/13/18		10		10
American Campus Communities Operating Partnership LP,
3.75%, 4/15/23		250		262
American International Group, Inc.,
4.88%, 6/1/22		275		310
AvalonBay Communities, Inc.,
Series G
2.95%, 5/11/26		375		376
Bank of America Corp.,
MTN
4.00%, 1/22/25		830		862
4.20%, 8/26/24		225		239
4.25%, 10/22/26		313		333
5.00%, 1/21/44		180		213
Bank of New York Mellon Corp. (The),
MTN
3.65%, 2/4/24		400		434

The accompanying notes are an integral part of the financial statements.
8

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Core Plus Fixed Income Portfolio

	Face Amount (000)		Value (000)
Finance (cont'd)
BNP Paribas SA,
4.38%, 5/12/26 (b)	$	200	$	207
5.00%, 1/15/21		175		196
Boston Properties LP,
3.80%, 2/1/24		175		187
BPCE SA,
5.15%, 7/21/24 (b)		600		632
Brookfield Asset Management, Inc.,
5.80%, 4/25/17		235		240
Capital One Bank USA NA,
3.38%, 2/15/23		500		514
Capital One Financial Corp.,
2.45%, 4/24/19		150		153
Citigroup, Inc.,
5.50%, 9/13/25		525		600
6.68%, 9/13/43		120		158
8.13%, 7/15/39		175		276
Citizens Bank NA,
MTN
2.55%, 5/13/21		250		255
Cooperatieve Rabobank UA,
3.95%, 11/9/22		650		682
Credit Agricole SA,
3.88%, 4/15/24 (b)		500		546
7.88%, 1/23/24 (b)(c)(e)		200		201
Credit Suisse Group Funding Guernsey Ltd.,
4.55%, 4/17/26 (b)		325		342
Discover Bank,
7.00%, 4/15/20		250		285
Discover Financial Services,
3.95%, 11/6/24		300		308
Extra Space Storage LP,
3.13%, 10/1/35 (b)(f)		250		270
Federal Realty Investment Trust,
3.63%, 8/1/46		250		245
Five Corners Funding Trust,
4.42%, 11/15/23 (b)		500		541
GE Capital International Funding Co.,
4.42%, 11/15/35		215		242
Goldman Sachs Group, Inc. (The),
6.75%, 10/1/37		490		626
MTN
4.80%, 7/8/44		175		198
Goodman Funding Pty Ltd.,
6.38%, 4/15/21 (b)		425		498
Hartford Financial Services Group, Inc. (The),
5.50%, 3/30/20		295		329
HBOS PLC,
Series G
6.75%, 5/21/18 (b)		813		871
Healthcare Trust of America Holdings LP,
3.70%, 4/15/23 (f)		350		363

	Face Amount (000)		Value (000)
HSBC Finance Corp.,
6.68%, 1/15/21	$	820	$	944
HSBC Holdings PLC,
4.25%, 3/14/24		200		207
HSBC USA, Inc.,
3.50%, 6/23/24		225		234
ING Bank N.V.,
5.80%, 9/25/23 (b)		520		582
ING Groep N.V.,
6.00%, 4/16/20 (c)(e)(f)		200		195
Intesa Sanpaolo SpA,
5.25%, 1/12/24 (f)		410		443
Jefferies Finance LLC/JFIN Co-Issuer Corp.,
7.38%, 4/1/20 (b)		380		372
JPMorgan Chase & Co.,
3.13%, 1/23/25		950		972
3.20%, 6/15/26		275		283
4.13%, 12/15/26		300		321
MTN
2.30%, 8/15/21		250		251
LeasePlan Corp. N.V.,
2.88%, 1/22/19 (b)(f)		475		480
Liberty Mutual Group, Inc.,
4.85%, 8/1/44 (b)		150		157
Macquarie Bank Ltd.,
6.63%, 4/7/21 (b)(f)		490		565
MetLife, Inc.,
5.70%, 6/15/35		175		212
Mizuho Financial Group, Inc.,
2.63%, 4/12/21 (b)		600		608
Nationwide Building Society,
3.90%, 7/21/25 (b)		200		216
6.25%, 2/25/20 (b)		645		733
New York Life Global Funding,
1.70%, 9/14/21 (b)(f)		600		597
PNC Financial Services Group, Inc. (The),
3.90%, 4/29/24		210		225
Realty Income Corp.,
3.25%, 10/15/22		400		414
Royal Bank of Scotland Group PLC,
3.88%, 9/12/23		650		641
Santander UK Group Holdings PLC,
2.88%, 10/16/20		375		379
3.13%, 1/8/21		350		357
Skandinaviska Enskilda Banken AB,
2.63%, 11/17/20 (b)		500		515
Standard Chartered PLC,
3.05%, 1/15/21 (b)(f)		325		335
TD Ameritrade Holding Corp.,
3.63%, 4/1/25		500		537
Toronto-Dominion Bank (The),
3.63%, 9/15/31 (c)(f)		425		427

The accompanying notes are an integral part of the financial statements.
9

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Core Plus Fixed Income Portfolio

	Face Amount (000)		Value (000)
Finance (cont'd)
Travelers Cos., Inc. (The),
3.75%, 5/15/46	$	175	$	185
UBS Group Funding Co.,
2.95%, 9/24/20 (b)		525		538
UnitedHealth Group, Inc.,
2.88%, 3/15/23		800		835
3.75%, 7/15/25		375		412
WEA Finance LLC/Westfield UK & Europe Finance PLC,
3.25%, 10/5/20 (b)		450		469
Wells Fargo & Co.,
MTN
4.10%, 6/3/26		750		797
				29,621
Industrials (17.1%)
21st Century Fox America, Inc.,
4.75%, 9/15/44		275		302
AbbVie, Inc.,
3.20%, 5/14/26		325		330
Air Liquide Finance SA,
1.75%, 9/27/21 (b)		250		250
Albea Beauty Holdings SA,
8.38%, 11/1/19 (b)		250		262
Altria Group, Inc.,
5.38%, 1/31/44		285		360
Amazon.com, Inc.,
3.80%, 12/5/24		475		527
Anadarko Petroleum Corp.,
5.55%, 3/15/26 (f)		375		425
6.45%, 9/15/36		250		293
Anheuser-Busch InBev Finance, Inc.,
3.70%, 2/1/24		250		271
4.90%, 2/1/46		425		508
Apple, Inc.,
2.45%, 8/4/26		350		351
4.45%, 5/6/44		300		337
Aramark Services, Inc.,
4.75%, 6/1/26 (b)		375		378
AT&T, Inc.,
4.50%, 3/9/48 (b)		750		757
Barrick Gold Corp.,
4.10%, 5/1/23 (f)		255		275
Baxalta, Inc.,
4.00%, 6/23/25		625		668
BHP Billiton Finance USA Ltd.,
5.00%, 9/30/43		150		178
Boston Scientific Corp.,
3.85%, 5/15/25		425		453
BP Capital Markets PLC,
3.12%, 5/4/26		500		512
3.25%, 5/6/22		275		290

	Face Amount (000)		Value (000)
CBS Corp.,
4.60%, 1/15/45	$	175	$	180
Celgene Corp.,
3.88%, 8/15/25 (f)		375		402
CEVA Group PLC,
7.00%, 3/1/21 (b)		370		302
Charter Communications Operating LLC/ Charter Communications Operating Capital,
4.91%, 7/23/25 (b)		550		608
6.48%, 10/23/45 (b)		300		364
Citrix Systems, Inc.,
0.50%, 4/15/19		200		227
CNH Industrial Capital LLC,
4.38%, 11/6/20 (f)		300		314
CNOOC Finance 2013 Ltd.,
3.00%, 5/9/23		540		547
Coca-Cola Co.,
3.20%, 11/1/23		375		404
Comcast Corp.,
4.60%, 8/15/45		230		266
DCP Midstream LLC,
5.35%, 3/15/20 (b)		169		174
Dollar General Corp.,
3.25%, 4/15/23		400		414
Eldorado Gold Corp.,
6.13%, 12/15/20 (b)		380		385
Enable Midstream Partners LP,
3.90%, 5/15/24		200		187
Ensco PLC,
5.75%, 10/1/44		225		139
Experian Finance PLC,
2.38%, 6/15/17 (b)		635		638
Express Scripts Holding Co.,
4.50%, 2/25/26		275		302
Exxon Mobil Corp.,
4.11%, 3/1/46		300		336
Ford Motor Credit Co., LLC,
3.20%, 1/15/21		400		411
General Motors Co.,
6.60%, 4/1/36		450		543
Goldcorp, Inc.,
3.70%, 3/15/23		293		304
Hanesbrands, Inc.,
4.63%, 5/15/24 (b)		187		193
4.88%, 5/15/26 (b)		288		296
HCA, Inc.,
4.75%, 5/1/23		445		465
Heathrow Funding Ltd.,
4.88%, 7/15/21 (b)		525		574
Hilcorp Energy I LP/Hilcorp Finance Co.,
5.75%, 10/1/25 (b)		315		315
Home Depot, Inc.,
5.88%, 12/16/36		225		309

The accompanying notes are an integral part of the financial statements.
10

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Core Plus Fixed Income Portfolio

	Face Amount (000)		Value (000)
Industrials (cont'd)
Illumina, Inc.,
0.00%, 6/15/19 (f)	$	328	$	341
Intel Corp.,
2.95%, 12/15/35		356		492
International Paper Co.,
3.00%, 2/15/27		500		501
Kinder Morgan, Inc.,
4.30%, 6/1/25 (f)		400		416
Kraft Heinz Foods Co.,
4.38%, 6/1/46		325		345
Lockheed Martin Corp.,
3.10%, 1/15/23		725		766
LyondellBasell Industries N.V.,
4.63%, 2/26/55		300		299
Mallinckrodt International Finance SA/ Mallinckrodt CB LLC,
5.50%, 4/15/25 (b)		500		477
MasTec, Inc.,
4.88%, 3/15/23		415		412
McDonald's Corp.,
MTN
4.60%, 5/26/45		325		366
Medtronic, Inc.,
4.63%, 3/15/45		325		383
Microsoft Corp.,
4.45%, 11/3/45		200		228
Mylan N.V.,
3.95%, 6/15/26 (b)		575		580
NBC Universal Media LLC,
5.95%, 4/1/41		150		202
NetApp, Inc.,
2.00%, 12/15/17		200		200
Netflix, Inc.,
5.50%, 2/15/22		255		276
Noble Energy, Inc.,
3.90%, 11/15/24		225		230
5.05%, 11/15/44		200		198
NOVA Chemicals Corp.,
5.25%, 8/1/23 (b)		463		475
Novartis Capital Corp.,
4.40%, 5/6/44		250		296
Nuance Communications, Inc.,
2.75%, 11/1/31		286		288
Numericable-SFR SA,
7.38%, 5/1/26 (b)		200		205
Occidental Petroleum Corp.,
4.40%, 4/15/46		275		304
Omnicom Group, Inc.,
3.65%, 11/1/24		230		245
ON Semiconductor Corp.,
Series B
2.63%, 12/15/26		290		347

	Face Amount (000)		Value (000)
Ooredoo International Finance Ltd.,
3.25%, 2/21/23 (b)	$	450	$	462
Oracle Corp.,
2.95%, 5/15/25		131		135
PepsiCo, Inc.,
3.60%, 3/1/24		475		521
Philip Morris International, Inc.,
2.50%, 8/22/22		495		509
Phillips 66 Partners LP,
4.68%, 2/15/45		150		143
Priceline Group, Inc. (The),
0.90%, 9/15/21		275		296
Rowan Cos., Inc.,
5.85%, 1/15/44		100		70
Shell International Finance BV,
3.25%, 5/11/25		400		422
Siemens Financieringsmaatschappij N.V.,
2.35%, 10/15/26 (b)		550		544
SK Telecom Co., Ltd.,
2.13%, 5/1/18 (b)		200		202
Southern Copper Corp.,
5.25%, 11/8/42 (f)		300		285
Spectra Energy Capital LLC,
3.30%, 3/15/23		475		471
Telstra Corp., Ltd.,
3.13%, 4/7/25 (b)		240		252
Teva Pharmaceutical Finance Netherlands III BV,
2.20%, 7/21/21		485		484
Thermo Fisher Scientific, Inc.,
2.95%, 9/19/26		325		323
Total Capital International SA,
2.88%, 2/17/22		500		525
Transurban Finance Co., Pty Ltd.,
3.38%, 3/22/27 (b)		350		353
Tyco International Finance SA,
3.90%, 2/14/26		350		382
Tyson Foods, Inc.,
4.88%, 8/15/34		225		250
United Airlines Pass-Through Trust,
Series A
4.00%, 4/11/26		636		683
United Technologies Corp.,
4.50%, 6/1/42		165		192
Verizon Communications, Inc.,
4.67%, 3/15/55		675		713
Visa, Inc.,
3.15%, 12/14/25		425		449
Volkswagen Group of America Finance LLC,
2.40%, 5/22/20 (b)		525		529
Wal-Mart Stores, Inc.,
5.25%, 9/1/35		440		585
Whole Foods Market, Inc.,
5.20%, 12/3/25 (b)		475		517

The accompanying notes are an integral part of the financial statements.
11

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Core Plus Fixed Income Portfolio

	Face Amount (000)		Value (000)
Industrials (cont'd)
Williams Partners LP/ACMP Finance Corp.,
4.88%, 5/15/23	$	175	$	177
Woodside Finance Ltd.,
3.70%, 9/15/26 (b)		525		529
Yahoo!, Inc.,
0.00%, 12/1/18		300		309
ZF North America Capital, Inc.,
4.50%, 4/29/22 (b)		475		505
				38,015
Utilities (1.0%)
Duke Energy Corp.,
2.65%, 9/1/26		525		516
Entergy Louisiana LLC,
3.05%, 6/1/31		400		411
Exelon Generation Co., LLC,
6.25%, 10/1/39		445		497
Jersey Central Power & Light Co.,
4.70%, 4/1/24 (b)		700		768
				2,192
				69,828
Mortgages — Other (8.2%)
Alternative Loan Trust,
0.71%, 5/25/47 (c)		191		164
Banc of America Alternative Loan Trust,
1.18%, 7/25/46 (c)		315		227
5.50%, 10/25/35		1,370		1,345
5.86%, 10/25/36		725		459
6.00%, 4/25/36		183		186
Banc of America Funding Trust,
5.25%, 7/25/37		425		436
ChaseFlex Trust,
6.00%, 2/25/37		1,112		903
Eurosail PLC,
1.33%, 6/13/45 (c)	GBP	350		408
Fannie Mae Connecticut Avenue Securities,
4.53%, 5/25/25 (c)	$	671		699
5.43%, 11/25/24 (c)		698		755
5.53%, 7/25/25 (c)		500		534
Farringdon Mortgages No. 2 PLC,
2.03%, 7/15/47 (c)	GBP	297		364
First Horizon Alternative Mortgage Securities Trust,
6.25%, 8/25/36	$	572		447
Freddie Mac Structured Agency Credit Risk Debt Notes,
3.83%, 10/25/27 (c)		400		416
4.28%, 9/25/24 (c)		602		624
4.53%, 8/25/24 (c)		312		327
4.78%, 11/25/23 (c)		700		742
5.08%, 10/25/24 (c)		948		1,007

	Face Amount (000)		Value (000)
Freddie Mac Whole Loan Securities Trust,
3.00%, 7/25/46	$	286	$	293
3.50%, 5/25/45 - 7/25/46		1,548		1,600
3.87%, 5/25/45 (b)(c)		249		225
4.00%, 5/25/45		131		137
Grifonas Finance PLC,
0.09%, 8/28/39 (c)	EUR	544		457
HarborView Mortgage Loan Trust,
0.72%, 1/19/38 (c)	$	275		238
IM Pastor 3 FTH,
0.00%, 3/22/43 (c)	EUR	554		498
Impac CMB Trust,
1.26%, 4/25/35 (c)	$	276		217
JP Morgan Mortgage Trust,
3.13%, 6/25/37 (c)		255		236
6.00%, 6/25/37		185		181
Lehman Mortgage Trust,
5.50%, 11/25/35 - 2/25/36		1,113		1,047
6.50%, 9/25/37		1,342		1,025
Oncilla Mortgage Funding PLC,
1.78%, 12/12/43 (c)	GBP	384		499
Paragon Mortgages No. 13 PLC,
0.93%, 1/15/39 (c)		300		335
RALI Trust,
5.50%, 12/25/34	$	878		863
6.00%, 11/25/36		320		256
				18,150
Municipal Bonds (1.2%)
City of Chicago, IL, O'Hare International Airport Revenue
6.40%, 1/1/40		255		370
City of New York, NY, Series G-1
5.97%, 3/1/36		270		368
Illinois State Toll Highway Authority, Highway Revenue, Build America Bonds
6.18%, 1/1/34		477		640
Municipal Electric Authority of Georgia,
6.64%, 4/1/57		283		385
6.66%, 4/1/57		320		430
New York City, NY, Transitional Finance Authority Future Tax Secured Revenue
5.27%, 5/1/27		320		398
				2,591
Sovereign (5.1%)
Brazil Notas do Tesouro Nacional, Series F,
10.00%, 1/1/21	BRL	5,400		1,587
Cyprus Government International Bond,
3.88%, 5/6/22	EUR	1,525		1,789
Guatemala Government Bond,
4.50%, 5/3/26 (b)	$	375		392
Hungary Government International Bond,
5.75%, 11/22/23		1,348		1,590

The accompanying notes are an integral part of the financial statements.
12

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Core Plus Fixed Income Portfolio

	Face Amount (000)		Value (000)
Sovereign (cont'd)
Indonesia Government International Bond,
5.88%, 1/15/24	$	1,150	$	1,359
Mexico Government International Bond,
3.60%, 1/30/25 (f)		500		520
Peruvian Government International Bond,
7.35%, 7/21/25 (f)		1,300		1,804
Petroleos de Venezuela SA,
6.00%, 11/15/26		550		232
Petroleos Mexicanos,
6.38%, 1/23/45		225		216
6.88%, 8/4/26 (b)		150		170
Poland Government Bond,
3.25%, 7/25/25	PLN	5,280		1,425
Provincia de Cordoba,
7.13%, 6/10/21 (b)	$	200		211
				11,295
U.S. Agency Security (0.9%)
Federal Home Loan Bank,
0.88%, 10/1/18		2,070		2,070
U.S. Treasury Securities (11.2%)
U.S. Treasury Bonds,
3.13%, 2/15/42		275		320
3.75%, 8/15/41		2,000		2,570
U.S. Treasury Inflation Indexed Bond,
0.25%, 1/15/25		5,075		5,172
U.S. Treasury Notes,
1.00%, 8/31/19		2,600		2,609
1.13%, 2/28/21		1,000		1,001
1.38%, 6/30/18		2,100		2,122
1.50%, 5/31/19		10,000		10,169
1.63%, 5/15/26		1,000		1,002
				24,965
Total Fixed Income Securities (Cost $202,001)				205,644
	Shares
Short-Term Investments (16.4%)
Securities held as Collateral on Loaned Securities (1.4%)
Investment Company (1.4%)
Morgan Stanley Institutional Liquidity Funds — Government Portfolio — Institutional Class (See Note G) (Cost $3,209)		3,209,388		3,209
Investment Company (11.4%)
Morgan Stanley Institutional Liquidity Funds — Government Portfolio — Institutional Class (See Note G) (Cost $25,383)		25,382,828		25,383

	Face Amount (000)		Value (000)
U.S. Treasury Securities (2.5%)
U.S. Treasury Bill 0.34%, 10/20/16 (g)	$	1,488	$	1,488
U.S. Treasury Note 0.88%, 4/30/17		4,000		4,008
				5,496
Certificates of Deposit (0.9%)
International Bank (0.9%)
Bank of Montreal,
1.23%, 5/3/17		2,010		2,011
Commercial Paper (0.2%)
International Bank (0.2%)
Credit Agricole SA,
1.25%, 2/9/17 (h)		475		473
Total Short-Term Investments (Cost $36,571)				36,572
Total Investments (108.9%) (Cost $238,572) Including $6,604 of Securities Loaned (i)(j)				242,216
Liabilities in Excess of Other Assets (–8.9%)				(19,800	)
Net Assets (100.0%)			$	222,416

(a) Security is subject to delayed delivery.

(b) 144A security — Certain conditions for public sale may exist. Unless otherwise noted, these securities are deemed to be liquid.

(c) Variable/Floating Rate Security — Interest rate changes on these instruments are based on changes in a designated base rate. The rates shown are those in effect on September 30, 2016.

(d) Inverse Floating Rate Security — Interest rate fluctuates with an inverse relationship to an associated interest rate. Indicated rate is the effective rate at September 30, 2016.

(e) Perpetual — One or more securities do not have a predetermined maturity date. Rates for these securities are fixed for a period of time, after which they revert to a floating rate. Interest rates in effect are as of September 30, 2016.

(f) All or a portion of this security was on loan at September 30, 2016.

(g) Rate shown is the yield to maturity at September 30, 2016.

(h) The rates shown are the effective yields at the date of purchase.

(i) Securities are available for collateral in connection with securities purchased on a forward commitment basis, open foreign currency forward exchange contracts, futures contracts and swap agreements.

(j) At September 30, 2016, the aggregate cost for federal income tax purposes is approximately $238,681,000. The aggregate gross unrealized appreciation is approximately $7,244,000 and the aggregate gross unrealized depreciation is approximately $3,709,000 resulting in net unrealized appreciation of approximately $3,535,000.

@ Value is less than $500.

IO Interest Only.

MTN Medium Term Note.

PAC Planned Amortization Class.

REMIC Real Estate Mortgage Investment Conduit.

STRIPS Separate Trading of Registered Interest and Principal of Securities.

TBA To Be Announced.

The accompanying notes are an integral part of the financial statements.
13

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Core Plus Fixed Income Portfolio

Foreign Currency Forward Exchange Contracts:

The Portfolio had the following foreign currency forward exchange contracts open at September 30, 2016:

Counterparty	Contracts to Deliver (000)		In Exchange For (000)		Delivery Date	Unrealized Appreciation (Depreciation) (000)
Australia and New Zealand Banking Group	AUD	23	$	18	10/5/16	$	(—	@)
Australia and New Zealand Banking Group	CAD	1,337	$	1,030	10/5/16		11
Australia and New Zealand Banking Group	EUR	1,719	NZD	2,650	10/5/16		(1	)
Australia and New Zealand Banking Group	NZD	2,650	EUR	1,707	10/5/16		(12	)
Australia and New Zealand Banking Group	NZD	2,673	$	1,947	10/5/16		1
Australia and New Zealand Banking Group	PLN	2,783	$	731	10/5/16		4
Australia and New Zealand Banking Group	TRY	60	$	20	10/5/16		—	@
Australia and New Zealand Banking Group	$	16	EUR	14	10/5/16		(—	@)
Australia and New Zealand Banking Group	$	25	GBP	19	10/5/16		(—	@)
Australia and New Zealand Banking Group	$	11	JPY	1,109	10/5/16		(—	@)
Australia and New Zealand Banking Group	$	1,932	NZD	2,673	10/5/16		15
Australia and New Zealand Banking Group	$	20	TRY	60	10/5/16		—	@
Australia and New Zealand Banking Group	$	47	ZAR	667	10/5/16		2
Citibank NA	NOK	8,640	$	1,082	10/5/16		1
Citibank NA	$	1,021	CAD	1,337	10/5/16		(2	)
Citibank NA	$	4,544	EUR	4,044	10/5/16		(1	)
HSBC Bank PLC	EUR	9	$	11	10/5/16		(—	@)
HSBC Bank PLC	GBP	1,196	$	1,575	10/5/16		24
HSBC Bank PLC	$	1,532	GBP	1,177	10/5/16		(6	)
HSBC Bank PLC	$	2	SEK	15	10/5/16		(—	@)
JPMorgan Chase Bank NA	RUB	59,802	$	908	10/5/16		(44	)
JPMorgan Chase Bank NA	SEK	15	$	2	10/5/16		—	@
JPMorgan Chase Bank NA	$	785	BRL	2,549	10/5/16		(2	)
JPMorgan Chase Bank NA	$	1,549	BRL	5,051	10/5/16		3
JPMorgan Chase Bank NA	$	15	HUF	4,011	10/5/16		—	@
JPMorgan Chase Bank NA	$	1,044	NOK	8,640	10/5/16		37
JPMorgan Chase Bank NA	$	1,440	PLN	5,512	10/5/16		2
JPMorgan Chase Bank NA	$	915	RUB	59,802	10/5/16		37
JPMorgan Chase Bank NA	ZAR	667	$	49	10/5/16		(—	@)
UBS AG	BRL	7,600	$	2,331	10/5/16		(5	)
UBS AG	EUR	4,048	$	4,553	10/5/16		5
UBS AG	HUF	4,011	$	15	10/5/16		(—	@)
UBS AG	JPY	1,109	$	11	10/5/16		—	@
UBS AG	MXN	46,382	$	2,494	10/5/16		102
UBS AG	PLN	2,728	$	708	10/5/16		(5	)
UBS AG	PLN	4,630	$	1,199	10/5/16		(12	)
UBS AG	RON	354	$	89	10/5/16		(—	@)
UBS AG	$	17	AUD	23	10/5/16		—	@
UBS AG	$	2,482	MXN	46,382	10/5/16		(91	)
UBS AG	$	1,182	PLN	4,630	10/5/16		29
UBS AG	$	89	RON	354	10/5/16		—	@
Australia and New Zealand Banking Group	NZD	2,650	EUR	1,714	11/4/16		1
Australia and New Zealand Banking Group	TRY	60	$	20	11/4/16		(—	@)
Australia and New Zealand Banking Group	$	18	AUD	23	11/4/16		—	@
Australia and New Zealand Banking Group	$	1,945	NZD	2,673	11/4/16		(1	)
Citibank NA	CAD	1,337	$	1,021	11/4/16		2
Citibank NA	EUR	4,044	$	4,551	11/4/16		1
Citibank NA	$	1,082	NOK	8,640	11/4/16		(1	)
HSBC Bank PLC	GBP	1,177	$	1,533	11/4/16		6
HSBC Bank PLC	SEK	15	$	2	11/4/16		—	@
JPMorgan Chase Bank NA	BRL	5,051	$	1,536	11/4/16		(4	)
JPMorgan Chase Bank NA	PLN	5,512	$	1,439	11/4/16		(1	)
JPMorgan Chase Bank NA	$	48	ZAR	667	11/4/16		—	@
UBS AG	$	15	HUF	4,011	11/4/16		—	@
UBS AG	$	11	JPY	1,109	11/4/16		(—	@)
UBS AG	$	90	RON	354	11/4/16		—	@
						$	95

The accompanying notes are an integral part of the financial statements.
14

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Core Plus Fixed Income Portfolio

Futures Contracts:

The Portfolio had the following futures contracts open at September 30, 2016:

	Number of Contracts		Value (000)			Expiration Date	Unrealized Appreciation (Depreciation) (000)
Long:
U.S. Treasury 2 yr. Note		87	$	19,007		Dec-16	$	1
U.S. Treasury 5 yr. Note		124		15,068		Dec-16		13
U.S. Treasury Long Bond		16		2,691		Dec-16		(37	)
U.S. Treasury Ultra Bond		61		11,216		Dec-16		(198	)
Short:
U.S. Treasury 10 yr. Note		4		(525	)	Dec-16		1
German Euro Bund		15		(2,792	)	Dec-16		(6	)
U.S. Treasury 10 yr. Ultra Long Bond		99		(14,271	)	Dec-16		23
							$	(203	)

Credit Default Swap Agreements:

The Portfolio had the following credit default swap agreements open at September 30, 2016:

Swap Counterparty and Reference Obligation	Buy/Sell Protection	Notional Amount (000)		Pay/Receive Fixed Rate			Termination Date	Upfront Payment Paid (000)		Unrealized Depreciation (000)			Value (000)			Credit Rating of Reference Obligation† (Unaudited)
Barclays Bank PLC Quest Diagnostics, Inc.	Buy	$	995		1.00	%	3/20/19	$	19	$	(39	)	$	(20	)	BBB+
Deutsche Bank AG CMBX.NA.BB.60	Sell		515		5.00		5/11/63		4		(94	)		(90	)	NR
		$	1,510					$	23	$	(133	)	$	(110	)

@ Value is less than $500.

† Credit rating as issued by Standard & Poor's.

NR Not Rated.

AUD — Australian Dollar

BRL — Brazilian Real

CAD — Canadian Dollar

EUR — Euro

GBP — British Pound

HUF — Hungarian Forint

JPY — Japanese Yen

MXN — Mexican Peso

NOK — Norwegian Krone

NZD — New Zealand Dollar

PLN — Polish Zloty

RON — Romanian New Leu

RUB — Russian Ruble

SEK — Swedish Krona

TRY — Turkish Lira

ZAR — South African Rand

The accompanying notes are an integral part of the financial statements.
15

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Core Plus Fixed Income Portfolio

Portfolio Composition*

Classification	Percentage of Total Investments
Agency Fixed Rate Mortgages		18.5	%
Industrials		15.9
Short-Term Investments		14.0
Finance		12.4
U.S. Treasury Securities		10.4
Other**		9.8
Mortgages — Other		7.6
Commercial Mortgage-Backed Securities		6.3
Asset-Backed Securities		5.1
Total Investments		100.0	%***

* Percentages indicated are based upon total investments (excluding Securities held as Collateral on Loaned Securities) as of September 30, 2016.

** Industries and/or investment types representing less than 5% of total investments.

*** Does not include open long/short futures contracts with an underlying face amount of approximately $65,570,000 with net unrealized depreciation of approximately $203,000. Does not include open foreign currency forward exchange contracts with net unrealized appreciation of approximately $95,000 and does not include open swap agreements with total unrealized depreciation of approximately $133,000.

The accompanying notes are an integral part of the financial statements.
16

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Core Plus Fixed Income Portfolio

Statement of Assets and Liabilities	September 30, 2016 (000)
Assets:
Investments in Securities of Unaffiliated Issuers, at Value⁽¹⁾ (Cost $209,980)	$	213,624
Investment in Security of Affiliated Issuer, at Value (Cost $28,592)		28,592
Total Investments in Securities, at Value (Cost $238,572)		242,216
Receivable for Investments Sold		6,748
Interest and Paydown Receivable		1,385
Receivable for Portfolio Shares Sold		385
Receivable for Variation Margin on Futures Contracts		347
Unrealized Appreciation on Foreign Currency Forward Exchange Contracts		283
Premium Paid on Open Swap Agreements		23
Receivable from Affiliate		6
Tax Reclaim Receivable		—	@
Other Assets		63
Total Assets		251,456
Liabilities:
Payable for Investments Purchased		24,650
Collateral on Securities Loaned, at Value		3,209
Payable for Advisory Fees		311
Payable for Portfolio Shares Redeemed		288
Unrealized Depreciation on Foreign Currency Forward Exchange Contracts		188
Payable for Trustees' Fees and Expenses		138
Unrealized Depreciation on Swap Agreements		133
Payable for Sub Transfer Agency Fees — Class I		18
Payable for Sub Transfer Agency Fees — Class A		2
Payable for Sub Transfer Agency Fees — Class L		—	@
Payable for Sub Transfer Agency Fees — Class C		—	@
Payable for Professional Fees		16
Payable for Administration Fees		14
Payable for Custodian Fees		13
Payable for Shareholder Services Fees — Class A		5
Payable for Distribution and Shareholder Services Fees — Class L		—	@
Payable for Distribution and Shareholder Services Fees — Class C		3
Payable for Transfer Agency Fees — Class I		2
Payable for Transfer Agency Fees — Class A		1
Payable for Transfer Agency Fees — Class L		1
Payable for Transfer Agency Fees — Class C		1
Other Liabilities		47
Total Liabilities		29,040
Net Assets	$	222,416
Net Assets Consist Of:
Paid-in-Capital	$	662,691
Accumulated Undistributed Net Investment Income		2,646
Accumulated Net Realized Loss		(446,318	)
Unrealized Appreciation (Depreciation) on:
Investments		3,644
Futures Contracts		(203	)
Swap Agreements		(133	)
Foreign Currency Forward Exchange Contracts		95
Foreign Currency Translations		(6	)
Net Assets	$	222,416

The accompanying notes are an integral part of the financial statements.
17

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Core Plus Fixed Income Portfolio

Statement of Assets and Liabilities (cont'd)	September 30, 2016 (000)
CLASS I:
Net Assets	$	193,976
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		17,289,438
Net Asset Value, Offering and Redemption Price Per Share	$	11.22
CLASS A:
Net Assets	$	24,071
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		2,143,149
Net Asset Value, Redemption Price Per Share	$	11.23
Maximum Sales Load		4.25	%
Maximum Sales Charge	$	0.50
Maximum Offering Price Per Share	$	11.73
CLASS L:
Net Assets	$	841
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		74,903
Net Asset Value, Offering and Redemption Price Per Share	$	11.23
CLASS C:
Net Assets	$	3,528
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		315,960
Net Asset Value, Offering and Redemption Price Per Share	$	11.17
⁽¹⁾ Including: Securities on Loan, at Value:	$	6,604

@ Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
18

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Core Plus Fixed Income Portfolio

Statement of Operations	Year Ended September 30, 2016 (000)
Investment Income:
Interest from Securities of Unaffiliated Issuers (Net of $1 of Foreign Taxes Withheld)	$	7,146
Dividends from Security of Affiliated Issuer (Note G)		56
Income from Securities Loaned — Net		22
Total Investment Income		7,224
Expenses:
Advisory Fees (Note B)		726
Sub Transfer Agency Fees — Class I		215
Sub Transfer Agency Fees — Class A		13
Sub Transfer Agency Fees — Class L		—	@
Sub Transfer Agency Fees — Class C		—	@
Administration Fees (Note C)		155
Professional Fees		101
Registration Fees		62
Pricing Fees		53
Custodian Fees (Note F)		47
Shareholder Reporting Fees		41
Shareholder Services Fees — Class A (Note D)		25
Distribution and Shareholder Services Fees — Class L (Note D)		2
Distribution and Shareholder Services Fees — Class C (Note D)		12
Transfer Agency Fees — Class I (Note E)		6
Transfer Agency Fees — Class A (Note E)		4
Transfer Agency Fees — Class L (Note E)		2
Transfer Agency Fees — Class C (Note E)		3
Trustees' Fees and Expenses		6
Other Expenses		25
Total Expenses		1,498
Reimbursement of Class Specific Expenses — Class I (Note B)		(221	)
Reimbursement of Class Specific Expenses — Class A (Note B)		(6	)
Reimbursement of Class Specific Expenses — Class L (Note B)		(2	)
Reimbursement of Class Specific Expenses — Class C (Note B)		(1	)
Waiver of Advisory Fees (Note B)		(93	)
Rebate from Morgan Stanley Affiliate (Note G)		(25	)
Reimbursement of Custodian Fees (Note F)		(260	)
Net Expenses		890
Net Investment Income		6,334
Realized Gain (Loss):
Investments Sold		14,318
Foreign Currency Forward Exchange Contracts		(655	)
Foreign Currency Transactions		32
Futures Contracts		767
Swap Agreements		(284	)
Net Realized Gain		14,178
Change in Unrealized Appreciation (Depreciation):
Investments		4,941
Foreign Currency Forward Exchange Contracts		35
Foreign Currency Translations		(5	)
Futures Contracts		(124	)
Swap Agreements		235
Net Change in Unrealized Appreciation (Depreciation)		5,082
Net Realized Gain and Change in Unrealized Appreciation (Depreciation)		19,260
Net Increase in Net Assets Resulting from Operations	$	25,594

@ Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
19

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Core Plus Fixed Income Portfolio

Statements of Changes in Net Assets	Year Ended September 30, 2016 (000)			Year Ended September 30, 2015 (000)
Increase (Decrease) in Net Assets:
Operations:
Net Investment Income	$	6,334		$	6,672
Net Realized Gain		14,178			2,949
Net Change in Unrealized Appreciation (Depreciation)		5,082			(7,292	)
Net Increase in Net Assets Resulting from Operations		25,594			2,329
Distributions from and/or in Excess of:
Class I:
Net Investment Income		(7,381	)		(6,016	)
Class A:
Net Investment Income		(245	)		(96	)
Class L:
Net Investment Income		(12	)		(7	)
Class C:
Net Investment Income		(25	)		(—	@)*
Total Distributions		(7,663	)		(6,119	)
Capital Share Transactions:⁽¹⁾
Class I:
Subscribed		49,744			41,541
Distributions Reinvested		7,372			6,008
Redeemed		(76,546	)		(39,648	)
Class A:
Subscribed		26,992			2,479
Distributions Reinvested		245			96
Redeemed		(8,071	)		(1,892	)
Class L:
Exchanged		517			—
Subscribed		—			225
Distributions Reinvested		11			6
Redeemed		(70	)		—
Class C:
Subscribed		3,299			50	*
Distributions Reinvested		24			—	@*
Redeemed		(24	)		(—	@)*
Net Increase in Net Assets Resulting from Capital Share Transactions		3,493			8,865
Total Increase in Net Assets		21,424			5,075
Net Assets:
Beginning of Period		200,992			195,917
End of Period (Including Accumulated Undistributed Net Investment Income of $2,646 and $4,482)	$	222,416		$	200,992
(1) Capital Share Transactions:
Class I:
Shares Subscribed		4,712			4,007
Shares Issued on Distributions Reinvested		721			583
Shares Redeemed		(7,510	)		(3,848	)
Net Increase (Decrease) in Class I Shares Outstanding		(2,077	)		742
Class A:
Shares Subscribed		2,520			239
Shares Issued on Distributions Reinvested		23			9
Shares Redeemed		(749	)		(183	)
Net Increase in Class A Shares Outstanding		1,794			65
Class L:
Shares Exchanged		48			—
Shares Subscribed		—			21
Shares Issued on Distributions Reinvested		1			1
Shares Redeemed		(7	)		—
Net Increase in Class L Shares Outstanding		42			22
Class C:
Shares Subscribed		311			5	*
Shares Issued on Distributions Reinvested		2			—	@@*
Shares Redeemed		(2	)		(—	@@)*
Net Increase in Class C Shares Outstanding		311			5

* For the period April 30, 2015 through September 30, 2015.

@ Amount is less than $500.

@@ Amount is less than 500 shares.

The accompanying notes are an integral part of the financial statements.
20

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Core Plus Fixed Income Portfolio

	Class I
	Year Ended September 30,
Selected Per Share Data and Ratios	2016††			2015			2014			2013			2012
Net Asset Value, Beginning of Period	$	10.18		$	10.36		$	9.91		$	10.48		$	9.92
Income (Loss) from Investment Operations:
Net Investment Income†		0.34			0.33			0.31			0.32			0.39
Net Realized and Unrealized Gain (Loss)		1.11			(0.20	)		0.45			(0.36	)		0.63
Total from Investment Operations		1.45			0.13			0.76			(0.04	)		1.02
Distributions from and/or in Excess of:
Net Investment Income		(0.41	)		(0.31	)		(0.31	)		(0.53	)		(0.46	)
Net Asset Value, End of Period	$	11.22		$	10.18		$	10.36		$	9.91		$	10.48
Total Return++		14.80	%**		1.15	%		7.82	%		(0.42	)%		10.62	%
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	193,976		$	197,057		$	192,868		$	187,014		$	227,331
Ratio of Expenses to Average Net Assets ⁽¹⁾		0.43	%+^^^		0.51	%+^^		0.61	%+		0.71	%+^		0.62	%+
Ratio of Net Investment Income to Average Net Assets ⁽¹⁾		3.31	%+^^^		3.24	%+^^		3.02	%+		3.14	%+^		3.88	%+
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.01	%		0.01	%		0.01	%		0.01	%		0.01	%
Portfolio Turnover Rate		262	%		348	%		296	%		226	%		189	%
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		0.74	%		0.73	%		0.81	%		0.73	%		N/A
Net Investment Income to Average Net Assets		3.00	%		3.02	%		2.82	%		3.12	%		N/A

†† Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class I shares. The Ratio of Expenses to Average Net Assets and the Ratio of Net Investment Income to Average Net Assets would be unchanged as the change to current period custodian fees was offset against current period expense waivers/reimbursements with no impact to net expenses or net investment income.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value as of the last business day of the period.

** Performance was positively impacted by approximately 7.72% due to the receipt of proceeds from the settlement of class action suits involving the Portfolio's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class I shares would have been approximately 7.08%.

+ The Ratios of Expenses and Net Investment Income reflect the rebate of certain Portfolio expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets."

^^^ Effective January 4, 2016, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 0.42% for Class I shares. Prior to January 4, 2016, the maximum ratio was 0.52% for Class I shares.

^^ Effective October 6, 2014, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 0.52% for Class I shares. Prior to October 6, 2014, the maximum ratio was 0.62% for Class I shares.

^ Effective September 16, 2013, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 0.62% for Class I shares.

The accompanying notes are an integral part of the financial statements.
21

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Core Plus Fixed Income Portfolio

	Class A
	Year Ended September 30,
Selected Per Share Data and Ratios	2016††			2015			2014			2013			2012
Net Asset Value, Beginning of Period	$	10.19		$	10.37		$	9.93		$	10.50		$	9.94
Income (Loss) from Investment Operations:
Net Investment Income†		0.30			0.30			0.27			0.29			0.37
Net Realized and Unrealized Gain (Loss)		1.12			(0.21	)		0.45			(0.36	)		0.62
Total from Investment Operations		1.42			0.09			0.72			(0.07	)		0.99
Distributions from and/or in Excess of:
Net Investment Income		(0.38	)		(0.27	)		(0.28	)		(0.50	)		(0.43	)
Net Asset Value, End of Period	$	11.23		$	10.19		$	10.37		$	9.93		$	10.50
Total Return++		14.31	%**		0.90	%		7.35	%		(0.68	)%		10.31	%
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	24,071		$	3,553		$	2,941		$	3,152		$	3,673
Ratio of Expenses to Average Net Assets ⁽¹⁾		0.76	%+^^^		0.86	%+^^		0.96	%+		0.96	%+^		0.87	%+
Ratio of Net Investment Income to Average Net Assets ⁽¹⁾		2.82	%+^^^		2.87	%+^^		2.67	%+		2.89	%+^		3.63	%+
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.02	%		0.01	%		0.01	%		0.01	%		0.01	%
Portfolio Turnover Rate		262	%		348	%		296	%		226	%		189	%
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		1.15	%		1.07	%		1.11	%		0.98	%		N/A
Net Investment Income to Average Net Assets		2.43	%		2.66	%		2.52	%		2.87	%		N/A

†† Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class A shares. The Ratio of Expenses to Average Net Assets and the Ratio of Net Investment Income to Average Net Assets would be unchanged as the change to current period custodian fees was offset against current period expense waivers/reimbursements with no impact to net expenses or net investment income.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

** Performance was positively impacted by approximately 7.76% due to the receipt of proceeds from the settlement of class action suits involving the Portfolio's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class A shares would have been approximately 6.55%.

^^^ Effective January 4, 2016, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 0.77% for Class A shares. Prior to January 4, 2016, the maximum ratio was 0.87% for Class A shares.

^^ Effective October 6, 2014, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 0.87% for Class A shares. Prior to October 6, 2014, the maximum ratio was 0.97% for Class A shares.

^ Effective September 16, 2013, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 0.97% for Class A shares.

The accompanying notes are an integral part of the financial statements.
22

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Core Plus Fixed Income Portfolio

	Class L
	Year Ended September 30,												Period from April 27, 2012^ to
Selected Per Share Data and Ratios	2016††			2015			2014			2013			September 30, 2012
Net Asset Value, Beginning of Period	$	10.18		$	10.37		$	9.92		$	10.49		$	10.14
Income (Loss) from Investment Operations:
Net Investment Income†		0.28			0.27			0.25			0.27			0.11
Net Realized and Unrealized Gain (Loss)		1.12			(0.21	)		0.45			(0.36	)		0.35
Total from Investment Operations		1.40			0.06			0.70			(0.09	)		0.46
Distributions from and/or in Excess of:
Net Investment Income		(0.35	)		(0.25	)		(0.25	)		(0.48	)		(0.11	)
Net Asset Value, End of Period	$	11.23		$	10.18		$	10.37		$	9.92		$	10.49
Total Return++		14.10	%**		0.59	%		7.19	%		(0.95	)%		4.59	%#
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	841		$	333		$	108		$	88		$	130
Ratio of Expenses to Average Net Assets ⁽¹⁾		1.03	%+^^^^		1.11	%+^^^		1.21	%+		1.21	%+^^		1.16	%+*
Ratio of Net Investment Income to Average Net Assets ⁽¹⁾		2.65	%+^^^^		2.65	%+^^^		2.42	%+		2.64	%+^^		2.60	%+*
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.01	%		0.02	%		0.01	%		0.01	%		0.01	%*
Portfolio Turnover Rate		262	%		348	%		296	%		226	%		189	%#
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		1.82	%		1.76	%		3.10	%		1.27	%		N/A
Net Investment Income to Average Net Assets		1.86	%		2.00	%		0.53	%		2.58	%		N/A

†† Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class L shares. The Ratio of Expenses to Average Net Assets and the Ratio of Net Investment Income to Average Net Assets would be unchanged as the change to current period custodian fees was offset against current period expense waivers/reimbursements with no impact to net expenses or net investment income.

^ Commencement of Offering.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value as of the last business day of the period.

^^^^ Effective January 4, 2016, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 1.02% for Class L shares. Prior to January 4, 2016, the maximum ratio was 1.12% for Class L shares.

^^^ Effective October 6, 2014, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 1.12% for Class L shares. Prior to October 6, 2014, the maximum ratio was 1.22% for Class L shares.

^^ Effective September 16, 2013, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 1.22% for Class L shares.

# Not Annualized.

* Annualized.

The accompanying notes are an integral part of the financial statements.
23

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Core Plus Fixed Income Portfolio

	Class C
Selected Per Share Data and Ratios	Year Ended September 30, 2016††			Period from April 30, 2015^ to September 30, 2015
Net Asset Value, Beginning of Period	$	10.16		$	10.44
Income (Loss) from Investment Operations:
Net Investment Income†		0.22			0.10
Net Realized and Unrealized Gain (Loss)		1.12			(0.31	)
Total from Investment Operations		1.34			(0.21	)
Distributions from and/or in Excess of:
Net Investment Income		(0.33	)		(0.07	)
Net Asset Value, End of Period	$	11.17		$	10.16
Total Return++		13.52	%**		(2.02	)%#
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	3,528		$	49
Ratio of Expenses to Average Net Assets ⁽¹⁾		1.51	%+^^		1.61	%+*
Ratio of Net Investment Income to Average Net Assets ⁽¹⁾		2.04	%+^^		2.23	%+*
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.02	%		0.01	%*
Portfolio Turnover Rate		262	%		348	%#
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		2.00	%		14.06	%*
Net Investment Income (Loss) to Average Net Assets		1.55	%		(10.22	)%*

†† Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class C shares. The Ratio of Expenses to Average Net Assets and the Ratio of Net Investment Income to Average Net Assets would be unchanged as the change to current period custodian fees was offset against current period expense waivers/reimbursements with no impact to net expenses or net investment income.

^ Commencement of Offering.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

** Performance was positively impacted by approximately 7.75% due to the receipt of proceeds from the settlement of class action suits involving the Portfolio's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class C shares would have been approximately 5.77%.

^^ Effective January 4, 2016, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 1.52% for Class C shares. Prior to January 4, 2016, the maximum ratio was 1.62% for Class C shares.

# Not Annualized.

* Annualized.

The accompanying notes are an integral part of the financial statements.
24

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements

Morgan Stanley Institutional Fund Trust ("MSIFT" or the "Fund'') is registered under the Investment Company Act of 1940, as amended (the "Act''), as an open-end management investment company. The Fund is comprised of nine separate, active portfolios (individually referred to as a "Portfolio", collectively as the "Portfolios"). The Fund applies investment company accounting and reporting guidance. All Portfolios are considered diversified for purposes of the Act.

The accompanying financial statements relate to the Core Plus Fixed Income Portfolio. The Portfolio seeks above-average total return over a market cycle of three to five years. The Portfolio offers four classes of shares — Class I, Class A, Class L and Class C.

On April 30, 2015, the Portfolio suspended offering Class L shares to all investors. Existing Class L shareholders may invest through reinvestment of dividends and distributions.

A. Significant Accounting Policies: The following significant accounting policies are in conformity with U.S. generally accepted accounting principles ("GAAP"). Such policies are consistently followed by the Fund in the preparation of its financial statements. GAAP may require management to make estimates and assumptions that affect the reported amounts and disclosures in the financial statements. Actual results may differ from those estimates.

Morgan Stanley Investment Management Inc. (the "Adviser") determines that the closing price, last sale price or the mean between the last reported bid and asked prices are not reflective of a security's market value, portfolio securities are valued at their fair value as determined in good faith under procedures established by and under the general supervision of the Trustees. Occasionally, developments affecting the closing prices of securities and other assets may occur between the times at which valuations of such securities are determined (that is, close of the foreign market on which the securities trade) and the close of business of the New York Stock Exchange ("NYSE"). If developments occur during such periods that are expected to materially affect the value of such securities, such valuations may be adjusted to reflect the estimated fair value of such securities as of the close of the NYSE, as determined in good faith by the Trustees or by the Adviser using a pricing service and/or procedures approved by the Trustees; (5) quotations of foreign portfolio securities, other assets and liabilities and forward contracts stated in foreign currency are translated into U.S. dollar equivalents at the prevailing market rates prior to the close of the NYSE; and (6) investments in mutual funds, including the Morgan Stanley Institutional Liquidity Funds, are valued at the net asset value ("NAV") as of the close of each business day.

The Trustees have responsibility for determining in good faith the fair value of the investments, and the Trustees may appoint others, such as the Fund's Adviser or a valuation committee, to assist the Trustees in determining fair value and to make the actual calculations pursuant to the fair valuation methodologies previously approved by the Trustees. Under procedures approved by the Trustees, the Fund's Adviser has formed a Valuation Committee whose members are approved by the Trustees. The Valuation Committee provides administration and oversight of the Fund's valuation policies and procedures, which are reviewed at least annually by the Trustees. These procedures allow the Fund to utilize independent pricing services, quotations from securities and financial instrument dealers, and other market sources to determine fair value.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

and ad hoc basis to review such securities and considers a number of factors, including valuation methodologies and significant unobservable valuation inputs, when arriving at fair value. The Valuation Committee may employ a market-based approach which may use related or comparable assets or liabilities, recent transactions, market multiples, book values, and other relevant information for the investment to determine the fair value of the investment. An income-based valuation approach may also be used in which the anticipated future cash flows of the investment are discounted to calculate fair value. Discounts may also be applied due to the nature or duration of any restrictions on the disposition of the investments. Due to the inherent uncertainty of valuations of such investments, the fair values may differ significantly from the values that would have been used had an active market existed. The Valuation Committee employs various methods for calibrating these valuation approaches including a regular review of valuation methodologies, key inputs and assumptions, transactional back-testing or disposition analysis, and reviews of any related market activity.

2. Fair Value Measurement: Financial Accounting Standards Board ("FASB") Accounting Standards Codification^TM ("ASC") 820, "Fair Value Measurement" ("ASC 820"), defines fair value as the value that the Fund would receive to sell an investment or pay to transfer a liability in a timely transaction with an independent buyer in the principal market, or in the absence of a principal market the most advantageous market for the investment or liability. ASC 820 establishes a three-tier hierarchy to distinguish between (1) inputs that reflect the assumptions market participants would use in valuing an asset or liability developed based on market data obtained from sources independent of the reporting entity (observable inputs) and (2) inputs that reflect the reporting entity's own assumptions about the assumptions market participants would use in valuing an asset or liability developed based on the best information available in the circumstances (unobservable inputs) and to establish classification of fair value measurements for disclosure purposes. Various inputs are used in determining the value of the Fund's investments. The inputs are summarized in the three broad levels listed below.

• Level 1 – unadjusted quoted prices in active markets for identical investments

• Level 2 – other significant observable inputs (including quoted prices for similar investments, interest rates, prepayment speeds, credit risk, etc.)

• Level 3 – significant unobservable inputs including the Fund's own assumptions in determining the fair value of investments. Factors considered in making this determination may include, but are not limited to, information obtained by contacting the issuer, analysts, or the appropriate stock exchange (for exchange-traded securities), analysis of the issuer's financial statements or other available documents and, if necessary, available information concerning other securities in similar circumstances

The inputs or methodology used for valuing securities are not necessarily an indication of the risk associated with investing in those securities and the determination of the significance of a particular input to the fair value measurement in its entirety requires judgment and considers factors specific to each security.

The following is a summary of the inputs used to value the Portfolio's investments as of September 30, 2016.

Investment Type	Level 1 Unadjusted quoted prices (000)		Level 2 Other significant observable inputs (000)		Level 3 Significant unobservable inputs (000)		Total (000)
Assets:
Fixed Income Securities
Agency Adjustable Rate Mortgage	$	—	$	251	$	—	$	251
Agency Fixed Rate Mortgages		—		44,316		—		44,316
Asset-Backed Securities		—		12,107		—		12,107
Collateralized Mortgage Obligations — Agency Collateral Series		—		5,092		—		5,092
Commercial Mortgage-Backed Securities		—		14,979		—		14,979
Corporate Bonds		—		69,828		—		69,828
Mortgages — Other		—		18,150		—		18,150
Municipal Bonds		—		2,591		—		2,591
Sovereign		—		11,295		—		11,295
U.S. Agency Security		—		2,070		—		2,070
U.S. Treasury Securities		—		24,965		—		24,965
Total Fixed Income Securities		—		205,644		—		205,644

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

Investment Type	Level 1 Unadjusted quoted prices (000)			Level 2 Other significant observable inputs (000)			Level 3 Significant unobservable inputs (000)		Total (000)
Short-Term Investments
Investment Company	$	28,592		$	—		$	—	$	28,592
U.S. Treasury Securities		—			5,496			—		5,496
Certificates of Deposit		—			2,011			—		2,011
Commercial Paper		—			473			—		473
Total Short-Term Investments		28,592			7,980			—		36,572
Foreign Currency Forward Exchange Contracts		—			283			—		283
Futures Contracts		38			—			—		38
Total Assets		28,630			213,907			—		242,537
Liabilities:
Foreign Currency Forward Exchange Contracts		—			(188	)		—		(188	)
Futures Contracts		(241	)		—			—		(241	)
Credit Default Swap Agreements		—			(133	)		—		(133	)
Total Liabilities		(241	)		(321	)		—		(562	)
Total	$	28,389		$	213,586		$	—	$	241,975

3. Foreign Currency Translation and Foreign Investments: The books and records of the Portfolio are maintained in U.S. dollars. Foreign currency amounts are translated into U.S. dollars as follows:

– investments, other assets and liabilities at the prevailing rate of exchange on the valuation date;

– investment transactions and investment income at the prevailing rates of exchange on the dates of such transactions.

investments in securities are included in the reported net realized and unrealized gains (losses) on investment transactions and balances. However, pursuant to U.S. federal income tax regulations, gains and losses from certain foreign currency transactions and the foreign currency portion of gains and losses realized on sales and maturities of foreign denominated debt securities are treated as ordinary income for U.S. federal income tax purposes.

Net realized gains (losses) on foreign currency transactions represent net foreign exchange gains (losses) from foreign currency forward exchange contracts, disposition of foreign currencies, currency gains (losses) realized between the trade and settlement dates on securities transactions, and the difference between the amount of investment income and foreign withholding taxes recorded on the Portfolio's books and the U.S. dollar equivalent amounts actually received or paid. Net unrealized currency gains (losses) from valuing foreign currency denominated assets and liabilities at period end exchange rates are reflected as a component of unrealized appreciation (depreciation) in the Statement of Assets and Liabilities. The change in unrealized currency gains (losses) on foreign currency translations for the period is reflected in the Statement of Operations.

Foreign security and currency transactions may involve certain considerations and risks not typically associated with those of U.S. dollar denominated transactions as a result of, among other factors, fluctuations of exchange rates in relation to the U.S. dollar, the possibility of lower levels of governmental supervision and regulation of foreign securities markets and the possibility of political or economic instability.

Governmental approval for foreign investments may be required in advance of making an investment under certain circumstances in some countries, and the extent of foreign investments in domestic companies may be subject to limitation in other countries. Foreign ownership limitations also may be imposed by the charters of individual companies to prevent, among other concerns, violations of foreign investment limitations. As a result, an additional class of shares (identified as "Foreign" in the Portfolio of Investments) may be created and offered for investment. The "local" and "foreign shares" market values may differ. In the absence of trading of the foreign shares in such markets, the Portfolio values the

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

foreign shares at the closing exchange price of the local shares.

4. Derivatives: The Portfolio may, but is not required to, use derivative instruments for a variety of purposes, including hedging, risk management, portfolio management or to earn income. Derivatives are financial instruments whose value is based, in part, on the value of an underlying asset, interest rate, index or financial instrument. Prevailing interest rates and volatility levels, among other things, also affect the value of derivative instruments. A derivative instrument often has risks similar to its underlying asset and may have additional risks, including imperfect correlation between the value of the derivative and the underlying asset, risks of default by the counterparty to certain transactions, magnification of losses incurred due to changes in the market value of the securities, instruments, indices or interest rates to which the derivative instrument relates, risks that the transactions may not be liquid and risks arising from margin requirements. The use of derivatives involves risks that are different from, and possibly greater than, the risks associated with other portfolio investments. Derivatives may involve the use of highly specialized instruments that require investment techniques and risk analyses different from those associated with other portfolio investments. All of the Portfolio's holdings, including derivative instruments, are marked-to-market each day with the change in value reflected in unrealized appreciation (depreciation). Upon disposition, a realized gain or loss is recognized.

Certain derivative transactions may give rise to a form of leverage. Leverage magnifies the potential for gain and the risk of loss. Leverage associated with derivative transactions may cause the Portfolio to liquidate portfolio positions when it may not be advantageous to do so to satisfy its obligations or to meet earmarking or segregation requirements, pursuant to applicable Securities and Exchange Commission rules and regulations, or may cause the Portfolio to be more volatile than if the Portfolio had not been leveraged. Although the Adviser seeks to use derivatives to further the Portfolio's investment objectives, there is no assurance that the use of derivatives will achieve this result.

Following is a description of the derivative instruments and techniques that the Portfolio used during the period and their associated risks:

Futures: A futures contract is a standardized, exchange-traded agreement to buy or sell a specific quantity of an underlying asset, reference rate or index at a specific price at a specific future time. The value of a futures contract tends to increase and decrease in tandem with the value of the underlying instrument. Depending on the terms of the particular contract, futures contracts are settled through either physical delivery of the underlying instrument on the settlement date or by payment of a cash settlement amount on the settlement date. During the period the futures contract is open, payments are received from or made to the broker based upon changes in the value of the contract (the variation margin). A decision as to whether, when and how to use futures contracts involves the exercise of skill and judgment and even a well-conceived futures transaction may be unsuccessful because of market behavior or unexpected events. In addition to the derivatives risks discussed above, the prices of futures contracts can be highly volatile, using futures contracts can lower total return, and the potential loss from futures contracts can exceed the Portfolio's initial investment in such contracts. No assurance can be given that a liquid market will exist for any particular futures contract at any particular time. There is also the risk of loss by the Portfolio of margin deposits in the event of bankruptcy of a broker with which the Portfolio has open positions in the futures contract.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

credit risk. In a cleared swap, the Portfolio's ultimate counterparty is a clearinghouse rather than a swap dealer, bank or other financial institution. OTC swap agreements are not entered into or traded on exchanges and often there is no central clearing or guaranty function for OTC swaps. These OTC swaps are often subject to credit risk or the risk of default or non-performance by the counterparty. Both OTC and cleared swaps could result in losses if interest rates, foreign currency exchange rates or other factors are not correctly anticipated by the Portfolio or if the reference index, security or investments do not perform as expected. During the period swap agreements are open, payments are received from or made to the clearinghouse or counterparty based upon changes in the value of the contract (variation margin). The Dodd-Frank Wall Street Reform and Consumer Protection Act and related regulatory developments require the clearing and exchange-trading of certain standardized swap transactions. Mandatory exchange-trading and clearing is occurring on a phased-in basis.

The Portfolio's use of swaps during the period included those based on the credit of an underlying security commonly referred to as "credit default swaps." The Portfolio may be either the buyer or seller in a credit default swap. Where the Portfolio is the buyer of a credit default swap contract, it would typically be entitled to receive the par (or other agreed-upon) value of a referenced debt obligation from the counterparty to the contract only in the event of a default or similar event by the issuer of the debt obligation. If no default occurs, the Portfolio would have paid to the counterparty a periodic stream of payments over the term of the contract and received no benefit from the contract. When the Portfolio is the seller of a credit default swap contract, it typically receives the stream of payments but is obligated to pay an amount equal to the par (or other agreed-upon) value of a referenced debt obligation upon the default or similar event by the issuer of the referenced debt obligation. The use of credit default swaps could result in losses to the Portfolio if the Adviser fails to correctly evaluate the creditworthiness of the issuer of the referenced debt obligation.

referenced obligation, other deliverable obligations or underlying securities comprising the referenced index or (ii) pay a net settlement amount in the form of cash or securities equal to the notional amount of the swap agreement less the recovery value of the referenced obligation or underlying securities comprising the referenced index. If the Portfolio is a buyer of protection and a credit event occurs, as defined under the terms of that particular swap agreement, the Portfolio will either (i) receive from the seller of protection an amount equal to the notional amount of the swap agreement and deliver the referenced obligation, other deliverable obligations or underlying securities comprising the referenced index or (ii) receive a net settlement amount in the form of cash or securities equal to the notional amount of the swap agreement less the recovery value of the referenced obligation or underlying securities comprising the referenced index. Recovery values are estimated by market makers considering either industry standard recovery rates or entity specific factors and considerations until a credit event occurs. If a credit event has occurred, the recovery value is determined by a facilitated auction whereby a minimum number of allowable broker bids, together with a specified valuation method, are used to calculate the settlement value. The Portfolio's maximum risk of loss from counterparty risk, either as the protection seller or as the protection buyer, is the fair value of the swap agreement.

The current credit rating of each individual issuer is listed in the table following the Portfolio of Investments and serves as an indicator of the current status of the payment/performance risk of the credit derivative. Alternatively, for credit default swaps on an index of credits, the quoted market prices and current values serve as an indicator of the current status of the payment/performance risk of the credit derivative. Generally, lower credit ratings and increasing market values, in absolute terms, represent a deterioration of the credit and a greater likelihood of an adverse credit event of the issuer.

When the Portfolio has an unrealized loss on a swap agreement, the Portfolio has instructed the custodian to pledge cash or liquid securities as collateral with a value approximately equal to the amount of the unrealized loss. Collateral pledges are monitored and subsequently adjusted if and when the swap valuations fluctuate. If

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

applicable, cash collateral is included with "Due from (to) Broker" in the Statement of Assets and Liabilities.

Upfront payments paid or received by the Portfolio will be reflected as an asset or liability, respectively, in the Statement of Assets and Liabilities.

Foreign Currency Forward Exchange Contracts: In connection with its investments in foreign securities, the Portfolio also entered into contracts with banks, brokers or dealers to purchase or sell securities or foreign currencies at a future date. A foreign currency forward exchange contract ("currency contract") is a negotiated agreement between the contracting parties to exchange a specified amount of currency at a specified future time at a specified rate. The rate can be higher or lower than the spot rate between the currencies that are the subject of the contract. Currency contracts may be used to protect against uncertainty in the level of future foreign currency exchange rates or to gain or modify exposure to a particular currency. In addition, the Portfolio may use cross currency hedging or proxy hedging with respect to currencies in which the Portfolio has or expects to have portfolio or currency exposure. Cross currency hedges involve the sale of one currency against the positive exposure to a different currency and may be used for hedging purposes or to establish an active exposure to the exchange rate between any two currencies. To the extent hedged by the use of currency contracts, the precise matching of the currency contract amounts and the value of the securities involved will not generally be possible because the future value of such securities in foreign currencies will change as a consequence of market movements in the value of those securities between the date on which the contract is entered into and the date it matures. Furthermore, such transactions may reduce or preclude the opportunity for gain if the value of the currency should move in the direction opposite to the position taken. There is additional risk to the extent that currency contracts create exposure to currencies in which the Portfolio's securities are not denominated. Unanticipated changes in currency prices may result in poorer overall performance for the Portfolio than if it had not entered into such contracts. The use of currency contracts involves the risk of loss from the insolvency or bankruptcy of the counterparty to the contract or the failure of the counterparty to make payments or otherwise comply with the terms of the contract. A currency contract is marked-to-market daily and the change in

market value is recorded by the Portfolio as unrealized gain or loss. The Portfolio records realized gains (losses) when the currency contract is closed equal to the difference between the value of the currency contract at the time it was opened and the value at the time it was closed.

FASB ASC 815, "Derivatives and Hedging" ("ASC 815"), is intended to improve financial reporting about derivative instruments by requiring enhanced disclosures to enable investors to better understand how and why the Portfolio uses derivative instruments, how these derivative instruments are accounted for and their effects on the Portfolio's financial position and results of operations.

The following tables set forth the fair value of the Portfolio's derivative contracts by primary risk exposure as of September 30, 2016.

Asset Derivatives
Statement of Assets and
Liabilities Location

Primary Risk
Exposure

Value
(000)

Foreign Currency
Forward Exchange
Contracts

Unrealized Appreciation on
Foreign Currency Forward
Exchange Contracts

Currency Risk

283

Futures Contracts

Variation Margin on
Futures Contracts

Interest Rate Risk

(a)

Total

321

Liability Derivatives
Statement of Assets and
Liabilities Location

Primary Risk
Exposure

Value
(000)

Foreign Currency
Forward Exchange
Contracts

Unrealized Depreciation on
Foreign Currency Forward
Exchange Contracts

Currency Risk

(188

)

Futures Contracts

Variation Margin on
Futures Contracts

Interest Rate Risk

(241

)(a)

Swap Agreements

Unrealized Depreciation on
Swap Agreements

Credit Risk

(133

)

Total

(562

)

(a) This amount represents the cumulative appreciation (depreciation) as reported in the Portfolio of Investments. The Statement of Assets and Liabilities only reflects the current day's net variation margin.

The following tables set forth by primary risk exposure the Portfolio's realized gains (losses) and change in unrealized appreciation (depreciation) by type of derivative contract for the year ended September 30, 2016 in accordance with ASC 815.

Realized Gain (Loss)
Primary Risk Exposure	Derivative Type	Value (000)
Currency Risk	Foreign Currency Forward Exchange Contracts	$	(655	)
Interest Rate Risk	Futures Contracts		767
Credit Risk	Swap Agreements		64
Interest Rate Risk	Swap Agreements		(348	)
	Total	$	(172	)

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

Change in Unrealized Appreciation (Depreciation)
Primary Risk Exposure	Derivative Type	Value (000)
Currency Risk	Foreign Currency Forward Exchange Contracts	$	35
Interest Rate Risk	Futures Contracts		(124	)
Credit Risk	Swap Agreements		(118	)
Interest Rate Risk	Swap Agreements		353
	Total	$	146

At September 30, 2016, the Portfolio's derivative assets and liabilities are as follows:

Gross Amounts of Assets and Liabilities Presented in the Statement of Assets and Liabilities
Derivatives(b)	Assets(c) (000)		Liabilities(c) (000)
Foreign Currency Forward Exchange Contracts	$	283	$	(188	)
Swap Agreements		—		(133	)
Total	$	283	$	(321	)

(b) Excludes exchange traded derivatives.

(c) Absent an event of default or early termination, OTC derivative assets and liabilities are presented gross and not offset in the Statement of Assets and Liabilities.

The Portfolio typically enters into International Swaps and Derivatives Association, Inc. Master Agreements ("ISDA Master Agreements") or similar master agreements (collectively, "Master Agreements") with its contract counterparties for certain OTC derivatives in order to, among other things, reduce its credit risk to counterparties. ISDA Master Agreements include provisions for general obligations, representations, collateral and events of default or termination. Under an ISDA Master Agreement, the Portfolio typically may offset with the counterparty certain OTC derivative financial instruments' payables and/or receivables with collateral held and/or posted and create one single net payment (close-out netting) in the event of default, termination and/or potential deterioration in the credit quality of the counterparty. Various Master Agreements govern the terms of certain transactions with counterparties, including transactions such as swap, forward, repurchase and reverse repurchase agreements. These Master Agreements typically attempt to reduce the counterparty risk associated with such transactions by specifying credit protection mechanisms and providing standardization that improves legal certainty. Cross-termination provisions under Master Agreements typically provide that a default in connection with one transaction between the Portfolio and a counterparty gives the non-defaulting party the right to terminate any other transactions in place with the defaulting party to create one single net payment due to/due from the defaulting party and may be a feature in certain Master Agreements. In the event the Portfolio

exercises its right to terminate a Master Agreement after a counterparty experiences a termination event as defined in the Master Agreement, the return of collateral with market value in excess of the Portfolio's net liability may be delayed or denied.

The following tables present derivative financial instruments that are subject to enforceable netting arrangements as of September 30, 2016.

Gross Amounts Not Offset in the Statement of Assets and Liabilities
Counterparty	Gross Asset Derivatives Presented in Statement of Assets and Liabilities (000)		Financial Instrument (000)			Collateral Received (000)		Net Amount (not less than $0) (000)
Australia and New Zealand Banking Group	$	34	$	(14	)	$	—	$	20
Citibank NA		4		(4	)		—		0
HSBC Bank PLC		30		(6	)		—		24
JPMorgan Chase Bank NA		79		(51	)		—		28
UBS AG		136		(113	)		—		23
Total	$	283	$	(188	)	$	—	$	95
Gross Amounts Not Offset in the Statement of Assets and Liabilities
Counterparty	Gross Liability Derivatives Presented in Statement of Assets and Liabilities (000)		Financial Instrument (000)			Collateral Pledged (000)		Net Amount (not less than $0) (000)
Australia and New Zealand Banking Group	$	14	$	(14	)	$	—	$	0
Barclays Bank PLC		39		—			—		39
Citibank NA		4		(4	)		—		0
Deutsche Bank AG		94		—			—		94
HSBC Bank PLC		6		(6	)		—		0
JPMorgan Chase Bank NA		51		(51	)		—		0
UBS AG		113		(113	)		—		0
Total	$	321	$	(188	)	$	—	$	133

For the year ended September 30, 2016, the approximate average monthly amount outstanding for each derivative type is as follows:

Foreign Currency Forward Exchange Contracts:
Average monthly principal amount	$	31,583,000
Futures Contracts:
Average monthly original value	$	74,858,000
Swap Agreements:
Average monthly notional amount	$	2,998,000

5. Securities Lending: The Portfolio lends securities to qualified financial institutions, such as broker-dealers, to earn additional income. Any increase or decrease in the

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

fair value of the securities loaned that might occur and any interest earned or dividends declared on those securities during the term of the loan would remain in the Portfolio. The Portfolio would receive cash or securities as collateral in an amount equal to or exceeding 100% of the current fair value of the loaned securities. The collateral is marked-to-market daily by State Street Bank and Trust Company ("State Street"), the securities lending agent, to ensure that a minimum of 100% collateral coverage is maintained.

Based on pre-established guidelines, the securities lending agent invests any cash collateral that is received in an affiliated money market portfolio and repurchase agreements. Securities lending income is generated from the earnings on the invested collateral and borrowing fees, less any rebates owed to the borrowers and compensation to the lending agent, and is recorded as "Income from Securities Loaned — Net" in the Portfolio's Statement of Operations. Risks in securities lending transactions are that a borrower may not provide additional collateral when required or return the securities when due, and that the value of the short-term investments will be less than the amount of cash collateral plus any rebate that is required to be returned to the borrower.

The Portfolio has the right under the lending agreement to recover the securities from the borrower on demand.

The following table presents financial instruments that are subject to enforceable netting arrangements as of September 30, 2016.

Gross Amounts Not Offset in the Statement of Assets and Liabilities
Gross Asset Amounts Presented in Statement of Assets and Liabilities (000)			Financial Instrument (000)		Collateral Received (000)			Net Amount (not less than $0) (000)
$	6,604	(d)	$	—	$	(6,604	)(e)(f)	$	0

(d) Represents market value of loaned securities at period end.

(e) The Portfolio received cash collateral of approximately $3,209,000, which was subsequently invested in Morgan Stanley Institutional Liquidity Funds as reported in the Portfolio of Investments. In addition, the Portfolio received non-cash collateral of approximately $3,552,000 in the form of U.S. Government obligations, which the Portfolio cannot sell or repledge, and accordingly are not reflected in the Portfolio of Investments.

(f) The actual collateral received is greater than the amount shown here due to overcollateralization.

types of collateral pledged in securities lending transactions and other similar transactions that are accounted for as secured borrowing.

The following table displays a breakdown of transactions accounted for as secured borrowings, the gross obligations by class of collateral pledged, and the remaining contractual maturity of those transactions as of September 30, 2016.

	Remaining Contractual Maturity of the Agreements
	Overnight and Continuous (000)		<30 days (000)		Between 30 & 90 days (000)		>90 days (000)		Total (000)
Securities Lending Transactions
Corporate Bonds	$	1,772	$	—	$	—	$	—	$	1,772
Sovereign		1,437		—		—		—		1,437
Total	$	3,209	$	—	$	—	$	—	$	3,209
Total Borrowings	$	3,209	$	—	$	—	$	—	$	3,209
Gross amount of recognized liabilities for securities lending transactions									$	3,209

6. When-Issued/Delayed Delivery Securities: The Portfolio purchases and sells when-issued and delayed delivery securities. Securities purchased on a when-issued or delayed delivery basis are purchased for delivery beyond the normal settlement date at a stated price and yield, and no income accrues to the Portfolio on such securities prior to delivery date. Payment and delivery for when-issued and delayed delivery securities can take place a month or more after the date of the transaction. When the Portfolio enters into a purchase transaction on a when-issued or delayed delivery basis, securities are available for collateral in an amount at least equal in value to the Portfolio's commitments to purchase such securities. Purchasing securities on a when-issued or delayed delivery basis may involve a risk that the market price at the time of delivery may be lower than the agreed upon purchase price, in which case there could be an unrealized loss at the time of delivery. Purchasing investments on a when-issued or delayed delivery basis may be considered a form of leverage which may increase the impact that gains (losses) may have on the Portfolio.

7. Indemnifications: The Fund enters into contracts that contain a variety of indemnifications. The Fund's maximum exposure under these arrangements is unknown. However, the Fund has not had prior claims or losses pursuant to these contracts and expects the risk of loss to be remote.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

8. Dividends and Distributions to Shareholders: Dividend income and distributions to shareholders are recorded on the ex-dividend date. Dividends from net investment income, if any, are declared and paid quarterly. Net realized capital gains, if any, are distributed at least annually.

9. Security Transactions, Income and Expenses: Security transactions are accounted for on the trade date (date the order to buy or sell is executed). Realized gains and losses on the sale of investment securities are determined on the specific identified cost method. Dividend income and other distributions are recorded on the ex-dividend date (except for certain foreign dividends which may be recorded as soon as the Portfolio is informed of such dividends) net of applicable withholding taxes. Interest income is recognized on the accrual basis except where collection is in doubt. Discounts are accreted and premiums are amortized over the life of the respective securities. Most expenses of the Fund can be directly attributed to a particular Portfolio. Expenses which cannot be directly attributed are apportioned among the Portfolios based upon relative net assets or other appropriate methods. Income, expenses (other than class specific expenses — distribution and shareholder services, transfer agency and sub transfer agency fees) and realized and unrealized gains or losses are allocated to each class of shares based upon their relative net assets. Included in Realized Gain (Loss) on Investments Sold are proceeds from the one-time settlements of class action lawsuits involving the Portfolio's past holdings of approximately $13,333,000, the impact of which on the Portfolio's performance is disclosed in the Financial Highlights.

First $1 billion				Over $1 billion
	0.375	%			0.300	%

For the year ended September 30, 2016, the advisory fee rate (net of waivers/rebate) was equivalent to an annual effective rate of 0.31% of the Portfolio's average daily net assets.

The Adviser has agreed to reduce its advisory fee and/or reimburse the Portfolio so that total annual portfolio operating expenses, excluding certain investment related expenses, taxes,

interest and other extraordinary expenses (including litigation), will not exceed 0.52% for Class I shares, 0.87% for Class A shares, 1.12% for Class L shares and 1.62% for Class C shares. Effective January 4, 2016, the Adviser has agreed to reduce its advisory fee and/or reimburse the Portfolio so that total annual portfolio operating expenses will not exceed 0.42% for Class I shares, 0.77% for Class A shares, 1.02% for Class L shares and 1.52% for Class C shares. The fee waivers and/or expense reimbursements will continue for at least one year from the date of the Portfolio's prospectus or until such time as the Trustees act to discontinue all or a portion of such waivers and/or reimbursements when they deem such action is appropriate. For the year ended September 30, 2016, approximately $93,000 of advisory fees were waived and approximately $230,000 of other expenses were reimbursed by the Adviser pursuant to this arrangement.

C. Administration Fees: The Adviser also serves as Administrator to the Fund and provides administrative services pursuant to an Administration Agreement for an annual fee, accrued daily and paid monthly, of 0.08% of the Portfolio's average daily net assets. Under a Sub-Administration Agreement between the Administrator and State Street, State Street provides certain administrative services to the Fund. For such services, the Administrator pays State Street a portion of the fee the Administrator receives from the Portfolio.

D. Distribution and Shareholder Services Fees: Morgan Stanley Distribution, Inc. ("MSDI" or the "Distributor"), a wholly-owned subsidiary of the Adviser, and an indirect subsidiary of Morgan Stanley, serves as the Fund's Distributor of Portfolio shares pursuant to a Distribution Agreement. The Fund has adopted a Shareholder Services Plan with respect to Class A shares pursuant to Rule 12b-1 under the Act. Under the Shareholder Services Plan, the Portfolio pays the Distributor a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Portfolio's average daily net assets attributable to Class A shares.

The Fund has adopted a Distribution and Shareholder Services Plan with respect to Class L shares pursuant to Rule 12b-1 under the Act. Under the Distribution and Shareholder Services Plan, the Portfolio pays the Distributor a distribution fee, accrued daily and paid monthly, at an annual rate of 0.25% and a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Portfolio's average daily net assets attributable to Class L shares.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

The Fund has adopted a Distribution and Shareholder Services Plan with respect to Class C shares pursuant to Rule 12b-1 under the Act. Under the Distribution and Shareholder Services Plan, the Portfolio pays the Distributor a distribution fee, accrued daily and paid monthly, at an annual rate of 0.75% and a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Portfolio's average daily net assets attributable to Class C shares.

The distribution and shareholder services fees are used to support the expenses associated with servicing and maintaining accounts. The Distributor may compensate other parties for providing shareholder support services to investors who purchase Class A, Class L and Class C shares.

E. Dividend Disbursing and Transfer Agent: The Fund's dividend disbursing and transfer agent is Boston Financial Data Services, Inc. ("BFDS"). Pursuant to a Transfer Agency Agreement, the Fund pays BFDS a fee based on the number of classes, accounts and transactions relating to the Portfolios of the Fund.

F. Custodian Fees: State Street (the "Custodian") serves as Custodian for the Fund in accordance with a Custodian Agreement. The Custodian holds cash, securities, and other assets of the Fund as required by the Act. Custody fees are payable monthly based on assets held in custody, investment purchases and sales activity and account maintenance fees, plus reimbursement for certain out-of-pocket expenses.

In December 2015, the Fund's Custodian announced that it had identified inconsistencies in the way in which clients were invoiced for out-of-pocket expenses from 1998 until November 2015. The dollar amount difference between what was charged and what should have been charged, plus interest, was paid back to the Portfolio in September 2016 as a reimbursement. State Street reimbursed the Portfolio directly, which was recognized as a change in accounting estimate and was reflected as "Reimbursement of Custodian Fees" in the Statement of Operations. Pursuant to the expense limitations described in Note B, the Portfolio has experienced investment advisory fee waivers during the current period. Accordingly, the reimbursement of out-of-pocket expenses in the current period resulted in the reduction in the current period waiver of advisory fees.

G. Security Transactions and Transactions with Affiliates: For the year ended September 30, 2016, purchases and sales of investment securities for the Portfolio, other than

long-term U.S. Government securities and short-term investments, were approximately $43,802,000 and $52,806,000, respectively. For the year ended September 30, 2016, purchases and sales of long-term U.S. Government securities were approximately $445,145,000 and $435,052,000, respectively.

The Portfolio invests in the Institutional Class of the Morgan Stanley Institutional Liquidity Funds (the "Liquidity Funds"), an open-end management investment company managed by the Adviser, both directly and as a portion of the securities held as collateral on loaned securities. Advisory fees paid by the Portfolio are reduced by an amount equal to its pro-rata share of the advisory and administration fees paid by the Portfolio due to its investment in the Liquidity Funds. For the year ended September 30, 2016, advisory fees paid were reduced by approximately $25,000 relating to the Portfolio's investment in the Liquidity Funds.

A summary of the Portfolio's transactions in shares of the Liquidity Funds during the year ended September 30, 2016 is as follows:

Value September 30, 2015 (000)				Purchases at Cost (000)				Sales (000)				Dividend Income (000)				Value September 30, 2016 (000)
$	25,450			$	136,973			$	133,831			$	56			$	28,592

The Portfolio is permitted to purchase and sell securities ("cross-trade") from and to other Morgan Stanley Funds as well as other funds and client accounts for which the Adviser or an affiliate of the Adviser serves as investment adviser, pursuant to procedures approved by the Trustees in compliance with Rule 17a-7 under the Act (the "Rule"). Each cross-trade is executed at the current market price in compliance with provisions of the Rule. For the year ended September 30, 2016, the Portfolio did not engage in any cross-trade transactions.

The Portfolio has an unfunded Deferred Compensation Plan (the "Compensation Plan"), which allows each independent Trustee to defer payment of all, or a portion, of the fees he or she receives for serving on the Board of Trustees. Each eligible Trustee generally may elect to have the deferred amounts credited with a return equal to the total return on one or more of the Morgan Stanley funds that are offered as investment options under the Compensation Plan. Appreciation/depreciation and distributions received from these investments are recorded with an offsetting increase/decrease in the deferred compensation obligation and do not affect the NAV of the Portfolio.

H. Federal Income Taxes: It is the Portfolio's intention to continue to qualify as a regulated investment company and

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

distribute all of its taxable and tax-exempt income. Accordingly, no provision for federal income taxes is required in the financial statements.

The Portfolio may be subject to taxes imposed by countries in which it invests. Such taxes are generally based on income and/or capital gains earned or repatriated. Taxes are accrued based on net investment income, net realized gains and net unrealized appreciation as such income and/or gains are earned. Taxes may also be based on transactions in foreign currency and are accrued based on the value of investments denominated in such currency.

FASB ASC 740-10, "Income Taxes — Overall", sets forth a minimum threshold for financial statement recognition of the benefit of a tax position taken or expected to be taken in a tax return. Management has concluded there are no significant uncertain tax positions that would require recognition in the financial statements. If applicable, the Portfolio recognizes interest accrued related to unrecognized tax benefits in "Interest Expense" and penalties in ''Other Expenses" in the Statement of Operations. The Portfolio files tax returns with the U.S. Internal Revenue Service, New York and various states. Each of the tax years in the four-year period ended September 30, 2016, remains subject to examination by taxing authorities.

The tax character of distributions paid may differ from the character of distributions shown in the Statements of Changes in Net Assets due to short-term capital gains being treated as ordinary income for tax purposes. The tax character of distributions paid during fiscal years 2016 and 2015 was as follows:

2016 Distributions Paid From: Ordinary Income (000)				2015 Distributions Paid From: Ordinary Income (000)
$	7,663			$	6,119

The amount and character of income and gains to be distributed are determined in accordance with income tax regulations which may differ from GAAP. These book/tax differences are either considered temporary or permanent in nature.

Temporary differences are attributable to differing book and tax treatments for the timing of the recognition of gains (losses) on certain investment transactions and the timing of the deductibility of certain expenses.

Permanent differences, primarily due to differing treatments of gains (losses) related to foreign currency transactions, basis adjustments for swap transactions and paydown adjustments,

resulted in the following reclassifications among the components of net assets at September 30, 2016:

Accumulated Undistributed Net Investment Income (000)				Accumulated Net Realized Loss (000)				Paid-in-Capital (000)
$	(507	)		$	507			$	—

At September 30, 2016, the components of distributable earnings for the Portfolio on a tax basis were as follows:

Undistributed Ordinary Income (000)				Undistributed Long-Term Capital Gain (000)
$	2,731			$	—

At September 30, 2016, the Portfolio had available for federal income tax purposes unused capital losses which will expire on the indicated dates:

Amount (000)		Expiration
$	244,990	September 30, 2017
	201,462	September 30, 2018

To the extent that capital loss carryforwards are used to offset any future capital gains realized during the carryover period as provided by U.S. federal income tax regulations, no capital gains tax liability will be incurred by the Portfolio for gains realized and not distributed. To the extent that capital gains are offset, such gains will not be distributed to the shareholders. During the year ended September 30, 2016, the Portfolio utilized capital loss carryforwards for U.S. federal income tax purposes of approximately $14,610,000.

I. Credit Facility: As of April 4, 2016, the Fund and other Morgan Stanley funds participate in a $150,000,000 committed, unsecured revolving line of credit facility (the "facility") with State Street. This facility is to be used for temporary emergency purposes or funding of shareholder redemption requests. The interest rate on borrowings is based on the federal funds rate or one month libor rate plus a spread. The facility also has a commitment fee of 0.25% per annum based on the unused portion of the facility. During the year ended September 30, 2016, the Portfolio did not have any borrowings under the facility.

J. Other: At September 30, 2016, the Portfolio had record owners of 10% or greater. Investment activities of these shareholders could have a material impact on the Portfolio. The aggregate percentage of such owners was 69.7%.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Report of Independent Registered Public Accounting Firm

To the Shareholders and Board of Trustees of
Morgan Stanley Institutional Fund Trust —
Core Plus Fixed Income Portfolio

We have audited the accompanying statement of assets and liabilities, including the portfolio of investments, of Core Plus Fixed Income Portfolio (one of the portfolios constituting Morgan Stanley Institutional Fund Trust) (the "Portfolio") as of September 30, 2016, and the related statement of operations for the year then ended, the statements of changes in net assets for each of the two years in the period then ended and the financial highlights for each of the years or periods indicated therein. These financial statements and financial highlights are the responsibility of the Portfolio's management. Our responsibility is to express an opinion on these financial statements and financial highlights based on our audits.

We conducted our audits in accordance with the standards of the Public Company Accounting Oversight Board (United States). Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements and financial highlights are free of material misstatement. We were not engaged to perform an audit of the Portfolio's internal control over financial reporting. Our audits included consideration of internal control over financial reporting as a basis for designing audit procedures that are appropriate in the circumstances, but not for the purpose of expressing an opinion on the effectiveness of the Portfolio's internal control over financial reporting. Accordingly, we express no such opinion. An audit also includes examining, on a test basis, evidence supporting the amounts and disclosures in the financial statements and financial highlights, assessing the accounting principles used and significant estimates made by management, and evaluating the overall financial statement presentation. Our procedures included confirmation of securities owned as of September 30, 2016, by correspondence with the custodian and others or by other appropriate auditing procedures where replies from others were not received. We believe that our audits provide a reasonable basis for our opinion.

In our opinion, the financial statements and financial highlights referred to above present fairly, in all material respects, the financial position of Core Plus Fixed Income Portfolio (one of the portfolios constituting Morgan Stanley Institutional Fund Trust) at September 30, 2016, the results of its operations for the year then ended, the changes in its net assets for each of the two years in the period then ended and the financial highlights for each of the years or periods indicated therein, in conformity with U.S. generally accepted accounting principles.

Boston, Massachusetts
November 22, 2016

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Advisory Agreement Approval (unaudited)

Nature, Extent and Quality of Services

The Board reviewed and considered the nature and extent of the investment advisory services provided by the Adviser (as defined herein) under the advisory agreement, including portfolio management, investment research and equity and fixed income securities trading. The Board also reviewed and considered the nature and extent of the non-advisory, administrative services provided by the Adviser under the administration agreement, including accounting, operations, clerical, bookkeeping, compliance, business management and planning, legal services and the provision of supplies, office space and utilities at the Adviser's expense. The Board also considered the Adviser's investment in personnel and infrastructure that benefits the Portfolio. (The advisory and administration agreements together are referred to as the "Management Agreement.") The Board also considered that the Adviser serves a variety of other investment advisory clients and has experience overseeing service providers. The Board also compared the nature of the services provided by the Adviser with similar services provided by non-affiliated advisers as reported to the Board by Broadridge Financial Solutions, Inc. ("Broadridge").

The Board reviewed and considered the qualifications of the portfolio managers, the senior administrative managers and other key personnel of the Adviser who provide the administrative and advisory services to the Portfolio. The Board determined that the Adviser's portfolio managers and key personnel are well qualified by education and/or training and experience to perform the services in an efficient and professional manner. The Board concluded that the nature and extent of the advisory and administrative services provided were necessary and appropriate for the conduct of the business and investment activities of the Portfolio and supported its decision to approve the Management Agreement.

Performance, Fees and Expenses of the Portfolio

The Board reviewed the performance, fees and expenses of the Portfolio compared to its peers, as determined by Broadridge, and to appropriate benchmarks where applicable. The Board discussed with the Adviser the performance goals and the actual results achieved in managing the Portfolio. When considering a fund's performance, the Board and the Adviser place emphasis on trends and longer-term returns (focusing on one-year, three-year and five-year performance, as of December 31, 2015, or since inception, as applicable). When a fund underperforms its benchmark and/or its peer group average, the Board and the Adviser discuss the causes of such underperformance and, where necessary, they discuss specific changes to investment strategy or investment personnel. The Board noted that the Portfolio's performance was better than its peer group average for the one-, three- and five-year periods. The Board discussed with the Adviser the level of the advisory and administration fees (together, the "management fee") for this Portfolio relative to comparable funds and/or other accounts advised by the Adviser and/or compared to its peers as determined by Broadridge. In addition to the management fee, the Board also reviewed the Portfolio's total expense ratio. The Board noted that the Portfolio's management fee and total expense ratio were lower than its peer group averages. After discussion, the Board concluded that the Portfolio's performance (i) was competitive with its peer group average; and (ii) management fee and total expense ratio were competitive with its peer group averages.

Economies of Scale

The Board considered the size and growth prospects of the Portfolio and how that relates to the Portfolio's total expense ratio and particularly the Portfolio's management fee rate, which includes a breakpoint. In conjunction with its review of the Adviser's profitability, the Board discussed with the Adviser how a change in assets can affect the efficiency or effectiveness of managing the Portfolio and whether the management fee level is appropriate relative to current and projected asset levels and/or whether the management fee structure reflects economies of scale as asset levels change. The Board has determined that its review of the actual and/or potential economies of scale of the Portfolio supports its decision to approve the Management Agreement.

Profitability of the Adviser and Affiliates

The Board considered information concerning the costs incurred and profits realized by the Adviser and its affiliates during the last year from their relationship with the Portfolio and during the last two years from their relationship with the Morgan Stanley Fund Complex and reviewed with the Adviser the cost allocation methodology used to determine the profitability of the Adviser and affiliates. The Board has determined that its review of the analysis of the Adviser's expenses and profitability supports its decision to approve the Management Agreement.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Advisory Agreement Approval (unaudited) (cont'd)

Other Benefits of the Relationship

The Board considered other direct and indirect benefits to the Adviser and/or its affiliates derived from their relationship with the Fund and other funds advised by the Adviser. These benefits may include, among other things, fees for trading, distribution and/or shareholder servicing and for transaction processing and reporting platforms used by securities lending agents, and research received by the Adviser generated from commission dollars spent on funds' portfolio trading. The Board reviewed with the Adviser these arrangements and the reasonableness of the Adviser's costs relative to the services performed. The Board has determined that its review of the other benefits received by the Adviser or its affiliates supports its decision to approve the Management Agreement.

Resources of the Adviser and Historical Relationship Between the Portfolio and the Adviser

The Board considered whether the Adviser is financially sound and has the resources necessary to perform its obligations under the Management Agreement. The Board also reviewed and considered the historical relationship between the Portfolio and the Adviser, including the organizational structure of the Adviser, the policies and procedures formulated and adopted by the Adviser for managing the Portfolio's operations and the Board's confidence in the competence and integrity of the senior managers and key personnel of the Adviser. The Board concluded that the Adviser has the financial resources necessary to fulfill its obligations under the Management Agreement and that it is beneficial for the Portfolio to continue its relationship with the Adviser.

Other Factors and Current Trends

The Board considered the controls and procedures adopted and implemented by the Adviser and monitored by the Fund's Chief Compliance Officer and concluded that the conduct of business by the Adviser indicates a good faith effort on its part to adhere to high ethical standards in the conduct of the Portfolio's business.

General Conclusion

After considering and weighing all of the above factors, with various written materials and verbal information presented by the Adviser, the Board concluded that it would be in the best interest of the Portfolio and its shareholders to approve renewal of the Management Agreement for another year. In reaching this conclusion the Board did not give particular weight to any single piece of information or factor referenced above. The Board considered these factors and information over the course of the year and in numerous meetings, some of which were in executive session with only the independent Board members and their counsel present. It is possible that individual Board members may have weighed these factors, and the information presented, differently in reaching their individual decisions to approve the Management Agreement.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Privacy Notice (unaudited)

MORGAN STANLEY INVESTMENT MANAGEMENT INC.
AN IMPORTANT NOTICE CONCERNING OUR U.S. PRIVACY POLICY

We are required by federal law to provide you with a copy of our privacy policy annually. This policy applies to current and former individual investors in funds managed or sponsored by Morgan Stanley Investment Management Inc. ("MSIM") as well as current and former individual clients of MSIM. This policy is not applicable to partnerships, corporations, trusts or other non-individual clients or investors. Please note that we may amend this policy at any time, and will inform you of any changes as required by law.

WE RESPECT YOUR PRIVACY

We appreciate that you have provided us with your personal financial information. We strive to maintain the privacy of such information while we help you achieve your financial objectives. This Notice describes what non-public personal information we collect about you, why we collect it, when we may share it with others and how certain others may use it. It discusses the steps you may take to limit our sharing of certain information about you to affiliated companies in the Morgan Stanley family of companies ("other Morgan Stanley companies"). It also discloses how you may limit use of certain shared information for marketing purposes by other Morgan Stanley branded companies. Throughout this policy, we refer to the non-public information that personally identifies you or your accounts as "personal information.''

1. WHAT PERSONAL INFORMATION DO WE COLLECT ABOUT YOU?

We obtain personal information from applications and other forms you submit to us, from your dealings with us, from consumer reporting agencies, from our Web sites and from third parties and other sources.

For example:

• We may collect information such as your name, address, e-mail address, telephone/fax numbers, assets, income and investment objectives through subscription documents, applications and other forms you submit to us.

• We may obtain information about account balances, your use of account(s) and the types of products and services you prefer to receive from us through your dealings and transactions with us and other sources.

• We may obtain information about your creditworthiness and credit history from consumer reporting agencies.

• We may collect background information from and through third-party vendors to verify representations you have made and to comply with various regulatory requirements.

• If you interact with us through our public and private Web sites, we may collect information that you provide directly through online communications (such as an e-mail address). We may also collect information about your Internet service provider, your domain name, your computer's operating system and Web browser, your use of our Web sites and your product and service preferences, through the use of "cookies." Please consult the Terms of Use of these sites for more details.

2. WHEN DO WE DISCLOSE PERSONAL INFORMATION WE COLLECT ABOUT YOU?

We may disclose personal information we collect about you to other Morgan Stanley companies and to non-affiliated third parties.

a. Information We Disclose to Other Morgan Stanley Companies.

We may disclose personal information to other Morgan Stanley companies for a variety of reasons, including to manage your account(s) effectively, to service and process your transactions, to let you know about products and services offered by us and other Morgan Stanley companies, to manage our business, and as otherwise required or permitted by law. Offers for products and services from other Morgan Stanley companies are developed under conditions designed to safeguard your personal information.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Privacy Notice (unaudited) (cont'd)

b. Information We Disclose to Non-affiliated Third Parties.

We do not disclose personal information that we collect about you to non-affiliated third parties except to those who provide marketing services on our behalf, to financial institutions with whom we have joint marketing agreements, and as otherwise required or permitted by law. For example, we may disclose personal information to nonaffiliated third parties for servicing and processing transactions, to offer our own products and services, to protect against fraud, for institutional risk control, to respond to judicial process or to perform services on our behalf. When we share personal information with a non-affiliated third party, they are required to limit their use of personal information to the particular purpose for which it was shared and they are not allowed to share personal information with others except to fulfill that limited purpose or as may be permitted or required by law.

3. HOW DO WE PROTECT THE SECURITY AND CONFIDENTIALITY OF PERSONAL INFORMATION WE COLLECT ABOUT YOU?

We maintain physical, electronic and procedural security measures to help safeguard the personal information we collect about you. We have internal policies governing the proper handling of client information. Third parties that provide support or marketing services on our behalf may also receive personal information, and we require them to adhere to confidentiality standards with respect to such information.

4. HOW CAN YOU LIMIT THE SHARING OF CERTAIN TYPES OF PERSONAL INFORMATION WITH OTHER MORGAN STANLEY COMPANIES?

We offer you choices as to whether we share with other Morgan Stanley companies the personal information that was collected to determine your eligibility for products and services you request ("eligibility information"). Eligibility information does not include your identification information or personal information pertaining to our transactions or experiences with you. Please note that, even if you direct us not to share eligibility information with other Morgan Stanley companies ("opt-out"), we may still share personal information, including eligibility information, with those companies in circumstances excluded from the opt-out under applicable law, such as to process transactions or to service your account.

5. HOW CAN YOU LIMIT THE USE OF CERTAIN TYPES OF PERSONAL INFORMATION BY OTHER MORGAN STANLEY COMPANIES FOR MARKETING?

By following the opt-out instructions in Section 6 below, you may limit other Morgan Stanley branded companies from marketing their products or services to you based on personal information we disclose to them. This information may include, for example, your income and account history with us. Please note that, even if you choose to limit Other Morgan Stanley Companies from using personal information about you that we may share with them for marketing their products and services to you, Other Morgan Stanley Companies may use your personal information that they obtain from us to market to you in circumstances permitted by law, such as if the Other Morgan Stanley Company has its own relationship with you.

6. HOW CAN YOU SEND US AN OPT-OUT INSTRUCTION?

If you wish to limit our sharing of eligibility information about you with other Morgan Stanley companies or other Morgan Stanley companies' use of personal information for marketing purposes, as described in this notice, you may do so by:

• Calling us at (800) 548-7786
Monday–Friday between 8a.m. and 6p.m.(EST)

• Writing to us at the following address:

Boston Financial Data Services, Inc.
c/o Privacy Coordinator
P.O. Box 219804
Kansas City, Missouri 64121

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Privacy Notice (unaudited) (cont'd)

Your written request should include your name, address, telephone number and account number(s) to which the opt-out applies and whether you are opting out with respect to sharing of eligibility information (Section 4 above), or if information used for Marketing (Section 5 above) or both. Written opt-out requests should not be sent with any other correspondence. In order to process your request, we require that the request be provided by you directly and not through a third party.

Your opt-out preference will remain in effect with respect to this policy (as it may be amended) until you notify us otherwise. If you have a joint account, your direction for us not to share this information with other Morgan Stanley companies and for those other Morgan Stanley companies not to use your personal information for marketing will be applied to all account holders on that account. Please understand that if you limit our sharing or our affiliated companies' use of personal information, you and any joint account holder(s) may not receive information about Morgan Stanley products and services, including products or services that could help you manage your financial resources and achieve your investment objectives.

7. WHAT IF AN AFFILIATED COMPANY BECOMES A NON-AFFILIATED THIRD PARTY?

If, at any time in the future, an affiliated company becomes a non-affiliated third party, further disclosures of personal information made to the former affiliated company will be limited to those described in Section 2(b) above relating to non-affiliated third parties. If you elected under Section 6 to limit disclosures we make to affiliated companies, or use of personal information by affiliated companies, your election will not apply to use by any former affiliated company of your personal information in their possession once it becomes a non-affiliated third party.

SPECIAL NOTICE TO RESIDENTS OF VERMONT

The following section supplements our policy with respect to our individual clients who have a Vermont address and supersedes anything to the contrary in the above policy with respect to those clients only.

The state of Vermont requires financial institutions to obtain your consent prior to sharing personal information that they collect about you with affiliated companies and non-affiliated third parties other than in certain limited circumstances. Except as permitted by law, we will not share personal information we collect about you with non-affiliated third parties or other Morgan Stanley companies unless you provide us with your written consent to share such information ("opt-in").

If you wish to receive offers for investment products and services offered by or through other Morgan Stanley companies, please notify us in writing at the following address:

Boston Financial Data Services, Inc.
c/o Privacy Coordinator
P.O. Box 219804
Kansas City, Missouri 64121

Your authorization should include your name, address, telephone number and account number(s) to which the opt-in applies and should not be sent with any other correspondence. In order to process your authorization, we require that the authorization be provided by you directly and not through a third party.

SPECIAL NOTICE TO RESIDENTS OF CALIFORNIA

The following section supplements our policy with respect to our individual clients who have a California address and supersedes anything to the contrary in the above policy with respect to those clients only.

In response to a California law, if your account has a California home address, your personal information will not be disclosed to nonaffiliated third parties except as permitted by applicable California law, and we will limit sharing such information with our affiliates to comply with California privacy laws that apply to us.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited)

Independent Trustees:

Name, Age and Address of
Independent Trustee

Position(s)
Held with
Registrant

Length of Time
Served*

Principal Occupation(s) During Past 5 Years
and Other Relevant Professional Experience

Number of
Portfolios in
Fund Complex
Overseen by
Independent
Trustee**

Other Directorships
Held by Independent
Trustee***

Frank L. Bowman (71)
c/o Perkins Coie LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
August
2006

President, Strategic Decisions, LLC (consulting) (since February 2009); Director or Trustee of various Morgan Stanley Funds (since August 2006); Chairperson of the Compliance and Insurance Committee (since October 2015); formerly, Chairperson of the Insurance Sub-Committee of the Compliance and Insurance Committee (2007-2015); served as President and Chief Executive Officer of the Nuclear Energy Institute (policy organization) (February 2005-November 2008); retired as Admiral, U.S. Navy after serving over 38 years on active duty including 8 years as Director of the Naval Nuclear Propulsion Program in the Department of the Navy and the U.S. Department of Energy (1996-2004); served as Chief of Naval Personnel (July 1994-September 1996) and on the Joint Staff as Director of Political Military Affairs (June 1992-July 1994); knighted as Honorary Knight Commander of the Most Excellent Order of the British Empire; awarded the Officier de l'Orde National du Mérite by the French Government; elected to the National Academy of Engineering (2009).

Director of BP p.l.c.; Director of Naval and Nuclear Technologies LLP; Director Emeritus of the Armed Services YMCA of the USA; Director of the U.S. Naval Submarine League; Member of the National Security Advisory Council of the Center for U.S. Global Engagement and a member of the CNA Military Advisory Board; Chairman of the charity J Street Cup Golf; Trustee of Fairhaven United Methodist Church; and Director of other various non-profit organizations.

Kathleen A. Dennis (63)
c/o Perkins Coie LLP
Counsel to the Independent Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
August
2006

President, Cedarwood Associates (mutual fund and investment management consulting) (since July 2006); Chairperson of the Liquidity and Alternatives Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Senior Managing Director of Victory Capital Management (1993-2006).

Director of various non-profit organizations.

Nancy C. Everett (61)
c/o Perkins Coie LLP
Counsel to the Independent Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
January
2015

Chief Executive Officer, Virginia Commonwealth University Investment Company (since November 2015); Owner OBIR, LLC (institutional investment management consulting) (since June 2014); formerly, Managing Director, BlackRock, Inc. (February 2011-December 2013); and Chief Executive Officer, General Motors Asset Management (a/k/a Promark Global Advisors, Inc.) (June 2005-May 2010).

Member of Virginia Commonwealth University School of Business Foundation; formerly, Member of Virginia Commonwealth University Board of Visitors (2013-2015); Member of Committee on Directors for Emerging Markets Growth Fund, Inc. (2007-2010); Chairperson of Performance Equity Management, LLC (2006-2010); and Chairperson, GMAM Absolute Return Strategies Fund, LLC (2006-2010).

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Age and Address of
Independent Trustee

Position(s)
Held with
Registrant

Length of Time
Served*

Principal Occupation(s) During Past 5 Years
and Other Relevant Professional Experience

Number of
Portfolios in
Fund Complex
Overseen by
Independent
Trustee**

Other Directorships
Held by Independent
Trustee***

Jakki L. Haussler (59)
c/o Perkins Coie LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
January
2015

Chairman and Chief Executive Officer, Opus Capital Group (since January 1996); formerly, Director, Capvest Venture Fund, LP (May 2000-December 2011); Partner, Adena Ventures, LP (July 1999-December 2010); Director, The Victory Funds (February 2005-July 2008).

Director of Cincinnati Bell Inc. and Member, Audit Committee and Compensation Committee; Director of Northern Kentucky University Foundation and Member, Investment Committee; Member of Chase College of Law Transactional Law Practice Center Board of Advisors; Director of Best Transport; Director of Chase College of Law Board of Visitors; formerly, Member, University of Cincinnati Foundation Investment Committee; Member, Miami University Board of Visitors (2008-2011); Trustee of Victory Funds (2005-2008) and Chairman, Investment Committee (2007-2008) and Member, Service Provider Committee (2005-2008).

Dr. Manuel H. Johnson (67)
c/o Johnson Smick
International, Inc.
220 I Street, N.E. —
Suite 200
Washington, D.C. 20002

Trustee

Since
July
1991

Senior Partner, Johnson Smick International, Inc. (consulting firm); Chairperson of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since July 1991); Co-Chairman and a founder of the Group of Seven Council (G7C) (international economic commission); formerly, Chairperson of the Audit Committee (July 1991-September 2006), Vice Chairman of the Board of Governors of the Federal Reserve System and Assistant Secretary of the U.S. Treasury.

100

Director of NVR, Inc. (home construction).

Joseph J. Kearns (74)
c/o Kearns & Associates LLC
23823 Malibu Road
S-50-440
Malibu, CA 90265

Trustee

Since
August
1994

President, Kearns & Associates LLC (investment consulting); Chairperson of the Audit Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 1994); formerly, Deputy Chairperson of the Audit Committee (July 2003-September 2006) and Chairperson of the Audit Committee of various Morgan Stanley Funds (since August 1994); CFO of the J. Paul Getty Trust.

101

Director of Electro Rent Corporation (equipment leasing). Prior to December 31, 2013, Director of The Ford Family Foundation.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Age and Address of
Independent Trustee

Position(s)
Held with
Registrant

Length of Time
Served*

Principal Occupation(s) During Past 5 Years
and Other Relevant Professional Experience

Number of
Portfolios in
Fund Complex
Overseen by
Independent
Trustee**

Other Directorships
Held by Independent
Trustee***

Michael F. Klein (57)
c/o Perkins Coie LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
August
2006

Managing Director, Aetos Capital, LLC (since March 2000); Co-President, Aetos Alternatives Management, LLC (since January 2004) and Co-Chief Executive Officer of Aetos Capital LLC (since August 2013); Chairperson of the Fixed Income Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, Managing Director, Morgan Stanley & Co. Inc. and Morgan Stanley Dean Witter Investment Management, President, various Morgan Stanley Funds (June 1998-March 2000) and Principal, Morgan Stanley & Co. Inc. and Morgan Stanley Dean Witter Investment Management (August 1997-December 1999).

Director of certain investment funds managed or sponsored by Aetos Capital, LLC; Director of Sanitized AG and Sanitized Marketing AG (specialty chemicals).

Michael E. Nugent (80)
522 Fifth Avenue
New York, NY 10036

Chair of the
Board and
Trustee

Chair of the Boards since
July 2006 and Trustee since
July 1991

Chair of the Boards of various Morgan Stanley Funds (since July 2006); Chairperson of the Closed-End Fund Committee (since June 2012) and Director or Trustee of various Morgan Stanley Funds (since July 1991); formerly, Chairperson of the Insurance Committee (until July 2006); General Partner, Triumph Capital, L.P. (private investment partnership) (1988-2013).

100

None.

W. Allen Reed (69)
c/o Perkins Coie LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
August
2006

Chairperson of the Equity Sub-Committee of the Investment Committee (since October 2006) and Director or Trustee of various Morgan Stanley Funds (since August 2006); formerly, President and CEO of General Motors Asset Management; Chairman and Chief Executive Officer of the GM Trust Bank and Corporate Vice President of General Motors Corporation (August 1994-December 2005).

Director of Legg Mason, Inc.; formerly, Director of the Auburn University Foundation (2010-2015).

Fergus Reid (84)
c/o Joe Pietryka, Inc.
85 Charles Colman Blvd.
Pawling, NY 12564

Trustee

Since
June
1992

Chairman, Joe Pietryka, Inc.; Chairperson of the Governance Committee and Director or Trustee of various Morgan Stanley Funds (since June 1992).

100

Formerly, Trustee and Director of certain investment companies in the JP Morgan Fund Complex managed by JP Morgan Investment Management Inc. (1987-2012).

* This is the earliest date the Trustee began serving the Morgan Stanley Funds. Each Trustee serves an indefinite term, until his or her successor is elected.

** The Fund Complex includes (as of December 31, 2015) all open-end and closed-end funds (including all of their portfolios) advised by Morgan Stanley Investment Management Inc. (the "Adviser") and any funds that have an adviser that is an affiliated person of the Adviser (including, but not limited to, Morgan Stanley AIP GP LP).

*** This includes any directorships at public companies and registered investment companies held by the Trustee at any time during the past five years.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited) (cont'd)

Executive Officers:

Name, Age and Address of Executive Officer

Position(s) Held
with
Registrant

Length of
Time Served*

Principal Occupation(s) During Past 5 Years

John H. Gernon (53)
522 Fifth Avenue
New York, NY 10036

President and
Principal
Executive
Officer

Since
September
2013

President and Principal Executive Officer of the Equity and Fixed Income Funds and the Morgan Stanley AIP Funds (since September 2013) and the Liquidity Funds and various money market funds (since May 2014) in the Fund Complex; Managing Director of the Adviser; Head of Product (since 2006).

Stefanie V. Chang Yu (49)
522 Fifth Avenue
New York, NY 10036

Chief
Compliance
Officer

Since
December
1997

Managing Director of the Adviser and various entities affiliated with the Adviser; Chief Compliance Officer of various Morgan Stanley Funds and the Adviser (since January 2014); formerly, Vice President of various Morgan Stanley Funds (December 1997-January 2014).

Joseph C. Benedetti (51)
522 Fifth Avenue
New York, NY 10036

Vice President

Since
January
2014

Managing Director of the Adviser and various entities affiliated with the Adviser; Vice President of various Morgan Stanley Funds (since January 2014); formerly, Assistant Secretary of various Morgan Stanley Funds (October 2004-January 2014).

Francis J. Smith (51)
522 Fifth Avenue
New York, NY 10036

Treasurer and
Principal
Financial
Officer

Treasurer
since July
2003 and
Principal
Financial
Officer since
September
2002

Executive Director of the Adviser and various entities affiliated with the Adviser; Treasurer (since July 2003) and Principal Financial Officer of various Morgan Stanley Funds (since September 2002).

Mary E. Mullin (49)
522 Fifth Avenue
New York, NY 10036

Secretary

Since
June
1999

Executive Director of the Adviser; Secretary of various Morgan Stanley Funds (since June 1999).

* This is the earliest date the officer began serving the Morgan Stanley Funds. Each officer serves a one-year term, until his or her successor is elected and has qualified.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Adviser and Administrator

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

Distributor

Morgan Stanley Distribution, Inc.
522 Fifth Avenue
New York, New York 10036

Dividend Disbursing and Transfer Agent

Boston Financial Data Services, Inc.
2000 Crown Colony Drive
Quincy, Massachusetts 02169

Custodian

State Street Bank and Trust Company
One Lincoln Street
Boston, Massachusetts 02111

Legal Counsel

Dechert LLP
1095 Avenue of the Americas
New York, New York 10036

Counsel to the Independent Trustees

Perkins Coie LLP
30 Rockefeller Plaza
New York, New York 10112

Independent Registered Public Accounting Firm

Ernst & Young LLP
200 Clarendon Street
Boston, Massachusetts 02116

Reporting to Shareholders

Each Morgan Stanley fund provides a complete schedule of portfolio holdings in its semi-annual and annual reports within 60 days of the end of the fund's second and fourth fiscal quarters. The semi-annual and annual reports are filed electronically with the Securities and Exchange Commission (SEC) on Form N-CSRS and Form N-CSR, respectively. Morgan Stanley also delivers the semi-annual and annual reports to fund shareholders and makes these reports available on its public website, www.morganstanley.com/im. Each Morgan Stanley fund also files a complete schedule of portfolio holdings with the SEC for the fund's first and third fiscal quarters on Form N-Q. Morgan Stanley does not deliver the reports for the first and third fiscal quarters to shareholders, nor are the reports posted to the Morgan Stanley public website. You may, however, obtain the Form N-Q filings (as well as the Form N-CSR and N-CSRS filings) by accessing the SEC's website, www.sec.gov. You may also review and copy them at the SEC's Public Reference Room in Washington, DC. Information on the operation of the SEC's Public Reference Room may be obtained by calling the SEC toll free at 1 (800) SEC-0330. You can also request copies of these materials, upon payment of a duplicating fee, by electronic request at the SEC's email address (publicinfo@sec.gov) or by writing the Public Reference Room of the SEC, Washington, DC 20549-0102.

Proxy Voting Policies and Procedures and Proxy Voting Record

You may obtain a copy of the Fund's Proxy Voting Policy and Procedures and information regarding how the Fund voted proxies relating to portfolio securities during the most recent twelve-month period ended June 30, without charge, upon request, by calling toll free 1 (800) 548-7786 or by visiting our website at www.morganstanley.com/im. This information is also available on the SEC's website at www.sec.gov.

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable Portfolio of Morgan Stanley Institutional Funds Trust, which describes in detail the Portfolio's investment policies, risks, fees and expenses. Please read the prospectus carefully before you invest or send money. For additional information, including information regarding the investments comprising the Portfolio, please visit our website at www.morganstanley.com/im or call toll free 1 (800) 548-7786.

(This Page has been left blank intentionally.)

Printed in U.S.A.
This Report has been prepared for shareholders and may be distributed to others only if preceded or accompanied by a current prospectus.

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

IFTCPFIANN
1627522EXP. 11.30.17

INVESTMENT MANAGEMENT

Morgan Stanley Institutional Fund Trust

Corporate Bond Portfolio

Annual Report

September 30, 2016

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Table of Contents

Shareholders' Letter					2
Expense Example					3
Investment Overview					4
Portfolio of Investments					7
Statement of Assets and Liabilities					14
Statement of Operations					16
Statements of Changes in Net Assets					17
Financial Highlights					18
Notes to Financial Statements					22
Report of Independent Registered Public Accounting Firm					32
Investment Advisory Agreement Approval					33
Privacy Notice					35
Trustee and Officer Information					38

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Shareholders' Letter (unaudited)

Dear Shareholders,

We are pleased to provide this Annual report, in which you will learn how your investment in Corporate Bond Portfolio (the "Portfolio") performed during the latest twelve-month period.

As always, we thank you for selecting Morgan Stanley Investment Management, and look forward to working with you in the months and years ahead.

Sincerely,

John H. Gernon
President and Principal Executive Officer

October 2016

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Expense Example (unaudited)

Corporate Bond Portfolio

This example is based on an investment of $1,000 invested at the beginning of the six-month period ended September 30, 2016 and held for the entire six-month period (unless otherwise noted).

Actual Expenses

Hypothetical Example for Comparison Purposes

	Beginning Account Value 4/1/16		Actual Ending Account Value 9/30/16		Hypothetical Ending Account Value		Actual Expenses Paid During Period*		Hypothetical Expenses Paid During Period*		Net Expense Ratio During Period**
Corporate Bond Portfolio Class I	$	1,000.00	$	1,086.90	$	1,021.55	$	3.60	$	3.49		0.69	%***
Corporate Bond Portfolio Class A		1,000.00		1,084.50		1,020.10		5.11		4.95		0.98	***
Corporate Bond Portfolio Class L		1,000.00		1,082.70		1,018.25		7.03		6.81		1.35	***
Corporate Bond Portfolio Class C		1,000.00		1,080.50		1,016.05		9.31		9.02		1.79	***

** Annualized.

*** Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Overview (unaudited)

Corporate Bond Portfolio

The Portfolio seeks above-average total return over a market cycle of three to five years.

Performance

For the fiscal year ended September 30, 2016, the Portfolio's Class I shares had a total return based on net asset value and reinvestment of distributions per share of 17.79%, net of fees. The Portfolio's Class I shares outperformed against the Portfolio's benchmark, the Bloomberg Barclays U.S. Corporate Index (the "Index"), which returned 8.56%.

During calendar year 2016, the Portfolio received monies related to certain nonrecurring litigation settlements. If these monies were not received, any period returns which include these settlement monies would have been lower. For example, the 2016 fiscal year total return would have been 8.78% for Class I Shares as of September 30, 2016. The returns on the other Share Classes would also have been similarly impacted. These were one-time settlements, and as a result, the impact on the net asset value and consequently the performance will not likely be repeated in the future. Please call 1-800-548-7786 for additional information.

Factors Affecting Performance

• Concerns about global growth, monetary policy, the U.K. referendum, and commodities kept markets volatile during the period. The market traded well in the fourth quarter of 2015; however, asset prices suffered in the first quarter of 2016, as risk premia rose on commodity concerns. A rally over the last two quarters of 2016 has erased much of the rise in yields (as bond prices move inversely to yields).

• June marked the occurrence of a risk event that captured market attention, as the unexpected outcome of the U.K. referendum vote resulted in high volatility in the days following its conclusion. Asset prices quickly recovered, however, as strong demand for credit mitigated the potential negatives of the referendum outcome on the credit markets.

• The third quarter saw a return to focus on central bank policy, as Federal Open Market Committee (FOMC) members' median expectations projected one hike for 2016 at their September meeting. This suggests that a move in December is likely. The September meeting also confirmed that rate hikes

will likely occur at a slow pace, which should mitigate potential market volatility. This return to the pre-Brexit market pattern led to strong performance by most financial assets during the third quarter 2016.

• Over the 12-month reporting period, the Treasury yields fell and the yield curve flattened. With lower growth globally as well as diminished expectations for economic growth and inflation, intermediate and long rates rallied over the period. Specifically, the 5-, 10- and 30-year Treasury yields ended 24, 44 and 54 basis points lower, respectively.¹ U.S. 2-year Treasury yields ended the period higher, up 13 basis points.

• While quite volatile intra-period, credit spreads ended the period tighter. The corporate sector as a whole was 31 basis points tighter over the 12-month period.² In aggregate, BBB corporate spreads contracted 47 basis points, while single A corporate spreads were 20 basis points tighter.² Non-financials outperformed financials, with industrials spreads narrowing 44 basis points and financials tightening 8 basis points.²

• Another driver of credit spreads is the technical balance between supply and demand. Supply volume has been elevated across many of the credit markets. This has been most apparent in the U.S. investment grade market, where a combination of increased merger and acquisition activity and the fear that an interest rate tightening cycle could increase the future cost of long-term debt financing has caused corporate treasurers to turn to the bond markets. As a result, year-to-date new issue volumes have been running at record pace. This is to a lesser extent also true in the U.S. high yield and European investment grade markets. High supply volume has been met with high demand as global interest rates remain low and investors reach for yield.

• The Portfolio's investment grade exposure was overall a positive contributor to the Portfolio's returns. Strength in the credit market over the period resulted in tighter spreads across all major segments of the investment grade market. The Portfolio's emphasis on financial institutions, specifically the banking sector, was particularly

¹ Source for U.S. Treasury yields: Bloomberg L.P.

² Source for credit spread data: Barclays

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Overview (unaudited) (cont'd)

Corporate Bond Portfolio

advantageous for performance over the reporting period. The Portfolio has an underweight to industrials, attributable to deteriorating fundamentals and less favorable relative value within the industrials segment of the market. The industrials underweight contributed positively to performance over the period; however, most of this performance was realized by an overweight to the communications and consumer cyclical sectors.

• The Portfolio's positioning within the investment grade sectors of capital goods, energy, and basic industry detracted somewhat from overall investment grade performance, due to market volatility in these sub-sectors. Additionally, the Portfolio's utility sector positioning had a negative impact on overall performance within the investment grade segment of the credit market.

• An opportunistic allocation to below investment grade (or high yield) credits also contributed to the Portfolio's performance. As with the investment grade market, despite volatility over the period, the high yield market benefited from spread tightening and yield advantages that led to positive returns.

• During the year, the Portfolio's overweight to credit was favorable for performance as yields tightened during the period. Duration exposure was managed with futures.

Management Strategies

• Accommodative policy and low global yields remain supportive of global credit, particularly U.S. credit, and we continue to believe the strong technical environment in global credit markets suggests modest tightening into year-end. We remain cautious, however, as we enter the last quarter of 2016 and continue to observe potential risk factors that may derail the positive momentum and technical support in credit. Challenges in the financial system, weakening credit fundamentals, commodity volatility, and the potential for less central bank support are risks we remain cognizant of. While we continue to monitor these potential risks, we believe the robust technical environment, particularly in the U.S., will continue to dominate the price-action in global credit into year-end.

• Despite our favorable outlook on investment grade corporates, we remain cognizant that the business cycle is maturing. Company behavior in later-cycle environments is often tilted in favor of equity holders at the expense of bond holders. As a result, we remain reliant upon our active, value-oriented approach and bottom-up credit research process to help identify the best value opportunities, while avoiding those companies where we believe there is limited scope to earn attractive returns.

• Given this outlook, we continue to position the Portfolio to be overweight credit risk, particularly in the financial sector, where we believe that the fundamental story remains one of secular de-risking as banks look to shore up their balance sheets, increase liquidity and reduce their risky activities. In the non-financial segment of the investment grade market, the Portfolio is underweight, due to deteriorating fundamentals and stretched valuations.

• The Portfolio continues to hold small allocations to high yield bonds, as we believe that both fundamentals and valuations may well compensate investors for bearing risk.

* Minimum Investment

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Overview (unaudited) (cont'd)

Corporate Bond Portfolio

Performance Compared to the Bloomberg Barclays U.S. Corporate Index⁽¹⁾ and the Lipper Corporate Debt Funds BBB-Rated Index⁽²⁾

	Period Ended September 30, 2016 Total Returns⁽³⁾
				Average Annual
	One Year			Five Years			Ten Years			Since Inception⁽⁸⁾
Portfolio — Class I Shares w/o sales charges⁽⁴⁾		17.79	%		7.11	%		4.99	%		6.68	%
Portfolio — Class A Shares w/o sales charges⁽⁵⁾		17.41			6.84			4.78			4.81
Portfolio — Class A Shares with maximum 4.25% sales charges⁽⁵⁾		12.42			5.91			4.33			4.49
Portfolio — Class L Shares w/o sales charges⁽⁶⁾		17.06			6.51			—			5.55
Portfolio — Class C Shares w/o sales charges⁽⁷⁾		16.47			—			—			8.66
Portfolio — Class C Shares with maximum 1.00% deferred sales charges⁽⁷⁾		15.47			—			—			8.66
Bloomberg Barclays U.S. Corporate Index		8.56			5.14			5.91			7.13
Lipper Corporate Debt Funds BBB-Rated Index		9.26			5.18			5.68			6.72

⁽¹⁾ The Bloomberg Barclays U.S. Corporate Index is a broad-based benchmark that measures the investment grade, U.S. dollar-denominated, fixed rate, taxable corporate bond market. It includes USD-denominated securities publicly issued by U.S. and non-U.S. industrial, utility and financial issuers that meet specified maturity, liquidity and quality requirements.The Index is unmanaged and its returns do not include any sales charges or fees. Such costs would lower performance. It is not possible to invest directly in an index.

⁽²⁾ The Lipper Corporate Debt Funds BBB-Rated Index is an equally weighted performance index of the largest qualifying funds (based on net assets) in the Lipper Corporate Debt Funds BBB-Rated Funds classification. The Index, which is adjusted for capital gains distributions and income dividends, is unmanaged and should not be considered an investment. There are currently 30 funds represented in this Index. As of the date of this report, the Portfolio was in the Lipper Corporate Debt Funds BBB-Rated Funds classification.

⁽³⁾ Total returns for the Portfolio reflect expenses waived and/or reimbursed, if applicable, by the Adviser and Distributor. Without such waivers and/or reimbursements, total returns would have been lower.

⁽⁴⁾ Commenced operations on August 31, 1990.

⁽⁵⁾ Commenced operations on May 20, 2002.

⁽⁶⁾ Commenced operations on June 16, 2008.

⁽⁷⁾ Commenced operations on April 30, 2015.

⁽⁸⁾ For comparative purposes, average annual since inception returns listed for the Indexes refer to the inception date of Class I of the Portfolio, not the inception of the Indexes.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments

Corporate Bond Portfolio

	Face Amount (000)		Value (000)
Fixed Income Securities (94.5%)
Asset-Backed Securities (0.7%)
CVS Pass-Through Trust,
6.04%, 12/10/28	$	106	$	123
8.35%, 7/10/31 (a)		125		168
				291
Corporate Bonds (92.2%)
Finance (35.6%)
ABN Amro Bank N.V.
4.75%, 7/28/25 (a)		200		211
AerCap Ireland Capital Ltd./AerCap Global Aviation Trust
3.75%, 5/15/19		150		154
Air Lease Corp.
3.38%, 6/1/21		75		78
Alexandria Real Estate Equities, Inc.
3.95%, 1/15/27		75		79
Ally Financial, Inc.
4.25%, 4/15/21		75		77
American Campus Communities Operating Partnership LP
3.75%, 4/15/23		100		105
American Express Credit Corp.,
MTN
2.38%, 5/26/20		200		205
American International Group, Inc.
4.88%, 6/1/22		175		197
AvalonBay Communities, Inc.,
Series G
2.95%, 5/11/26		100		100
Bank of America Corp.,
MTN
4.00%, 4/1/24 - 1/22/25		350		370
4.25%, 10/22/26		166		176
4.75%, 4/21/45		50		54
5.00%, 1/21/44		125		148
Bank of New York Mellon Corp. (The),
MTN
3.65%, 2/4/24		60		65
BBVA Bancomer SA
6.50%, 3/10/21 (a)		150		164
BNP Paribas SA,
4.38%, 5/12/26 (a)		200		207
5.00%, 1/15/21		95		106
Boston Properties LP,
3.65%, 2/1/26		100		106
3.80%, 2/1/24		25		27
BPCE SA
5.15%, 7/21/24 (a)		200		211
Brixmor Operating Partnership LP
4.13%, 6/15/26		150		156
Brookfield Finance, Inc.
4.25%, 6/2/26		150		155

	Face Amount (000)		Value (000)
Capital One Bank USA NA
3.38%, 2/15/23	$	342	$	352
Capital One Financial Corp.
2.45%, 4/24/19		50		51
Chubb INA Holdings, Inc.
3.35%, 5/15/24		125		133
Citigroup, Inc.,
5.50%, 9/13/25		250		286
6.68%, 9/13/43		50		66
8.13%, 7/15/39		100		158
Citizens Bank NA,
MTN
2.55%, 5/13/21		250		255
CNA Financial Corp.
5.75%, 8/15/21		75		87
Cooperatieve Rabobank UA
3.95%, 11/9/22		250		262
Credit Suisse AG,
MTN
3.63%, 9/9/24		250		261
6.00%, 2/15/18		61		64
CubeSmart LP
3.13%, 9/1/26		50		50
Discover Bank
2.00%, 2/21/18		250		251
Discover Financial Services
3.95%, 11/6/24		75		77
Federal Realty Investment Trust
3.63%, 8/1/46		75		74
Five Corners Funding Trust
4.42%, 11/15/23 (a)		200		216
GE Capital International Funding Co.,
2.34%, 11/15/20		200		206
4.42%, 11/15/35		211		237
Goldman Sachs Group, Inc. (The),
2.35%, 11/15/21		175		175
MTN
4.80%, 7/8/44		125		141
6.25%, 2/1/41		75		98
6.75%, 10/1/37		230		294
Goodman Funding Pty Ltd.
6.38%, 4/15/21 (a)		250		293
Hartford Financial Services Group, Inc. (The)
5.50%, 3/30/20		275		307
Healthcare Trust of America Holdings LP
3.70%, 4/15/23 (b)		100		104
Hospitality Properties Trust
5.25%, 2/15/26		85		90
HSBC Finance Corp.
6.68%, 1/15/21		235		271
HSBC Holdings PLC,
2.65%, 1/5/22 (c)		200		199
6.50%, 5/2/36		100		127

The accompanying notes are an integral part of the financial statements.
7

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Corporate Bond Portfolio

	Face Amount (000)		Value (000)
Finance (cont'd)
HSBC USA, Inc.
3.50%, 6/23/24	$	100	$	104
ING Bank N.V.
5.80%, 9/25/23 (a)		100		112
JPMorgan Chase & Co.,
MTN
2.30%, 8/15/21		100		100
3.20%, 6/15/26		275		283
4.13%, 12/15/26		275		294
KeyBank NA
1.60%, 8/22/19		250		250
LeasePlan Corp. N.V.
2.88%, 1/22/19 (a)(b)		200		202
Liberty Mutual Group, Inc.
4.85%, 8/1/44 (a)		50		52
Lincoln National Corp.
7.00%, 6/15/40		75		97
Lloyds Banking Group PLC
3.10%, 7/6/21 (b)		200		205
Massachusetts Mutual Life Insurance Co.
4.50%, 4/15/65 (a)		50		49
Metropolitan Life Global Funding I
2.00%, 4/14/20 (a)		200		202
Mizuho Financial Group, Inc.
2.63%, 4/12/21 (a)		225		228
Nationwide Building Society
6.25%, 2/25/20 (a)		260		295
Pacific LifeCorp
6.00%, 2/10/20 (a)		150		167
PNC Financial Services Group, Inc. (The)
3.90%, 4/29/24		80		86
Prudential Financial, Inc.,
MTN
4.60%, 5/15/44		75		80
5.63%, 6/15/43 (d)		170		184
Realty Income Corp.
3.25%, 10/15/22		150		155
Royal Bank of Scotland Group PLC
3.88%, 9/12/23		200		197
Santander UK Group Holdings PLC
3.13%, 1/8/21		125		127
Santander UK PLC
5.00%, 11/7/23 (a)		200		209
Simon Property Group LP
2.50%, 7/15/21		125		128
Skandinaviska Enskilda Banken AB
2.63%, 11/17/20 (a)		200		206
Standard Chartered PLC
2.10%, 8/19/19 (a)		225		225
State Street Corp.
1.95%, 5/19/21		175		176

	Face Amount (000)		Value (000)
TD Ameritrade Holding Corp.
3.63%, 4/1/25	$	100	$	107
Toronto-Dominion Bank (The),
Series G
1.45%, 9/6/18		200		200
3.63%, 9/15/31 (b)(d)		175		176
Travelers Cos., Inc. (The)
3.75%, 5/15/46		50		53
UnitedHealth Group, Inc.,
2.75%, 2/15/23		55		57
2.88%, 3/15/23		255		266
3.75%, 7/15/25		150		165
Weingarten Realty Investors
3.38%, 10/15/22		150		155
Wells Fargo & Co.,
2.15%, 1/15/19		60		61
MTN
4.10%, 6/3/26		425		451
Westpac Banking Corp.
2.85%, 5/13/26 (b)		150		152
				14,592
Industrials (48.3%)
21st Century Fox America, Inc.
4.75%, 9/15/44		125		137
ABB Treasury Center USA, Inc.
4.00%, 6/15/21 (a)		50		55
AbbVie, Inc.,
3.20%, 5/14/26		100		101
4.70%, 5/14/45		75		81
Actavis Funding SCS,
4.75%, 3/15/45		130		143
4.85%, 6/15/44		50		55
Air Liquide Finance SA
2.25%, 9/27/23 (a)		200		201
Alfa SAB de CV
5.25%, 3/25/24 (a)		200		213
Alibaba Group Holding Ltd.
2.50%, 11/28/19		200		204
Altria Group, Inc.
5.38%, 1/31/44		55		70
Amazon.com, Inc.,
3.80%, 12/5/24		75		83
4.95%, 12/5/44		50		61
American Airlines Pass-Through Trust
4.00%, 7/15/25		170		181
Amgen, Inc.
4.66%, 6/15/51 (a)		109		117
Anadarko Petroleum Corp.,
5.55%, 3/15/26 (b)		25		28
6.45%, 9/15/36		125		146

The accompanying notes are an integral part of the financial statements.
8

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Corporate Bond Portfolio

	Face Amount (000)		Value (000)
Industrials (cont'd)
Anheuser-Busch InBev Finance, Inc.,
3.65%, 2/1/26	$	125	$	135
3.70%, 2/1/24		200		216
4.90%, 2/1/46		175		209
Apple, Inc.,
2.45%, 8/4/26		150		150
3.85%, 5/4/43		50		51
4.50%, 2/23/36		125		143
APT Pipelines Ltd.
4.20%, 3/23/25 (a)(b)		200		207
Aramark Services, Inc.
4.75%, 6/1/26 (a)		100		101
AstraZeneca PLC
6.45%, 9/15/37		125		175
AT&T, Inc.,
4.50%, 3/9/48 (a)		287		290
4.55%, 3/9/49 (a)		125		126
5.15%, 3/15/42		75		82
Automatic Data Processing, Inc.
3.38%, 9/15/25		50		55
Baidu, Inc.
3.25%, 8/6/18		200		205
Barrick Gold Corp.
4.10%, 5/1/23 (b)		100		108
Baxalta, Inc.
5.25%, 6/23/45		100		119
BHP Billiton Finance USA Ltd.,
3.85%, 9/30/23 (b)		50		55
5.00%, 9/30/43		75		89
Boston Scientific Corp.
3.85%, 5/15/25		100		107
BP Capital Markets PLC,
3.02%, 1/16/27		100		102
3.12%, 5/4/26		125		128
Brambles USA, Inc.
4.13%, 10/23/25 (a)		150		160
British Airways Pass-Through Trust
4.63%, 6/20/24 (a)		158		169
Buckeye Partners LP
4.15%, 7/1/23		175		179
Burlington Northern Santa Fe LLC,
4.40%, 3/15/42 (b)		75		84
4.55%, 9/1/44		50		58
Carrizo Oil & Gas, Inc.
6.25%, 4/15/23 (b)		100		99
Caterpillar, Inc.
3.80%, 8/15/42		50		51
CBS Corp.,
4.60%, 1/15/45		25		26
4.90%, 8/15/44		50		53
Celgene Corp.
3.88%, 8/15/25 (b)		125		134

	Face Amount (000)		Value (000)
CEVA Group PLC
7.00%, 3/1/21 (a)	$	75	$	61
Charter Communications Operating LLC/Charter Communications Operating Capital,
4.91%, 7/23/25 (a)		75		83
6.48%, 10/23/45 (a)		150		182
Cimarex Energy Co.
5.88%, 5/1/22		150		157
Cisco Systems, Inc.
1.85%, 9/20/21		275		277
Coca-Cola Co.
1.38%, 5/30/19		175		175
ConocoPhillips Co.
2.20%, 5/15/20 (b)		100		101
Crown Castle International Corp.,
3.40%, 2/15/21		100		105
4.45%, 2/15/26		75		83
CVS Health Corp.
2.13%, 6/1/21 (b)		75		76
Daimler Finance North America LLC
8.50%, 1/18/31		161		262
DCP Midstream LLC
5.35%, 3/15/20 (a)		38		39
Delphi Automotive PLC
3.15%, 11/19/20		125		130
Deutsche Telekom International Finance BV
8.75%, 6/15/30		75		117
Diamond 1 Finance Corp./Diamond 2 Finance Corp.
8.10%, 7/15/36 (a)		75		88
Dollar General Corp.
3.25%, 4/15/23		125		129
Eastman Chemical Co.
3.80%, 3/15/25		100		106
eBay, Inc.
2.50%, 3/9/18		100		101
Eldorado Gold Corp.
6.13%, 12/15/20 (a)		105		106
Enable Midstream Partners LP
3.90%, 5/15/24		125		117
Endeavor Energy Resources LP/EER Finance, Inc.
7.00%, 8/15/21 (a)		75		77
Energy Transfer Partners LP
6.50%, 2/1/42		125		131
Ensco PLC
5.75%, 10/1/44		50		31
Enterprise Products Operating LLC
4.45%, 2/15/43		175		172
Express Scripts Holding Co.
4.50%, 2/25/26		100		110
Exxon Mobil Corp.
4.11%, 3/1/46		75		84

The accompanying notes are an integral part of the financial statements.
9

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Corporate Bond Portfolio

	Face Amount (000)		Value (000)
Industrials (cont'd)
FedEx Corp.
3.20%, 2/1/25	$	100	$	105
Ford Motor Credit Co., LLC,
3.10%, 5/4/23		200		202
5.88%, 8/2/21		200		229
General Motors Co.
6.60%, 4/1/36		125		151
General Motors Financial Co., Inc.,
4.30%, 7/13/25		55		57
4.38%, 9/25/21		125		134
Gilead Sciences, Inc.,
3.65%, 3/1/26		25		27
4.50%, 2/1/45		25		27
4.80%, 4/1/44		50		56
GlaxoSmithKline Capital, Inc.
6.38%, 5/15/38		75		108
Goldcorp, Inc.
5.45%, 6/9/44		50		54
Hanesbrands, Inc.,
4.63%, 5/15/24 (a)		40		41
4.88%, 5/15/26 (a)		60		62
Harris Corp.
4.85%, 4/27/35		50		55
HCA, Inc.
4.75%, 5/1/23		130		136
Heathrow Funding Ltd.
4.88%, 7/15/21 (a)		190		208
Hess Corp.
6.00%, 1/15/40		40		41
Hilcorp Energy I LP/Hilcorp Finance Co.
5.75%, 10/1/25 (a)		55		55
Home Depot, Inc.,
2.13%, 9/15/26		50		49
3.35%, 9/15/25		25		27
5.88%, 12/16/36		109		150
Hutchison Whampoa International 14 Ltd.
1.63%, 10/31/17 (a)		200		200
International Paper Co.
3.00%, 2/15/27		150		150
John Deere Capital Corp.,
MTN
1.25%, 10/9/19		225		224
KFC Holding Co/Pizza Hut Holdings LLC/ Taco Bell of America LLC
5.25%, 6/1/26 (a)		100		106
Kinder Morgan Energy Partners LP
4.15%, 2/1/24		150		153
Kinder Morgan, Inc.,
4.30%, 6/1/25		50		52
5.55%, 6/1/45		50		51
Kraft Heinz Foods Co.
4.38%, 6/1/46		175		186

	Face Amount (000)		Value (000)
Kroger Co. (The)
6.90%, 4/15/38	$	80	$	112
Lam Research Corp.
3.90%, 6/15/26 (b)		100		104
Lockheed Martin Corp.
3.55%, 1/15/26		125		135
Lowe's Cos., Inc.
2.50%, 4/15/26		175		176
LyondellBasell Industries N.V.
4.63%, 2/26/55		75		75
Mallinckrodt International Finance SA/ Mallinckrodt CB LLC
5.50%, 4/15/25 (a)		100		95
MasTec, Inc.
4.88%, 3/15/23		90		89
McDonald's Corp.,
MTN
4.60%, 5/26/45		100		113
Mead Johnson Nutrition Co.
3.00%, 11/15/20		75		78
Medtronic, Inc.
4.63%, 3/15/45		200		236
Merck & Co., Inc.
2.80%, 5/18/23		125		131
Microsoft Corp.,
1.55%, 8/8/21		175		174
4.45%, 11/3/45		125		142
MPLX LP
4.00%, 2/15/25		100		99
Mylan N.V.
3.95%, 6/15/26 (a)		150		151
NBC Universal Media LLC
5.95%, 4/1/41		275		370
NetApp, Inc.
2.00%, 12/15/17		100		100
Netflix, Inc.
5.50%, 2/15/22		95		103
Newell Brands, Inc.
3.85%, 4/1/23		175		187
Nissan Motor Acceptance Corp.
2.55%, 3/8/21 (a)(b)		150		154
Noble Energy, Inc.
5.05%, 11/15/44		50		50
NOVA Chemicals Corp.
5.25%, 8/1/23 (a)		120		123
Novartis Capital Corp.
4.40%, 5/6/44		75		89
Omnicom Group, Inc.,
3.60%, 4/15/26		50		53
3.63%, 5/1/22		95		102
3.65%, 11/1/24		23		24
Ooredoo International Finance Ltd.
3.25%, 2/21/23 (a)		225		231

The accompanying notes are an integral part of the financial statements.
10

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Corporate Bond Portfolio

	Face Amount (000)		Value (000)
Industrials (cont'd)
Oracle Corp.
4.50%, 7/8/44	$	150	$	165
Orange SA
9.00%, 3/1/31		50		80
PepsiCo, Inc.
3.60%, 3/1/24		100		110
Philip Morris International, Inc.
4.50%, 3/20/42		150		170
Phillips 66
5.88%, 5/1/42		25		31
Phillips 66 Partners LP
4.68%, 2/15/45		25		24
Rowan Cos., Inc.
5.85%, 1/15/44		40		28
RR Donnelley & Sons Co.
7.88%, 3/15/21 (b)		10		11
Ryder System, Inc.,
MTN
2.65%, 3/2/20		50		51
Shell International Finance BV
1.38%, 9/12/19		175		175
Southern Copper Corp.
7.50%, 7/27/35		100		118
Spectra Energy Capital LLC
7.50%, 9/15/38		100		125
Telefonica Europe BV
8.25%, 9/15/30		84		123
Telstra Corp., Ltd.
3.13%, 4/7/25 (a)		65		68
Teva Pharmaceutical Finance Netherlands III BV
3.15%, 10/1/26		100		101
Thermo Fisher Scientific, Inc.
2.95%, 9/19/26		125		124
Time Warner, Inc.
7.70%, 5/1/32		91		130
TransCanada PipeLines Ltd.
7.63%, 1/15/39		75		111
Transurban Finance Co., Pty Ltd.,
3.38%, 3/22/27 (a)		75		76
4.13%, 2/2/26 (a)		95		102
Tyco International Finance SA
3.90%, 2/14/26		75		82
Tyson Foods, Inc.
4.88%, 8/15/34		50		55
Under Armour, Inc.
3.25%, 6/15/26		100		101
United Airlines Pass-Through Trust,
Class A
4.30%, 8/15/25		203		222
Vale Overseas Ltd.
6.88%, 11/21/36		75		73

	Face Amount (000)		Value (000)
Verizon Communications, Inc.,
4.67%, 3/15/55	$	278	$	294
5.01%, 8/21/54		210		233
Viacom, Inc.
5.85%, 9/1/43		50		57
Visa, Inc.
4.30%, 12/14/45		125		145
Vodafone Group PLC
4.38%, 2/19/43		50		50
Volkswagen Group of America Finance LLC
2.40%, 5/22/20 (a)		200		201
Wal-Mart Stores, Inc.,
3.30%, 4/22/24 (b)		150		164
5.25%, 9/1/35		75		100
Walgreens Boots Alliance, Inc.,
3.45%, 6/1/26		50		52
3.80%, 11/18/24		25		27
Whole Foods Market, Inc.
5.20%, 12/3/25 (a)		100		109
Williams Partners LP/ACMP Finance Corp.
4.88%, 5/15/23		125		127
WM Wrigley Jr. Co.
2.90%, 10/21/19 (a)		230		238
Woodside Finance Ltd.
3.70%, 9/15/26 (a)		150		151
				19,838
Utilities (8.3%)
Alabama Power Co.
3.75%, 3/1/45		125		130
Baltimore Gas & Electric Co.
2.40%, 8/15/26		75		75
Black Hills Corp.
3.15%, 1/15/27		75		76
Boston Gas Co.
4.49%, 2/15/42 (a)		125		139
CenterPoint Energy Houston Electric LLC
1.85%, 6/1/21		150		150
CMS Energy Corp.
6.25%, 2/1/20		200		228
DTE Energy Co.
1.50%, 10/1/19 (c)		100		100
Duke Energy Carolinas LLC
3.75%, 6/1/45		75		78
Duke Energy Corp.
2.65%, 9/1/26		150		148
Enel Finance International N.V.
6.00%, 10/7/39 (a)		100		121
Entergy Arkansas, Inc.
3.50%, 4/1/26		75		81
Entergy Louisiana LLC
3.05%, 6/1/31		75		77

The accompanying notes are an integral part of the financial statements.
11

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Corporate Bond Portfolio

	Face Amount (000)		Value (000)
Utilities (cont'd)
Exelon Generation Co., LLC
6.25%, 10/1/39	$	145	$	162
Fortis, Inc.
2.10%, 10/4/21 (a)		100		100
Jersey Central Power & Light Co.
4.70%, 4/1/24 (a)		200		219
Nevada Power Co., Series N
6.65%, 4/1/36		150		210
NextEra Energy Capital Holdings, Inc.
1.65%, 9/1/18		125		126
Oncor Electric Delivery Co., LLC
2.95%, 4/1/25		75		78
Public Service Electric & Gas Co.,
MTN
2.25%, 9/15/26		150		150
Sempra Energy
6.00%, 10/15/39		125		160
South Carolina Electric & Gas Co.
4.50%, 6/1/64		75		79
TransAlta Corp.
4.50%, 11/15/22 (b)		235		232
Virginia Electric & Power Co.
2.95%, 1/15/22 (b)		325		341
WEC Energy Group, Inc.
3.55%, 6/15/25		75		81
Xcel Energy, Inc.
3.30%, 6/1/25		75		79
				3,420
				37,850
Sovereign (0.5%)
Sinopec Group Overseas Development 2015 Ltd.
2.50%, 4/28/20 (a)		200		204
U.S. Treasury Security (0.9%)
U.S. Treasury Inflation Indexed Bond
0.25%, 1/15/25		381		388
Variable Rate Senior Loan Interest (0.2%)
Industrial (0.2%)
FMG Resources August 2006 Pty Ltd.,
Term B
3.75%, 6/30/19		89		89
Total Fixed Income Securities (Cost $36,928)				38,822

	Shares		Value (000)
Short-Term Investments (8.4%)
Securities held as Collateral on Loaned Securities (2.9%)
Investment Company (2.9%)
Morgan Stanley Institutional Liquidity Funds — Government Portfolio — Institutional Class (See Note G) (Cost $1,182)		1,181,730	$	1,182
Investment Company (4.6%)
Morgan Stanley Institutional Liquidity Funds — Government Portfolio — Institutional Class (See Note G) (Cost $1,884)		1,883,859		1,884
	Face Amount (000)
U.S. Treasury Security (0.9%)
U.S. Treasury Bill
0.41%, 3/23/17 (b)(e)(f) (Cost $359)	$	360		359
Total Short-Term Investments (Cost $3,425)				3,425
Total Investments (102.9%) (Cost $40,353) Including $2,414 of Securities Loaned (g)(h)				42,247
Liabilities in Excess of Other Assets (–2.9%)				(1,181	)
Net Assets (100.0%)			$	41,066

(a) 144A security — Certain conditions for public sale may exist. Unless otherwise noted, these securities are deemed to be liquid.

(b) All or a portion of this security was on loan at September 30, 2016.

(d) Variable/Floating Rate Security — Interest rate changes on these instruments are based on changes in a designated base rate. The rates shown are those in effect on September 30, 2016.

(e) Rate shown is the yield to maturity at September 30, 2016.

(f) All or a portion of the security was pledged to cover margin requirements for futures contracts and swap agreements.

(g) Securities are available for collateral in connection with open futures contracts and swap agreements.

(h) At September 30, 2016, the aggregate cost for federal income tax purposes is approximately $40,353,000. The aggregate gross unrealized appreciation is approximately $2,017,000 and the aggregate gross unrealized depreciation is approximately $123,000 resulting in net unrealized appreciation of approximately $1,894,000.

MTN Medium Term Note.

The accompanying notes are an integral part of the financial statements.
12

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Corporate Bond Portfolio

Futures Contracts:

The Portfolio had the following futures contracts open at September 30, 2016:

	Number of Contracts		Value (000)			Expiration Date	Unrealized Appreciation (Depreciation) (000)
Long:
U.S. Treasury 2 yr. Note		21	$	4,588		Dec-16	$	—	@
U.S. Treasury 5 yr. Note		3		364		Dec-16		(—	@)
U.S. Treasury Long Bond		5		841		Dec-16		(10	)
U.S. Treasury Ultra Bond		1		184		Dec-16		(1	)
Short:
U.S. Treasury 10 yr. Note		15		(1,967	)	Dec-16		2
U.S. Treasury 10 yr. Ultra Long Bond		22		(3,171	)	Dec-16		2
							$	(7	)

Credit Default Swap Agreements:

The Portfolio had the following credit default swap agreements open at September 30, 2016:

Swap Counterparty and Reference Obligation	Buy/Sell Protection	Notional Amount (000)		Pay/Receive Fixed Rate			Termination Date	Upfront Payment Paid (Received) (000)			Unrealized Depreciation (000)			Value (000)			Credit Rating of Reference Obligation† (Unaudited)
Barclays Bank PLC Quest Diagnostics, Inc.	Buy	$	200		1.00	%	3/20/19	$	4		$	(8	)	$	(4	)	BBB+
Morgan Stanley & Co., LLC* CDX.NA.HY.26	Buy		175		5.00		6/20/21		(8	)		(1	)		(9	)	NR
		$	375					$	(4	)	$	(9	)	$	(13	)

@ Value is less than $500.

† Credit rating as issued by Standard & Poor's.

* Cleared swap agreement, the broker is Morgan Stanley & Co., LLC.

NR Not rated.

Portfolio Composition*

Classification	Percentage of Total Investments
Industrials		48.3	%
Finance		35.5
Utilities		8.3
Short-Term Investments		5.5
Other**		2.4
Total Investments		100.0	%***

* Percentages indicated are based upon total investments (excluding Securities held as Collateral on Loaned Securities) as of September 30, 2016.

** Industries and/or investment types representing less than 5% of total investments.

*** Does not include open long/short futures contracts with an underlying face amount of approximately $11,115,000 with net unrealized depreciation of approximately $7,000. Does not include open swap agreements with total unrealized depreciation of approximately $9,000.

The accompanying notes are an integral part of the financial statements.
13

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Corporate Bond Portfolio

Statement of Assets and Liabilities	September 30, 2016 (000)
Assets:
Investments in Securities of Unaffiliated Issuers, at Value⁽¹⁾ (Cost $37,287)	$	39,181
Investment in Security of Affiliated Issuer, at Value (Cost $3,066)		3,066
Total Investments in Securities, at Value (Cost $40,353)		42,247
Interest Receivable		360
Receivable for Portfolio Shares Sold		156
Receivable for Investments Sold		16
Receivable for Variation Margin on Futures Contracts		11
Premium Paid on Open Swap Agreements		4
Receivable from Affiliate		—	@
Other Assets		37
Total Assets		42,831
Liabilities:
Collateral on Securities Loaned, at Value		1,182
Payable for Investments Purchased		399
Payable for Advisory Fees		81
Payable for Trustees' Fees and Expenses		23
Payable for Professional Fees		21
Payable for Portfolio Shares Redeemed		10
Unrealized Depreciation on Swap Agreements		8
Payable for Sub Transfer Agency Fees — Class I		6
Payable for Sub Transfer Agency Fees — Class L		—	@
Payable for Sub Transfer Agency Fees — Class C		—	@
Payable for Transfer Agency Fees — Class I		3
Payable for Transfer Agency Fees — Class A		1
Payable for Transfer Agency Fees — Class L		—	@
Payable for Transfer Agency Fees — Class C		1
Payable for Custodian Fees		3
Payable for Administration Fees		3
Payable for Shareholder Services Fees — Class A		1
Payable for Distribution and Shareholder Services Fees — Class L		1
Payable for Distribution and Shareholder Services Fees — Class C		—	@
Payable for Variation Margin on Swap Agreements		1
Other Liabilities		21
Total Liabilities		1,765
Net Assets	$	41,066
Net Assets Consist of:
Paid-in-Capital	$	92,524
Accumulated Undistributed Net Investment Income		486
Accumulated Net Realized Loss		(53,822	)
Unrealized Appreciation (Depreciation) on:
Investments		1,894
Futures Contracts		(7	)
Swap Agreements		(9	)
Net Assets	$	41,066

The accompanying notes are an integral part of the financial statements.
14

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Corporate Bond Portfolio

Statement of Assets and Liabilities (cont'd)	September 30, 2016 (000)
CLASS I:
Net Assets	$	31,873
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		2,585,300
Net Asset Value, Offering and Redemption Price Per Share	$	12.33
CLASS A:
Net Assets	$	6,916
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		560,526
Net Asset Value, Redemption Price Per Share	$	12.34
Maximum Sales Load		4.25	%
Maximum Sales Charge	$	0.55
Maximum Offering Price Per Share	$	12.89
CLASS L:
Net Assets	$	2,151
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		174,612
Net Asset Value, Offering and Redemption Price Per Share	$	12.32
CLASS C:
Net Assets	$	126
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		10,289
Net Asset Value, Offering and Redemption Price Per Share	$	12.27
⁽¹⁾ Including: Securities on Loan, at Value:	$	2,414

@ Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
15

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Corporate Bond Portfolio

Statement of Operations	Year Ended September 30, 2016 (000)
Investment Income:
Interest from Securities of Unaffiliated Issuers	$	1,385
Dividends from Security of Affiliated Issuer (Note G)		5
Income from Securities Loaned — Net		5
Total Investment Income		1,395
Expenses:
Advisory Fees (Note B)		132
Professional Fees		95
Registration Fees		53
Sub Transfer Agency Fees — Class I		41
Sub Transfer Agency Fees — Class A		2
Sub Transfer Agency Fees — Class L		1
Pricing Fees		37
Administration Fees (Note C)		28
Shareholder Services Fees — Class A (Note D)		7
Distribution and Shareholder Services Fees — Class L (Note D)		10
Distribution and Shareholder Services Fees — Class C (Note D)		1
Shareholder Reporting Fees		16
Transfer Agency Fees — Class I (Note E)		9
Transfer Agency Fees — Class A (Note E)		2
Transfer Agency Fees — Class L (Note E)		2
Transfer Agency Fees — Class C (Note E)		2
Custodian Fees (Note F)		12
Trustees' Fees and Expenses		3
Other Expenses		16
Total Expenses		469
Reimbursement of Class Specific Expenses — Class I (Note B)		(50	)
Reimbursement of Class Specific Expenses — Class C (Note B)		(1	)
Waiver of Advisory Fees (Note B)		(49	)
Waiver of Shareholder Servicing Fees — Class A (Note D)		(3	)
Rebate from Morgan Stanley Affiliate (Note G)		(2	)
Reimbursement of Custodian Fees (Note F)		(98	)
Net Expenses		266
Net Investment Income		1,129
Realized Gain (Loss):
Investments Sold		2,692
Futures Contracts		(334	)
Swap Agreements		(44	)
Net Realized Gain		2,314
Change in Unrealized Appreciation (Depreciation):
Investments		2,293
Futures Contracts		54
Swap Agreements		39
Net Change in Unrealized Appreciation (Depreciation)		2,386
Net Realized Gain and Change in Unrealized Appreciation (Depreciation)		4,700
Net Increase in Net Assets Resulting from Operations	$	5,829

The accompanying notes are an integral part of the financial statements.
16

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Corporate Bond Portfolio

Statements of Changes in Net Assets	Year Ended September 30, 2016 (000)			Year Ended September 30, 2015 (000)
Increase (Decrease) in Net Assets:
Operations:
Net Investment Income	$	1,129		$	1,248
Net Realized Gain		2,314			734
Net Change in Unrealized Appreciation (Depreciation)		2,386			(1,938	)
Net Increase in Net Assets Resulting from Operations		5,829			44
Distributions from and/or in Excess of:
Class I:
Net Investment Income		(954	)		(1,021	)
Class A:
Net Investment Income		(59	)		(14	)
Class L:
Net Investment Income		(51	)		(54	)
Class C:
Net Investment Income		(1	)		(—	@)*
Total Distributions		(1,065	)		(1,089	)
Capital Share Transactions:⁽¹⁾
Class I:
Subscribed		3,997			2,961
Distributions Reinvested		952			1,021
Redeemed		(8,505	)		(8,193	)
Class A:
Subscribed		6,507			427
Distributions Reinvested		57			12
Redeemed		(676	)		(281	)
Class L:
Exchanged		12			—
Subscribed		—			108
Distributions Reinvested		51			54
Redeemed		(345	)		(338	)
Class C:
Subscribed		211			10	*
Distributions Reinvested		1			—
Redeemed		(104	)		—
Net Increase (Decrease) in Net Assets Resulting from Capital Share Transactions		2,158			(4,219	)
Total Increase (Decrease) in Net Assets		6,922			(5,264	)
Net Assets:
Beginning of Period		34,144			39,408
End of Period (Including Accumulated Undistributed Net Investment Income of $486 and $437)	$	41,066		$	34,144
(1) Capital Share Transactions:
Class I:
Shares Subscribed		357			266
Shares Issued on Distributions Reinvested		86			92
Shares Redeemed		(767	)		(740	)
Net Decrease in Class I Shares Outstanding		(324	)		(382	)
Class A:
Shares Subscribed		564			38
Shares Issued on Distributions Reinvested		5			1
Shares Redeemed		(59	)		(25	)
Net Increase in Class A Shares Outstanding		510			14
Class L:
Shares Exchanged		1			—
Shares Subscribed		—			10
Shares Issued on Distributions Reinvested		5			5
Shares Redeemed		(32	)		(31	)
Net Decrease in Class L Shares Outstanding		(26	)		(16	)
Class C:
Shares Subscribed		18			1	*
Shares Issued on Distributions Reinvested		—	@@		—
Shares Redeemed		(9	)		—
Net Increase in Class C Shares Outstanding		9			1	*

* For the period April 30, 2015 through September 30, 2015.

@ Amount is less than $500.

@@ Amount is less than 500 shares.

The accompanying notes are an integral part of the financial statements.
17

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Corporate Bond Portfolio

	Class I
	Year Ended September 30,
Selected Per Share Data and Ratios	2016††			2015			2014			2013			2012
Net Asset Value, Beginning of Period	$	10.80		$	11.12		$	10.53		$	10.93		$	10.27
Income (Loss) from Investment Operations:
Net Investment Income†		0.37			0.37			0.38			0.32			0.36
Net Realized and Unrealized Gain (Loss)		1.51			(0.37	)		0.53			(0.40	)		0.73
Total from Investment Operations		1.88			—			0.91			(0.08	)		1.09
Distributions from and/or in Excess of:
Net Investment Income		(0.35	)		(0.32	)		(0.32	)		(0.32	)		(0.43	)
Net Asset Value, End of Period	$	12.33		$	10.80		$	11.12		$	10.53		$	10.93
Total Return++		17.79	%**		(0.04	)%		8.79	%		(0.77	)%		10.94	%
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	31,873		$	31,427		$	36,598		$	36,186		$	44,779
Ratio of Expenses to Average Net Assets⁽¹⁾		0.69	%+		0.70	%+		0.70	%+		1.18	%+^		1.00	%+
Ratio of Net Investment Income to Average Net Assets⁽¹⁾		3.28	%+		3.33	%+		3.47	%+		2.91	%+^		3.41	%+
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.01	%		0.00	%§		0.00	%§		0.00	%§		0.00	%§
Portfolio Turnover Rate		41	%		45	%		50	%		63	%		129	%
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		1.28	%		1.15	%		1.13	%		1.21	%		N/A
Net Investment Income to Average Net Assets		2.69	%		2.88	%		3.04	%		2.88	%		N/A

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value as of the last business day of the period.

** Performance was positively impacted by approximately 9.01% due to the receipt of proceeds from the settlement of class action suits involving the Portfolio's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class I shares would have been approximately 8.78%.

^ Effective September 16, 2013, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 0.70% for Class I shares.

§ Amount is less than 0.005%.

The accompanying notes are an integral part of the financial statements.
18

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Corporate Bond Portfolio

	Class A
	Year Ended September 30,
Selected Per Share Data and Ratios	2016††			2015			2014			2013			2012
Net Asset Value, Beginning of Period	$	10.81		$	11.12		$	10.53		$	10.92		$	10.27
Income (Loss) from Investment Operations:
Net Investment Income†		0.32			0.33			0.34			0.30			0.34
Net Realized and Unrealized Gain (Loss)		1.53			(0.37	)		0.53			(0.39	)		0.73
Total from Investment Operations		1.85			(0.04	)		0.87			(0.09	)		1.07
Distributions from and/or in Excess of:
Net Investment Income		(0.32	)		(0.27	)		(0.28	)		(0.30	)		(0.42	)
Net Asset Value, End of Period	$	12.34		$	10.81		$	11.12		$	10.53		$	10.92
Total Return++		17.41	%**		(0.37	)%		8.43	%		(0.83	)%		10.69	%
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	6,916		$	544		$	405		$	1,194		$	961
Ratio of Expenses to Average Net Assets⁽¹⁾		0.99	%+		1.05	%+		1.05	%+		1.34	%+^		1.15	%+
Ratio of Net Investment Income to Average Net Assets⁽¹⁾		2.78	%+		2.98	%+		3.12	%+		2.76	%+^		3.26	%+
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.01	%		0.00	%§		0.00	%§		0.00	%§		0.00	%§
Portfolio Turnover Rate		41	%		45	%		50	%		63	%		129	%
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		1.51	%		1.88	%		1.60	%		1.47	%		1.25	%
Net Investment Income to Average Net Assets		2.26	%		2.15	%		2.57	%		2.63	%		3.16	%

†† Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class A shares. The Ratio of Expenses to Average Net Assets and the Ratio of Net Investment Income to Average Net Assets would be unchanged as the change to current period custodian fees was offset against current period expense waivers/reimbursements with no impact to net expenses or net investment income.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

** Performance was positively impacted by approximately 8.97% due to the receipt of proceeds from the settlement of class action suits involving the Portfolio's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class A shares would have been approximately 8.44%.

^ Effective September 16, 2013, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 1.05% for Class A shares.

§ Amount is less than 0.005%.

The accompanying notes are an integral part of the financial statements.
19

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Corporate Bond Portfolio

	Class L
	Year Ended September 30,
Selected Per Share Data and Ratios	2016††			2015			2014			2013			2012
Net Asset Value, Beginning of Period	$	10.79		$	11.11		$	10.52		$	10.92		$	10.26
Income (Loss) from Investment Operations:
Net Investment Income†		0.30			0.30			0.31			0.26			0.30
Net Realized and Unrealized Gain (Loss)		1.51			(0.37	)		0.54			(0.40	)		0.74
Total from Investment Operations		1.81			(0.07	)		0.85			(0.14	)		1.04
Distributions from and/or in Excess of:
Net Investment Income		(0.28	)		(0.25	)		(0.26	)		(0.26	)		(0.38	)
Net Asset Value, End of Period	$	12.32		$	10.79		$	11.11		$	10.52		$	10.92
Total Return++		17.06	%**		(0.65	)%		8.15	%		(1.28	)%		10.38	%
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	2,151		$	2,163		$	2,405		$	2,649		$	3,149
Ratio of Expenses to Average Net Assets⁽¹⁾		1.33	%+		1.31	%+		1.30	%+		1.69	%+^		1.50	%+
Ratio of Net Investment Income to Average Net Assets⁽¹⁾		2.64	%+		2.72	%+		2.87	%+		2.40	%+^		2.91	%+
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.01	%		0.00	%§		0.00	%§		0.00	%§		0.00	%§
Portfolio Turnover Rate		41	%		45	%		50	%		63	%		129	%
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		1.75	%		1.73	%		1.66	%		1.70	%		N/A
Net Investment Income to Average Net Assets		2.22	%		2.30	%		2.51	%		2.39	%		N/A

†† Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class L shares. The Ratio of Expenses to Average Net Assets and the Ratio of Net Investment Income to Average Net Assets would be unchanged as the change to current period custodian fees was offset against current period expense waivers/reimbursements with no impact to net expenses or net investment income.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value as of the last business day of the period.

** Performance was positively impacted by approximately 9.05% due to the receipt of proceeds from the settlement of class action suits involving the Portfolio's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class L shares would have been approximately 8.01%.

^ Effective September 16, 2013, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 1.52% for Class L shares.

§ Amount is less than 0.005%.

The accompanying notes are an integral part of the financial statements.
20

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Corporate Bond Portfolio

	Class C
Selected Per Share Data and Ratios	Year Ended September 30, 2016††			Period from April 30, 2015^ to September 30, 2015
Net Asset Value, Beginning of Period	$	10.77		$	11.21
Income (Loss) from Investment Operations:
Net Investment Income†		0.22			0.10
Net Realized and Unrealized Gain (Loss)		1.53			(0.48	)
Total from Investment Operations		1.75			(0.38	)
Distributions from and/or in Excess of:
Net Investment Income		(0.25	)		(0.06	)
Net Asset Value, End of Period	$	12.27		$	10.77
Total Return++		16.47	%**		(3.40	)%#
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	126		$	10
Ratio of Expenses to Average Net Assets⁽¹⁾		1.79	%+		1.80	%+*
Ratio of Net Investment Income to Average Net Assets⁽¹⁾		1.90	%+		2.25	%+*
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.01	%		0.00	%§*
Portfolio Turnover Rate		41	%		45	%#
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		4.45	%		38.20	%*
Net Investment Loss to Average Net Assets		(0.76	)%		(34.15	)%*

†† Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class C shares. The Ratio of Expenses to Average Net Assets and the Ratio of Net Investment Income to Average Net Assets would be unchanged as the change to current period custodian fees was offset against current period expense waivers/reimbursements with no impact to net expenses or net investment income.

^ Commencement of Offering.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

** Performance was positively impacted by approximately 8.85% due to the receipt of proceeds from the settlement of class action suits involving the Portfolio's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class C shares would have been approximately 7.62%.

§ Amount is less than 0.005%.

# Not Annualized.

* Annualized.

The accompanying notes are an integral part of the financial statements.
21

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements

Morgan Stanley Institutional Fund Trust (''MSIFT" or the "Fund'') is registered under the Investment Company Act of 1940, as amended (the "Act''), as an open-end management investment company. The Fund is comprised of nine separate, active portfolios (individually referred to as a "Portfolio", collectively as the "Portfolios"). The Fund applies investment company accounting and reporting guidance. All Portfolios are considered diversified for purposes of the Act.

The accompanying financial statements relate to the Corporate Bond Portfolio. The Portfolio seeks above-average total return over a market cycle of three to five years. The Portfolio offers four classes of shares — Class I, Class A, Class L and Class C.

On April 30, 2015, the Portfolio suspended offering Class L shares to all investors. Existing Class L shareholders may invest through reinvestment of dividends and distributions.

market quotations are not readily available, including circumstances under which Morgan Stanley Investment Management Inc. (the "Adviser") determines that the closing price, last sale price or the mean between the last reported bid and asked prices are not reflective of a security's market value, portfolio securities are valued at their fair value as determined in good faith under procedures established by and under the general supervision of the Trustees. Occasionally, developments affecting the closing prices of securities and other assets may occur between the times at which valuations of such securities are determined (that is, close of the foreign market on which the securities trade) and the close of business of the New York Stock Exchange ("NYSE"). If developments occur during such periods that are expected to materially affect the value of such securities, such valuations may be adjusted to reflect the estimated fair value of such securities as of the close of the NYSE, as determined in good faith by the Trustees or by the Adviser using a pricing service and/or procedures approved by the Trustees; and (6) investments in mutual funds, including the Morgan Stanley Institutional Liquidity Funds, are valued at the net asset value ("NAV") as of the close of each business day.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

arriving at fair value. The Valuation Committee may employ a market-based approach which may use related or comparable assets or liabilities, recent transactions, market multiples, book values, and other relevant information for the investment to determine the fair value of the investment. An income-based valuation approach may also be used in which the anticipated future cash flows of the investment are discounted to calculate fair value. Discounts may also be applied due to the nature or duration of any restrictions on the disposition of the investments. Due to the inherent uncertainty of valuations of such investments, the fair values may differ significantly from the values that would have been used had an active market existed. The Valuation Committee employs various methods for calibrating these valuation approaches including a regular review of valuation methodologies, key inputs and assumptions, transactional back-testing or disposition analysis, and reviews of any related market activity.

• Level 1 – unadjusted quoted prices in active markets for identical investments

• Level 2 – other significant observable inputs (including quoted prices for similar investments,

interest rates, prepayment speeds, credit risk, etc.)

The following is a summary of the inputs used to value the Portfolio's investments as of September 30, 2016.

Investment Type	Level 1 Unadjusted quoted prices (000)			Level 2 Other significant observable inputs (000)			Level 3 Significant unobservable inputs (000)		Total (000)
Assets:
Fixed Income Securities
Asset-Backed Securities	$	—		$	291		$	—	$	291
Corporate Bonds		—			37,850			—		37,850
Sovereign		—			204			—		204
U.S. Treasury Security		—			388			—		388
Variable Rate Senior Loan Interest		—			89			—		89
Total Fixed Income Securities		—			38,822			—		38,822
Short-Term Investments
Investment Company		3,066			—			—		3,066
U.S. Treasury Security		—			359			—		359
Total Short-Term Investments		3,066			359			—		3,425
Futures Contracts		4			—			—		4
Total Assets		3,070			39,181			—		42,251
Liabilities:
Futures Contracts		(11	)		—			—		(11	)
Credit Default Swap Agreements		—			(9	)		—		(9	)
Total Liabilities		(11	)		(9	)		—		(20	)
Total	$	3,059		$	39,172		$	—	$	42,231

Transfers between investment levels may occur as the markets fluctuate and/or the availability of data used in an

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

investment's valuation changes. The Portfolio recognizes transfers between the levels as of the end of the period. As of September 30, 2016, the Portfolio did not have any investments transfer between investment levels.

3. Derivatives: The Portfolio may, but is not required to, use derivative instruments for a variety of purposes, including hedging, risk management, portfolio management or to earn income. Derivatives are financial instruments whose value is based, in part, on the value of an underlying asset, interest rate, index or financial instrument. Prevailing interest rates and volatility levels, among other things, also affect the value of derivative instruments. A derivative instrument often has risks similar to its underlying asset and may have additional risks, including imperfect correlation between the value of the derivative and the underlying asset, risks of default by the counterparty to certain transactions, magnification of losses incurred due to changes in the market value of the securities, instruments, indices or interest rates to which the derivative instrument relates, risks that the transactions may not be liquid and risks arising from margin requirements. The use of derivatives involves risks that are different from, and possibly greater than, the risks associated with other portfolio investments. Derivatives may involve the use of highly specialized instruments that require investment techniques and risk analyses different from those associated with other portfolio investments. All of the Portfolio's holdings, including derivative instruments, are marked-to-market each day with the change in value reflected in unrealized appreciation (depreciation). Upon disposition, a realized gain or loss is recognized.

Following is a description of the derivative instruments and techniques that the Portfolio used during the period and their associated risks:

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

party. Cleared swap transactions may help reduce counterparty credit risk. In a cleared swap, the Portfolio's ultimate counterparty is a clearinghouse rather than a swap dealer, bank or other financial institution. OTC swap agreements are not entered into or traded on exchanges and often there is no central clearing or guaranty function for OTC swaps. These OTC swaps are often subject to credit risk or the risk of default or non-performance by the counterparty. Both OTC and cleared swaps could result in losses if interest rates, foreign currency exchange rates or other factors are not correctly anticipated by the Portfolio or if the reference index, security or investments do not perform as expected. During the period swap agreements are open, payments are received from or made to the clearinghouse or counterparty based upon changes in the value of the contract (variation margin). The Dodd-Frank Wall Street Reform and Consumer Protection Act and related regulatory developments require the clearing and exchange-trading of certain standardized swap transactions. Mandatory exchange-trading and clearing is occurring on a phased-in basis.

If the Portfolio is a seller of protection and a credit event occurs, as defined under the terms of that

particular swap agreement, the Portfolio will either (i) pay to the buyer of protection an amount equal to the notional amount of the swap agreement and take delivery of the referenced obligation, other deliverable obligations or underlying securities comprising the referenced index or (ii) pay a net settlement amount in the form of cash or securities equal to the notional amount of the swap agreement less the recovery value of the referenced obligation or underlying securities comprising the referenced index. If the Portfolio is a buyer of protection and a credit event occurs, as defined under the terms of that particular swap agreement, the Portfolio will either (i) receive from the seller of protection an amount equal to the notional amount of the swap agreement and deliver the referenced obligation, other deliverable obligations or underlying securities comprising the referenced index or (ii) receive a net settlement amount in the form of cash or securities equal to the notional amount of the swap agreement less the recovery value of the referenced obligation or underlying securities comprising the referenced index. Recovery values are estimated by market makers considering either industry standard recovery rates or entity specific factors and considerations until a credit event occurs. If a credit event has occurred, the recovery value is determined by a facilitated auction whereby a minimum number of allowable broker bids, together with a specified valuation method, are used to calculate the settlement value. The Portfolio's maximum risk of loss from counterparty risk, either as the protection seller or as the protection buyer, is the fair value of the swap agreement.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

loss. Collateral pledges are monitored and subsequently adjusted if and when the swap valuations fluctuate. If applicable, cash collateral is included with "Due from (to) Broker" in the Statement of Assets and Liabilities.

Upfront payments paid or received by the Portfolio will be reflected as an asset or liability, respectively, in the Statement of Assets and Liabilities.

The following tables set forth the fair value of the Portfolio's derivative contracts by primary risk exposure as of September 30, 2016.

Asset Derivatives
Statement of Assets and
Liabilities Location

Primary Risk
Exposure

Value
(000)

Futures Contracts

Variation Margin on
Futures Contracts

Interest Rate Risk

(a)

Liability Derivatives
Statement of Assets and
Liabilities Location

Primary Risk
Exposure

Value
(000)

Futures Contracts

Variation Margin on
Futures Contracts

Interest Rate Risk

(11

)(a)

Swap Agreement

Unrealized Depreciation on
Swap Agreements

Credit Risk

)

Swap Agreement

Variation Margin on
Swap Agreements

Credit Risk

)(a)

Total

(20

)

Realized Gain (Loss)
Primary Risk Exposure	Derivative Type	Value (000)
Interest Rate Risk	Futures Contracts	$	(334	)
Credit Risk	Swap Agreements		2
Interest Rate Risk	Swap Agreements		(46	)
	Total	$	(378	)

Change in Unrealized Appreciation (Depreciation)
Primary Risk Exposure	Derivative Type	Value (000)
Interest Rate Risk	Futures Contracts	$	54
Credit Risk	Swap Agreements		(18	)
Interest Rate Risk	Swap Agreements		57
	Total	$	93

At September 30, 2016, the Portfolio's derivative assets and liabilities are as follows:

Gross Amounts of Assets and Liabilities Presented in the Statement of Assets and Liabilities
Derivatives(b)	Assets(c) (000)		Liabilities(c) (000)
Swap Agreement	$	—	$	(8	)

(b) Excludes exchange traded derivatives.

(c) Absent an event of default or early termination, OTC derivative assets and liabilities are presented gross and not offset in the Statement of Assets and Liabilities.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

value in excess of the Portfolio's net liability may be delayed or denied.

The following table presents derivative financial instruments that are subject to enforceable netting arrangements as of September 30, 2016.

Gross Amounts Not Offset in the Statement of Assets and Liabilities
Counterparty	Gross Liability Derivatives Presented in Statement of Assets and Liabilities (000)		Financial Instrument (000)		Collateral Pledged (000)		Net Amount (not less than $0) (000)
Barclays Bank PLC	$	8	$	—	$	—	$	8

For the year ended September 30, 2016, the approximate average monthly amount outstanding for each derivative type is as follows:

Futures Contracts:
Average monthly original value	$	13,961,000
Swap Agreements:
Average monthly notional amount	$	986,000

4. Senior Loans: Senior Loans are typically structured by a syndicate of lenders ("Lenders"), one or more of which administers the Senior Loan on behalf of the Lenders ("Agent"). Lenders may sell interests in Senior Loans to third parties ("Participations") or may assign all or a portion of their interest in a Senior Loan to third parties ("Assignments"). Senior Loans are exempt from registration under the Securities Act of 1933. Presently, Senior Loans are not readily marketable and are often subject to restrictions on resale.

5. Securities Lending: The Portfolio lends securities to qualified financial institutions, such as broker-dealers, to earn additional income. Any increase or decrease in the fair value of the securities loaned that might occur and any interest earned or dividends declared on those securities during the term of the loan would remain in the Portfolio. The Portfolio would receive cash or securities as collateral in an amount equal to or exceeding 100% of the current fair value of the loaned securities. The collateral is marked-to-market daily by State Street Bank and Trust Company ("State Street"), the securities lending agent, to ensure that a minimum of 100% collateral coverage is maintained.

earnings on the invested collateral and borrowing fees, less any rebates owed to the borrowers and compensation to the lending agent, and is recorded as "Income from Securities Loaned — Net" in the Portfolio's Statement of Operations. Risks in securities lending transactions are that a borrower may not provide additional collateral when required or return the securities when due, and that the value of the short-term investments will be less than the amount of cash collateral plus any rebate that is required to be returned to the borrower.

The Portfolio has the right under the lending agreement to recover the securities from the borrower on demand.

The following table presents financial instruments that are subject to enforceable netting arrangements as of September 30, 2016.

Gross Amounts Not Offset in the Statement of Assets and Liabilities
Gross Asset Amounts Presented in Statement of Assets and Liabilities (000)			Financial Instrument (000)		Collateral Received (000)			Net Amount (not less than $0) (000)
$	2,414	(d)	$	—	$	(2,414	)(e)(f)	$	0

(d) Represents market value of loaned securities at period end.

(e) The Portfolio received cash collateral of approximately $1,182,000, which was subsequently invested in Morgan Stanley Institutional Liquidity Funds as reported in the Portfolio of Investments. In addition, the Portfolio received non-cash collateral of approximately $1,291,000 in the form of U.S. Government agency securities and U.S. Government obligations, which the Portfolio cannot sell or repledge, and accordingly are not reflected in the Portfolio of Investments.

(f) The actual collateral received is greater than the amount shown here due to overcollateralization.

The Portfolio has adopted the disclosure provisions of FASB Accounting Standards Update No. 2014-11 ("ASU No. 2014-11"), "Transfers & Servicing (Topic 860): Repurchase-to-Maturity Transactions, Repurchase Financings, and Disclosures". ASU No. 2014-11 is intended to provide increased transparency about the types of collateral pledged in securities lending transactions and other similar transactions that are accounted for as secured borrowing.

The following table displays a breakdown of transactions accounted for as secured borrowings, the gross obligations by class of collateral pledged, and the

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

remaining contractual maturity of those transactions as of September 30, 2016.

Remaining Contractual Maturity of the Agreements
	Overnight and Continuous (000)		<30 days (000)		Between 30 & 90 days (000)		>90 days (000)		Total (000)
Securities Lending Transactions
Corporate Bonds	$	1,182	$	—	$	—	$	—	$	1,182
Total Borrowings	$	1,182	$	—	$	—	$	—	$	1,182
Gross amount of recognized liabilities for securities lending transactions									$	1,182

9. Security Transactions, Income and Expenses: Security transactions are accounted for on the trade date (date the order to buy or sell is executed). Realized gains and losses on the sale of investment securities are determined on the specific identified cost method. When the Portfolio buys an interest in a Senior Loan, it may receive a commitment fee which is paid to lenders on an ongoing basis based upon the undrawn portion committed by the lenders of the underlying Senior Loan. The Portfolio accrues the commitment fee over the expected term of the loan. When the Portfolio sells an interest in a Senior Loan, it may be required to pay fees or commissions to the purchaser of the interest. Fees received in connection with loan amendments are accrued as earned. Dividend income and other distributions are recorded on the ex-dividend date (except for certain foreign dividends which may be recorded as soon as the Portfolio is informed of such dividends) net of applicable withholding taxes. Interest income is recognized on the accrual basis except where collection is in doubt. Discounts are accreted and premiums are amortized over the life of the respective securities. Most expenses of the Fund can be directly attributed to a particular Portfolio. Expenses which cannot be directly attributed are apportioned among the Portfolios based upon relative net assets or other appropriate methods. Income, expenses (other than class specific expenses — distribution and shareholder services, transfer agency and sub transfer agency fees) and realized and unrealized gains or losses are allocated to each class of shares based upon their relative net assets. Included in Realized Gain (Loss) on Investments Sold are proceeds from the one-time settlements of class action lawsuits involving the Portfolio's past holdings of approximately $2,835,000, the impact of which on the Portfolio's performance is disclosed in the Financial Highlights.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

for at least one year from the date of the Portfolio's prospectus or until such time as the Trustees act to discontinue all or a portion of such waivers and/or reimbursements when they deem such action is appropriate. For the year ended September 30, 2016, approximately $49,000 of advisory fees were waived and approximately $51,000 of other expenses were reimbursed by the Adviser pursuant to this arrangement.

an annual rate of 0.25% of the Portfolio's average daily net assets attributable to Class C shares.

In December 2015, the Fund's Custodian announced that it had identified inconsistencies in the way in which clients were invoiced for out-of-pocket expenses from 1998 until November 2015. The dollar amount difference between what was charged and what should have been charged, plus interest, was paid back to the Portfolio in September 2016 as a reimbursement. State Street reimbursed the Portfolio directly, which was recognized as a change in accounting estimate and was reflected as "Reimbursement of Custodian Fees" in the Statement of Operations. Pursuant to the expense limitations described in Note B, the Portfolio has experienced investment advisory fee waivers and expenses reimbursed by the Adviser during the current period. Accordingly, the reimbursement of out-of-pocket expenses in the current period resulted in the reduction in the current period waiver of advisory fees and expenses reimbursed by the Adviser.

G. Security Transactions and Transactions with Affiliates: For the year ended September 30, 2016, purchases and sales of investment securities for the Portfolio, other than long-term U.S. Government securities and short-term investments, were approximately $16,844,000 and $13,620,000, respectively. For the year ended September 30, 2016, purchases of long-term U.S. Government securities were approximately $371,000 and there were no sales of long-term U.S. Government securities.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

The Portfolio invests in the Institutional Class of the Morgan Stanley Institutional Liquidity Funds (the "Liquidity Funds"), an open-end management investment company managed by the Adviser, both directly and as a portion of the securities held as collateral on loaned securities. Advisory fees paid by the Portfolio are reduced by an amount equal to its pro-rata share of the advisory and administration fees paid by the Portfolio due to its investment in the Liquidity Funds. For the year ended September 30, 2016, advisory fees paid were reduced by approximately $2,000 relating to the Portfolio's investment in the Liquidity Funds.

A summary of the Portfolio's transactions in shares of the Liquidity Funds during the year ended September 30, 2016 is as follows:

Value September 30, 2015 (000)				Purchases at Cost (000)				Sales (000)				Dividend Income (000)				Value September 30, 2016 (000)
$	1,911			$	19,856			$	18,701			$	5			$	3,066

H. Federal Income Taxes: It is the Portfolio's intention to continue to qualify as a regulated investment company and distribute all of its taxable and tax-exempt income. Accordingly, no provision for federal income taxes is required in the financial statements.

FASB ASC 740-10, "Income Taxes — Overall", sets forth a minimum threshold for financial statement recognition of the benefit of a tax position taken or expected to be taken in a tax return. Management has concluded there are no significant uncertain tax positions that would require recognition in the financial statements. If applicable, the Portfolio recognizes interest accrued related to unrecognized tax benefits in "Interest Expense" and penalties in "Other Expenses" in the Statement of Operations. The Portfolio files tax returns with the U.S. Internal Revenue Service, New York and various states. Each of the tax years in the four-year period ended September 30, 2016, remains subject to examination by taxing authorities.

2016 Distributions Paid From: Ordinary Income (000)				2015 Distributions Paid From: Ordinary Income (000)
$	1,065			$	1,089

Permanent differences, primarily due to basis adjustments for swap transactions, resulted in the following reclassifications among the components of net assets at September 30, 2016:

Accumulated Undistributed Net Investment Income (000)				Accumulated Net Realized Loss (000)				Paid-in- Capital (000)
$	(15	)		$	15			$	—

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

At September 30, 2016, the components of distributable earnings for the Portfolio on a tax basis were as follows:

Undistributed Ordinary Income (000)				Undistributed Long-Term Capital Gain (000)
$	483			$	—

At September 30, 2016, the Portfolio had available for federal income tax purposes unused capital losses which will expire on the indicated dates:

Amount (000)		Expiration
$	45,370	September 30, 2017
	8,130	September 30, 2018

Capital losses and specified ordinary losses, including currency losses, incurred after October 31 but within the taxable year are deemed to arise on the first day of the Portfolio's next taxable year. For the year ended September 30, 2016, the Portfolio deferred to October 1, 2016 for U.S. federal income tax purposes the following losses:

Post-October Currency And Specified Ordinary Losses (000)				Post-October Capital Losses (000)
$	—			$	333

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Report of Independent Registered Public Accounting Firm

To the Shareholders and Board of Trustees of
Morgan Stanley Institutional Fund Trust —
Corporate Bond Portfolio

We have audited the accompanying statement of assets and liabilities, including the portfolio of investments, of Corporate Bond Portfolio (one of the portfolios constituting Morgan Stanley Institutional Fund Trust) (the "Portfolio") as of September 30, 2016, and the related statement of operations for the year then ended, the statements of changes in net assets for each of the two years in the period then ended and the financial highlights for each of the years or periods indicated therein. These financial statements and financial highlights are the responsibility of the Portfolio's management. Our responsibility is to express an opinion on these financial statements and financial highlights based on our audits.

In our opinion, the financial statements and financial highlights referred to above present fairly, in all material respects, the financial position of Corporate Bond Portfolio (one of the portfolios constituting Morgan Stanley Institutional Fund Trust) at September 30, 2016, the results of its operations for the year then ended, the changes in its net assets for each of the two years in the periods then ended and the financial highlights for each of the years or periods indicated therein, in conformity with U.S. generally accepted accounting principles.

Boston, Massachusetts
November 22, 2016

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Advisory Agreement Approval (unaudited)

Nature, Extent and Quality of Services

Performance, Fees and Expenses of the Portfolio

The Board reviewed the performance, fees and expenses of the Portfolio compared to its peers, as determined by Broadridge, and to appropriate benchmarks where applicable. The Board discussed with the Adviser the performance goals and the actual results achieved in managing the Portfolio. When considering a fund's performance, the Board and the Adviser place emphasis on trends and longer-term returns (focusing on one-year, three-year and five-year performance, as of December 31, 2015, or since inception, as applicable). When a fund underperforms its benchmark and/or its peer group average, the Board and the Adviser discuss the causes of such underperformance and, where necessary, they discuss specific changes to investment strategy or investment personnel. The Board noted that the Portfolio's performance was better than its peer group average for the three- and five-year periods but below its peer group average for the one-year period. The Board discussed with the Adviser the level of the advisory and administration fees (together, the "management fee") for this Portfolio relative to comparable funds and/or other accounts advised by the Adviser and/or compared to its peers as determined by Broadridge. In addition to the management fee, the Board also reviewed the Portfolio's total expense ratio. When a fund's management fee and/or its total expense ratio are higher than its peers, the Board and the Adviser discuss the reasons for this and, where appropriate, they discuss possible waivers and/or caps. The Board noted that the Portfolio's management fee was lower than its peer group average but its total expense ratio was higher than its peer group average. After discussion, the Board concluded that the Portfolio's (i) performance was competitive with its peer group average; (ii) management fee was competitive with its peer group average; and (iii) total expense ratio was acceptable.

Economies of Scale

The Board considered the size and growth prospects of the Portfolio and how that relates to the Portfolio's total expense ratio and particularly the Portfolio's management fee rate, which does not include breakpoints. In conjunction with its review of the Adviser's profitability, the Board discussed with the Adviser how a change in assets can affect the efficiency or effectiveness of managing the Portfolio and whether the management fee level is appropriate relative to current and projected asset levels and/or whether the management fee structure reflects economies of scale as asset levels change. The Board has determined that its review of the actual and/or potential economies of scale of the Portfolio supports its decision to approve the Management Agreement.

Profitability of the Adviser and Affiliates

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Advisory Agreement Approval (unaudited) (cont'd)

Other Benefits of the Relationship

Resources of the Adviser and Historical Relationship Between the Portfolio and the Adviser

Other Factors and Current Trends

General Conclusion

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Privacy Notice (unaudited)

MORGAN STANLEY INVESTMENT MANAGEMENT INC.
AN IMPORTANT NOTICE CONCERNING OUR U.S. PRIVACY POLICY

WE RESPECT YOUR PRIVACY

1. WHAT PERSONAL INFORMATION DO WE COLLECT ABOUT YOU?

For example:

• We may obtain information about your creditworthiness and credit history from consumer reporting agencies.

• We may collect background information from and through third-party vendors to verify representations you have made and to comply with various regulatory requirements.

2. WHEN DO WE DISCLOSE PERSONAL INFORMATION WE COLLECT ABOUT YOU?

We may disclose personal information we collect about you to other Morgan Stanley companies and to non-affiliated third parties.

a. Information We Disclose to Other Morgan Stanley Companies. We may disclose personal information to other Morgan Stanley companies for a variety of reasons, including to manage your account(s) effectively, to service and process your transactions, to let you know about products and services offered by us and other Morgan Stanley companies, to manage our business, and as otherwise required or permitted by law. Offers for products and services from other Morgan Stanley companies are developed under conditions designed to safeguard your personal information.

b. Information We Disclose to Non-affiliated Third Parties. We do not disclose personal information that we collect about you to non-affiliated third parties except to those who provide marketing services on our behalf, to financial institutions with whom we have joint marketing agreements, and as otherwise required or permitted by law. For example, we may disclose personal

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Privacy Notice (unaudited) (cont'd)

information to nonaffiliated third parties for servicing and processing transactions, to offer our own products and services, to protect against fraud, for institutional risk control, to respond to judicial process or to perform services on our behalf. When we share personal information with a non-affiliated third party, they are required to limit their use of personal information to the particular purpose for which it was shared and they are not allowed to share personal information with others except to fulfill that limited purpose or as may be permitted or required by law.

3. HOW DO WE PROTECT THE SECURITY AND CONFIDENTIALITY OF PERSONAL INFORMATION WE COLLECT ABOUT YOU?

4. HOW CAN YOU LIMIT THE SHARING OF CERTAIN TYPES OF PERSONAL INFORMATION WITH OTHER MORGAN STANLEY COMPANIES?

5. HOW CAN YOU LIMIT THE USE OF CERTAIN TYPES OF PERSONAL INFORMATION BY OTHER MORGAN STANLEY COMPANIES FOR MARKETING?

6. HOW CAN YOU SEND US AN OPT-OUT INSTRUCTION?

• Calling us at (800) 548-7786
Monday-Friday between 8a.m. and 6p.m.(EST)

• Writing to us at the following address:

Boston Financial Data Services, Inc.
c/o Privacy Coordinator
P.O. Box 219804
Kansas City, Missouri 64121

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Privacy Notice (unaudited) (cont'd)

7. WHAT IF AN AFFILIATED COMPANY BECOMES A NON-AFFILIATED THIRD PARTY?

SPECIAL NOTICE TO RESIDENTS OF VERMONT

If you wish to receive offers for investment products and services offered by or through other Morgan Stanley companies, please notify us in writing at the following address:

Boston Financial Data Services, Inc.
c/o Privacy Coordinator
P.O. Box 219804
Kansas City, Missouri 64121

SPECIAL NOTICE TO RESIDENTS OF CALIFORNIA

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited)

Independent Trustees:

Name, Age and Address of
Independent Trustee

Position(s)
Held with
Registrant

Length of Time
Served*

During Past 5 Years
and Other Relevant
Professional Experience

Number of
Principal Occupation(s)
Overseen by
Independent
Trustee**

Portfolios in
Fund Complex
Other Directorships
Held by Independent
Trustee***

Frank L. Bowman (71)
c/o Perkins Coie LLP
Counsel to the Independent Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since August 2006

Kathleen A. Dennis (63)
c/o Perkins Coie LLP
Counsel to the Independent Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since August 2006

Director of various non-profit organizations.

Nancy C. Everett (61)
c/o Perkins Coie LLP
Counsel to the Independent Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since January 2015

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Age and Address of
Independent Trustee

Position(s)
Held with
Registrant

Length of Time
Served*

During Past 5 Years
and Other Relevant
Professional Experience

Number of
Principal Occupation(s)
Overseen by
Independent
Trustee**

Portfolios in
Fund Complex
Other Directorships
Held by Independent
Trustee***

Jakki L. Haussler (59)
c/o Perkins Coie LLP
Counsel to the Independent Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since January 2015

Dr. Manuel H. Johnson (67)
c/o Johnson Smick
International, Inc.
220 I Street, N.E. — Suite 200
Washington, D.C. 20002

Trustee

Since July 1991

100

Director of NVR, Inc. (home construction).

Joseph J. Kearns (74)
c/o Kearns & Associates LLC
23823 Malibu Road
S-50-440
Malibu, CA 90265

Trustee

Since August 1994

101

Director of Electro Rent Corporation (equipment leasing). Prior to December 31, 2013, Director of The Ford Family Foundation.

Michael F. Klein (57)
c/o Perkins Coie LLP
Counsel to the Independent Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since August 2006

Director of certain investment funds managed or sponsored by Aetos Capital, LLC; Director of Sanitized AG and Sanitized Marketing AG (specialty chemicals).

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Age and Address of
Independent Trustee

Position(s)
Held with
Registrant

Length of Time
Served*

Principal Occupation(s)
During Past 5 Years
and Other Relevant
Professional Experience

Number of
Portfolios in
Fund Complex
Overseen by
Independent
Trustee**

Other Directorships
Held by Independent
Trustee***

Michael E. Nugent (80)
522 Fifth Avenue
New York, NY 10036

Chair of the Board and Trustee

Chair of the Boards since July 2006 and Trustee since July 1991

100

None.

W. Allen Reed (69)
c/o Perkins Coie LLP
Counsel to the Independent Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since August 2006

Director of Legg Mason, Inc.; formerly, Director of the Auburn University Foundation (2010-2015).

Fergus Reid (84)
c/o Joe Pietryka, Inc.
85 Charles Colman Blvd.
Pawling, NY 12564

Trustee

Since June 1992

Chairman, Joe Pietryka, Inc.; Chairperson of the Governance Committee and Director or Trustee of various Morgan Stanley Funds (since June 1992).

100

Formerly, Trustee and Director of certain investment companies in the JP Morgan Fund Complex managed by JP Morgan Investment Management Inc. (1987-2012).

* This is the earliest date the Trustee began serving the Morgan Stanley Funds. Each Trustee serves an indefinite term, until his or her successor is elected.

*** This includes any directorships at public companies and registered investment companies held by the Trustee at any time during the past five years.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited) (cont'd)

Executive Officers:

Name, Age and Address of Executive Officer

Position(s) Held
with
Registrant

Length of Time
Served*

Principal Occupation(s) During Past 5 Years

John H. Gernon (53)
522 Fifth Avenue
New York, NY 10036

President and Principal Executive Officer

Since September 2013

Stefanie V. Chang Yu (49)
522 Fifth Avenue
New York, NY 10036

Chief Compliance Officer

Since December 1997

Joseph C. Benedetti (51)
522 Fifth Avenue
New York, NY 10036

Vice President

Since January 2014

Francis J. Smith (51)
522 Fifth Avenue
New York, NY 10036

Treasurer and Principal Financial Officer

Treasurer since July 2003 and Principal Financial Officer since September 2002

Executive Director of the Adviser and various entities affiliated with the Adviser; Treasurer (since July 2003) and Principal Financial Officer of various Morgan Stanley Funds (since September 2002).

Mary E. Mullin (49)
522 Fifth Avenue
New York, NY 10036

Secretary

Since June 1999

Executive Director of the Adviser; Secretary of various Morgan Stanley Funds (since June 1999).

* This is the earliest date the officer began serving the Morgan Stanley Funds. Each officer serves a one-year term, until his or her successor is elected and has qualified.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Adviser and Administrator

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

Distributor

Morgan Stanley Distribution, Inc.
522 Fifth Avenue
New York, New York 10036

Dividend Disbursing and Transfer Agent

Boston Financial Data Services, Inc.
2000 Crown Colony Drive
Quincy, Massachusetts 02169

Custodian

State Street Bank and Trust Company
One Lincoln Street
Boston, Massachusetts 02111

Counsel to the Independent Trustees

Perkins Coie LLP
30 Rockefeller Plaza
New York, New York 10112

Independent Registered Public Accounting Firm

Ernst & Young LLP
200 Clarendon Street
Boston, Massachusetts 02116

Reporting to Shareholders

Proxy Voting Policies and Procedures and Proxy Voting Record

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable Portfolio of Morgan Stanley Institutional Funds Trust, which describes in detail the Portfolio's investment policies, risks, fees and expenses. Please read the prospectus carefully before you invest or send money. For additional information, including information regarding the investments comprising the Portfolio, please visit our website at www.morganstanley.com/im or call toll free 1 (800) 548-7786.

(This Page has been left blank intentionally.)

Printed in U.S.A.
This Report has been prepared for shareholders and may be distributed to others only if preceded or accompanied by a current prospectus.

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

IFTCBANN
1627566 EXP. 11.30.17

INVESTMENT MANAGEMENT

Morgan Stanley Institutional Fund Trust

Global Multi-Asset Income Portfolio

Annual Report

September 30, 2016

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Table of Contents

Shareholders' Letter					2
Expense Example					3
Investment Overview					4
Portfolio of Investments					7
Statement of Assets and Liabilities					23
Statement of Operations					25
Statements of Changes in Net Assets					26
Financial Highlights					27
Notes to Financial Statements					31
Report of Independent Registered Public Accounting Firm					45
Investment Advisory Agreement Approval					46
Federal Tax Notice					48
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Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Shareholders' Letter (unaudited)

Dear Shareholders,

We are pleased to provide this Annual report, in which you will learn how your investment in Global Multi-Asset Income Portfolio (the "Portfolio") performed during the latest twelve-month period.

As always, we thank you for selecting Morgan Stanley Investment Management, and look forward to working with you in the months and years ahead.

Sincerely,

John H. Gernon
President and Principal Executive Officer

October 2016

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Expense Example (unaudited)

Global Multi-Asset Income Portfolio

This example is based on an investment of $1,000 invested at the beginning of the six-month period ended September 30, 2016 and held for the entire six-month period (unless otherwise noted).

Actual Expenses

Hypothetical Example for Comparison Purposes

	Beginning Account Value 4/1/16		Actual Ending Account Value 9/30/16		Hypothetical Ending Account Value		Actual Expenses Paid During Period*		Hypothetical Expenses Paid During Period*		Net Expense Ratio During Period**
Global Multi-Asset Income Portfolio Class I	$	1,000.00	$	1,040.00	$	1,020.40	$	4.69	$	4.65		0.92	%***
Global Multi-Asset Income Portfolio Class A		1,000.00		1,038.60		1,018.75		6.37		6.31		1.25	***
Global Multi-Asset Income Portfolio Class C		1,000.00		1,034.40		1,014.90		10.27		10.18		2.02	***
Global Multi-Asset Income Portfolio Class IS		1,000.00		1,040.20		1,020.70		4.39		4.34		0.86	***

** Annualized.

*** Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Overview (unaudited)

Global Multi-Asset Income Portfolio

The Portfolio's investment objective is to maximize current income and to seek capital appreciation over time.

Performance

For the fiscal year ended September 30, 2016, the Portfolio's Class I shares had a total return based on net asset value and reinvestment of distributions per share of 8.39%, net of fees. The Portfolio's Class I shares underperformed against the Portfolio's benchmarks, the Bloomberg Barclays Global Aggregate Index, which returned 8.83% and the Customized MSIM Global Allocation Income Index (the "Customized Index", which is comprised of 30% MSCI All Country World Index, 50% Bloomberg Barclays Global Aggregate Index, 5% Dow Jones Brookfield Global Infrastructure Index, 5% FTSE EPRA/NAREIT Developed Index, 5% Bloomberg Barclays Global High Yield Index and 5% JP Morgan EMBI Global Index, which returned 11.26%.

Factors Affecting Performanceⁱ

• In the 12 months ended September 30, 2016, global equities outperformed bonds and commodities, with the MSCI All Country World Index up +12.0%, the Bloomberg Barclays Global Aggregate Index up +8.8%, and the S&P GSCI Index, a broad index of commodity prices, falling –12.2%.ⁱⁱ (Except where noted, equity market returns are represented by the MSCI regional or country index and are calculated in U.S. dollars [USD].)

• Within equities, the U.S. outperformed, with the S&P 500 Index up +15.4%. A tightening labor market contributed to the first U.S. rate hike in seven years in December 2015, but repeated global growth scares in 2016 (China in January, Brexit in June) encouraged the Federal Reserve to keep rates on hold for the remainder of the period, extending the "goldilocks" environment for equities as U.S. growth held up on a relative basis. European equities underperformed (+2.5% USD, +7.0% local), driven by generally disappointing monetary policy from the European Central Bank (ECB), comparatively greater exposure to emerging market growth and the threat of knock-on effects from Brexit. Japan (+12.1% USD, –5.2% local) was the regional laggard in local currency terms, as growth resumed slowing (though narrowly avoided slipping back into recession), but outperformed in USD terms as the effectiveness of Bank of Japan (BOJ) monetary policy appeared to reach a limit, contributing to a strong rally in the yen (+18.3% versus USD). Emerging markets (EM) were the top performer (+16.8%

USD, +13.0% local), as massive credit easing by the People's Bank of China (PBOC) stabilized Chinese growth. Within emerging markets, Brazil rose +57.6% in USD, as growth and inflation began to improve, while the impeachment of President Dilma Rousseff ushered in a new administration and the hope of meaningful economic reforms.

• Within bonds, global government yields fell to all-time lows in July and sentiment indicators reached extreme bearishness, as the U.K.'s vote to exit the European Union added to uncertainty in the already sluggish global growth outlook, extending expectations for extremely low rates almost indefinitely. In the U.S., the 10-year yield fell –44 basis points (bps) to 1.59%, while the 2-year yield rose +13 bps to 0.76%, helped by a 25 bps hike in the policy rate. U.S. credit spreads tightened on resilient domestic activity and stabilization in the oil price (which returned to $52 per barrel by the end of the period after bottoming at $28 in January). U.S. investment grade credit spreads fell –31 bps to 1.38%, and U.S. high yield spreads fell –150 bps to 4.80%. Elsewhere in developed markets, deflationary fears coupled with negative policy rates contributed to the German 10-year yield falling –71 bps to –0.12%, and the Japanese 10-year yield falling –45 bps to –0.09%. The U.K. 10-year yield fell –102 bps to 0.75%, as the market prepared for a hard Brexit. Emerging sovereign spreads fell –114 bps to 3.60%, as emerging market growth and commodity prices stabilized.

• Within currencies, the U.S. dollar fell –0.9% on a trade-weighted basis, as rate hike expectations were pushed out further. Relative to the U.S. dollar, the British pound fell –14.2% following Brexit, the Mexican peso fell –12.4% on fears of a Trump presidency in the U.S., and the Chinese renminbi fell –4.7% as the government attempted to regain control of its monetary policy amid record capital outflows. The top-performing currencies were the Brazilian real, which rose +22.6% versus USD as economic and political risks subsided, and the Japanese yen, which rose +18.3% as the market appeared to accept that "Abenomics" had failed.

ⁱ Certain of the Portfolio's investment themes may, in whole or part, be implemented through the use of derivatives, including the purchase and sale of futures, options, swaps, structured investments (including commodity-linked notes) and other related instruments and techniques. The Portfolio may also invest in foreign currency forward exchange contracts, which are also derivatives, in connection with its investments in foreign securities. The Portfolio may use derivative instruments for a variety of purposes, including hedging, risk management, portfolio management or to earn income. As a result, the use of derivatives had a material effect on the Portfolio's performance during the period.

ⁱⁱ Data sources used in preparation of this commentary include FactSet and Bloomberg LP. Data as of September 30, 2016.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Overview (unaudited) (cont'd)

Global Multi-Asset Income Portfolio

• Active positions within equities detracted from performance. Overweight positions in eurozone broad and domestically-focused equities versus U.S. equities were the top detractors, in addition to underweight positions in global aerospace, China-exposed auto manufacturers, and U.S. oil and gas refiners, all hedged. However, these losses were somewhat offset by gains from directional overweight positions in global equities. Writing call options on broad global equity market indices had a small positive impact on performance.

• Active positions within fixed income detracted from performance. Underweight positions in U.S. and German 10-year rates and an overweight position in U.S. 10-year inflation breakevens detracted from performance. An overweight position in U.S. high yield spreads and a Mexican 2s10s flattener (underweight 2-year rates versus overweight 10-year rates) contributed positively, as did overweight positions in Argentine and Greek government bonds.

• Active positions within high-yielding assets had a negative impact on performance. An overweight allocation to U.S. high yield spreads contributed positively; however, these gains were offset by losses from underweight positions in global infrastructure equities and real estate investment trusts (REITs).

• Active currency positions (implemented via currency forwards and futures) negatively impacted performance. Overweight positions in the Swedish krona (versus the Australian dollar, Swiss franc, Chinese renminbi, euro) and the Mexican peso, as well as underweight positions in China-sensitive currencies (Australian dollar, New Zealand dollar, South Korean won, Thai baht) versus G-3 currencies (U.S dollar, euro, yen) detracted from performance. Positive contributors included an underweight in the Chinese renminbi and overweight positions in oil-sensitive currencies (Norwegian kroner, Canadian dollar, Russian ruble).

Management Strategies

• As of September 30, 2016, the Portfolio is slightly underweight equities and underweight fixed income. We believe the global economy faces a "new mediocre" regime, with tepid growth hovering around 2% globally, and "low-flation" preventing full policy normalization. In addition, excessive global debt levels are rendering incremental

monetary policy ineffective, limiting the possibility for a renewed credit cycle to revive growth.

• We are underweight global bonds and bond proxies, such as consumer staples stocks. We believe valuations remain expensive given better-than-expected global growth following Brexit, as the global bond market appears to have extrapolated lower rates for longer to mean low rates forever. At current growth trends, we estimate that "fair value" for government bond yields will reach 1.90% in the U.S. by year end (versus 1.59% at the end of September), and 0.25% in Germany (compared to –0.12% at the end of September).

• We are underweight U.S. equities. The U.S. appears most likely to tighten policy, given relatively resilient growth, and we expect the prospect of higher rates, coupled with weak earnings growth, to interrupt the "goldilocks" environment and cause a multiple re-rating for U.S. stocks. We expect U.S. earnings to disappoint (we expect 5% growth over the next year, versus consensus at 11%). In addition, U.S. equity valuations are once again near cycle highs, with the S&P 500 Index trading at 16.9x forward earnings, and sentiment is overbought.

• We are overweight eurozone domestic equities. Despite post-Brexit expectations for a slowdown in eurozone growth, domestically-led (or non-export related) growth is back above trend, inflation is turning up, and the fiscal impulse is no longer contractionary. We expect 8% earnings growth for domestically-exposed eurozone stocks versus 5% U.S. earnings growth. We believe eurozone versus U.S. relative valuations have meaningful upside potential, while sentiment is extremely bearish.

• We are neutral emerging market equities. We continue to believe China is a risk to global growth, and we expect growth there to slow in 2017 as stimulus ebbs and excesses keep building. As the credit impulse leads activity by roughly nine months, we estimate that Chinese growth will rebound briefly in the second half of 2016 before slowing in the first half of 2017, weighing on export-sensitive EM economies. In addition, emerging market equites are expensive excluding energy and financials.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Overview (unaudited) (cont'd)

Global Multi-Asset Income Portfolio

• We are neutral Japanese equities. After a slight uptick in recent months, we expect Japanese growth to fall back to 0% over the next 12 months, compared to 1% expected by consensus. We expect weak growth to weigh on earnings, along with the strong yen. That said, Japanese equities have underperformed significantly, and relative valuations remain near historic lows.

* Minimum Investment

** Commenced operations on April 30, 2015.

In accordance with SEC regulations, the Portfolio's performance shown assumes that all recurring fees (including management fees) were deducted and all dividends and distributions were reinvested. The performance of Class A, Class C and Class IS shares will vary from the performance of Class I shares based upon their different inception dates and will be negatively impacted by additional fees assessed to those classes (where applicable).

Performance Compared to the Bloomberg Barclays Global Aggregate Index⁽¹⁾, the Customized MSIM Global Allocation Income Index⁽²⁾, and the Lipper Flexible Portfolio Funds Index⁽³⁾

	Period Ended September 30, 2016 Total Returns⁽⁴⁾
				Average Annual
	One Year			Five Years		Ten Years		Since Inception⁽⁷⁾
Portfolio — Class I Shares w/o sales charges⁽⁵⁾		8.39	%		—		—		1.01	%
Portfolio — Class A Shares w/o sales charges⁽⁵⁾		8.10			—		—		0.65
Portfolio — Class A Shares with maximum 5.25% sales charges⁽⁵⁾		2.39			—		—		–3.08

	Period Ended September 30, 2016 Total Returns⁽⁴⁾
				Average Annual
	One Year			Five Years		Ten Years		Since Inception⁽⁷⁾
Portfolio — Class C Shares w/o sales charges⁽⁶⁾		7.11	%		—		—		–0.17	%
Portfolio — Class C Shares with maximum 1.00% deferred sales charges⁽⁶⁾		6.11			—		—		–0.17
Portfolio — Class IS Shares w/o sales charges⁽⁵⁾		8.44			—		—		1.05
Bloomberg Barclays Global Aggregate Index		8.83			—		—		5.11
Customized MSIM Global Allocation Income Index		11.26			—		—		3.43
Lipper Flexible Portfolio Funds Index		9.79			—		—		1.04

⁽¹⁾ The Bloomberg Barclays Global Aggregate Index provides a broadbased measure of the global investment grade fixed-rate debt markets. Total Returns shown in unhedged USD. The Index is unmanaged and its returns do not include any sales charges or fees. Such costs would lower performance. It is not possible to invest directly in an index.

⁽²⁾ The Customized MSIM Global Allocation Income Index is comprised of 30% MSCI All Country World Index (benchmark that measures the equity market performance of developed and emerging markets), 50% Bloomberg Barclays Global Aggregate Index (benchmark that provides a broadbased measure of the global investment grade fixed-rate debt markets), 5% Dow Jones Brookfield Global Infrastructure Index (benchmark that measures the stock performance of companies that exhibit strong infrastructure charateristics), 5% FTSE EPRA/NAREIT Developed Index (benchmark that is designed to reflect stock performance of companies engaged in North American, European, and Asian real estate markets), 5% Bloomberg Barclays Global High Yield Index (benchmark that is a multi currency flagship measure of global high yield debt market), and 5% JP Morgan EMBI Global Index (benchmark that tracks returns for U.S. dollar-denominated debt instruments issued by emerging market sovereign and quasi sovereign entities). The Index is unmanaged and its returns do not include any sales charges or fees. Such costs would lower performance. It is not possible to invest directly in an index.

⁽³⁾ The Lipper Flexible Portfolio Funds Index is an equally weighted performance index of the largest qualifying funds (based on net assets) in the Lipper Flexible Portfolio Funds classification. The Index, which is adjusted for capital gains distributions and income dividends, is unmanaged and should not be considered an investment. There are currently 30 funds represented in this Index. As of the date of this report, the Portfolio was in the Lipper Flexible Portfolio Funds classification.

⁽⁴⁾ Total returns for the Portfolio reflect expenses waived and/or reimbursed, if applicable, by the Adviser. Without such waivers and/or reimbursements, total returns would have been lower.

⁽⁵⁾ Commenced operations on April 30, 2015.

⁽⁶⁾ Commenced operations on May 08, 2015.

⁽⁷⁾ For comparative purposes, average annual since inception returns listed for the Indexes refer to the inception date of the Class I of the Portfolio, not the inception of the Indexes.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments

Global Multi-Asset Income Portfolio

	Face Amount (000)		Value (000)
Fixed Income Securities (50.3%)
Agency Fixed Rate Mortgages (5.3%)
United States (5.3%)
Federal Home Loan Mortgage Corporation,
Gold Pools:
3.50%, 2/1/45	$	49	$	53
Federal National Mortgage Association,
Conventional Pools:
4.50%, 10/1/44 - 11/1/44		55		61
October TBA:
2.50%, 10/1/31 (a)		50		52
3.00%, 10/1/31 - 10/1/46 (a)		392		408
3.50%, 10/1/46 (a)		150		158
4.00%, 10/1/46 (a)		50		54
				786
Commercial Mortgage-Backed Securities (1.2%)
United States (1.2%)
GS Mortgage Securities Trust,
4.93%, 8/10/46 (b)(c)		70		65
Wells Fargo Commercial Mortgage Trust,
4.24%, 5/15/48 (b)		51		42
WF-RBS Commercial Mortgage Trust,
4.27%, 5/15/45 (b)(c)		40		37
4.63%, 8/15/46 (b)(c)		35		32
				176
Corporate Bonds (10.6%)
Australia (0.6%)
Australia & New Zealand Banking Group Ltd.,
5.13%, 9/10/19	EUR	50		64
Transurban Finance Co., Pty Ltd.,
4.13%, 2/2/26 (c)	$	25		27
				91
Belgium (0.2%)
Anheuser-Busch InBev Finance, Inc.,
4.70%, 2/1/36		25		29
Canada (0.2%)
Royal Bank of Canada,
1.50%, 7/29/19		25		25
France (0.4%)
BNP Paribas SA,
5.00%, 1/15/21		50		56
Israel (0.1%)
Teva Pharmaceutical Finance Netherlands III BV,
2.20%, 7/21/21		10		10
Netherlands (0.8%)
ABN Amro Bank N.V.,
3.63%, 10/6/17	EUR	50		58
Cooperatieve Rabobank UA,
3.75%, 11/9/20		50		64
				122

	Face Amount (000)		Value (000)
United Kingdom (0.7%)
Barclays Bank PLC,
6.00%, 1/23/18	EUR	50	$	60
Diageo Capital PLC,
1.50%, 5/11/17	$	50		50
				110
United States (7.6%)
Air Lease Corp.,
2.13%, 1/15/20 (d)		25		25
Apple, Inc.,
4.45%, 5/6/44		25		28
AT&T, Inc.,
4.50%, 3/9/48 (c)		63		64
Bank of America Corp.,
Series G
3.50%, 4/19/26		25		26
Baxalta, Inc.,
4.00%, 6/23/25		25		27
Boston Properties LP,
3.85%, 2/1/23		50		53
Charter Communications Operating LLC/ Charter Communications Operating Capital,
4.91%, 7/23/25 (c)		25		28
Citigroup, Inc.,
5.50%, 9/13/25		50		57
General Motors Financial Co., Inc.,
4.30%, 7/13/25		30		31
Gilead Sciences, Inc.,
3.65%, 3/1/26		25		27
Goldman Sachs Group, Inc. (The),
6.75%, 10/1/37		50		64
HSBC USA, Inc.,
3.50%, 6/23/24		100		104
JPMorgan Chase & Co.,
3.20%, 6/15/26		50		51
McDonald's Corp.,
MTN
3.38%, 5/26/25		50		53
Merck & Co., Inc.,
2.80%, 5/18/23		50		52
Microsoft Corp.,
1.55%, 8/8/21		25		25
Monongahela Power Co.,
5.40%, 12/15/43 (c)		50		63
MPLX LP,
4.00%, 2/15/25		50		49
NBC Universal Media LLC,
4.38%, 4/1/21		50		56
Omnicom Group, Inc.,
3.63%, 5/1/22		50		54
Prudential Financial, Inc.,
MTN
6.63%, 12/1/37		50		65

The accompanying notes are an integral part of the financial statements.
7

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Multi-Asset Income Portfolio

	Face Amount (000)		Value (000)
United States (cont'd)
UnitedHealth Group, Inc.,
2.88%, 3/15/23	$	25	$	26
Verizon Communications, Inc.,
3.50%, 11/1/24		25		27
Visa, Inc.,
3.15%, 12/14/25		25		26
Wal-Mart Stores, Inc.,
2.55%, 4/11/23		25		26
Wells Fargo & Co.,
MTN
4.10%, 6/3/26		25		27
				1,134
				1,577
Sovereign (27.9%)
Argentina (1.1%)
Argentine Republic Government International Bond,
7.50%, 4/22/26 (c)		150		170
Australia (0.5%)
Australia Government Bond,
3.25%, 4/21/25	AUD	80		68
Austria (0.2%)
Austria Government Bond,
1.20%, 10/20/25 (c)	EUR	30		38
Belgium (0.9%)
Belgium Government Bond,
0.80%, 6/22/25 (c)		115		138
Brazil (1.3%)
Brazil Notas do Tesouro Nacional, Series F,
10.00%, 1/1/21 - 1/1/25	BRL	640		187
Canada (2.0%)
Canadian Government Bond,
1.50%, 6/1/23	CAD	70		56
3.25%, 6/1/21		280		240
				296
France (2.6%)
France Government Bond OAT,
0.00%, 5/25/21	EUR	140		161
0.50%, 5/25/25		100		117
3.25%, 5/25/45		34		60
5.50%, 4/25/29		30		55
				393
Germany (2.8%)
Bundesrepublik Deutschland,
1.00%, 8/15/25		125		156
2.50%, 1/4/21		140		179
4.25%, 7/4/39		25		52
4.75%, 7/4/34		15		31
				418

	Face Amount (000)		Value (000)
Greece (0.2%)
Hellenic Republic Government Bond,
3.00%, 2/24/23 - 2/24/42 (e)	EUR	40	$	34
Hungary (0.4%)
Hungary Government International Bond,
5.75%, 11/22/23	$	50		59
Ireland (0.1%)
Ireland Government Bond,
5.40%, 3/13/25	EUR	10		16
Italy (1.3%)
Italy Buoni Poliennali Del Tesoro,
1.50%, 6/1/25		25		29
1.65%, 3/1/32 (c)		30		34
2.35%, 9/15/24 (c)		80		106
5.00%, 9/1/40		10		18
				187
Japan (7.8%)
Japan Government Ten Year Bond,
0.50%, 9/20/24	JPY	36,000		375
1.10%, 6/20/21		6,000		63
1.70%, 6/20/18		31,000		316
Japan Government Thirty Year Bond,
1.70%, 6/20/33		17,400		214
2.00%, 9/20/40		14,900		201
				1,169
Mexico (0.3%)
Mexican Bonos,
6.50%, 6/10/21	MXN	600		32
Petroleos Mexicanos,
6.38%, 1/23/45	$	10		9
				41
Netherlands (0.4%)
Netherlands Government Bond,
0.25%, 7/15/25 (c)	EUR	50		58
New Zealand (0.3%)
New Zealand Government Bond,
4.50%, 4/15/27	NZD	50		44
Peru (0.2%)
Peruvian Government International Bond,
4.13%, 8/25/27	$	20		23
Poland (0.9%)
Poland Government Bond,
2.50%, 7/25/26	PLN	510		129
4.00%, 10/25/23		30		8
				137
South Africa (0.1%)
South Africa Government Bond,
8.00%, 1/31/30	ZAR	300		20

The accompanying notes are an integral part of the financial statements.
8

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Multi-Asset Income Portfolio

	Face Amount (000)		Value (000)
Spain (0.7%)
Spain Government Bond,
1.15%, 7/30/20	EUR	16	$	19
1.30%, 10/31/26 (c)		5		6
2.15%, 10/31/25 (c)		20		25
Spain Government Inflation Linked Bond,
1.00%, 11/30/30 (c)		40		49
1.80%, 11/30/24 (c)		10		13
				112
United Kingdom (3.8%)
United Kingdom Gilt,
2.00%, 9/7/25	GBP	70		101
2.75%, 9/7/24		130		198
4.25%, 6/7/32 - 9/7/39		135		262
				561
				4,169
U.S. Treasury Securities (5.3%)
United States (5.3%)
U.S. Treasury Bonds,
2.50%, 2/15/45	$	10		10
3.88%, 8/15/40		150		196
U.S. Treasury Inflation Indexed Bond,
0.25%, 1/15/25		173		176
U.S. Treasury Notes,
1.38%, 1/31/21		160		162
2.13%, 5/15/25		95		99
2.38%, 6/30/18		140		144
				787
Total Fixed Income Securities (Cost $7,203)				7,495
	Shares
Common Stocks (31.8%)
Australia (2.0%)
Ansell Ltd.		438		8
APA Group		139		1
ARB Corp., Ltd.		1,214		17
AusNet Services		209		—	@
Automotive Holdings Group Ltd.		3,381		11
BlueScope Steel Ltd.		3,006		18
BWP Trust REIT		4,859		12
Challenger Ltd.		2,323		18
Downer EDI Ltd.		2,717		11
DUET Group		6,101		12
Goodman Group REIT		862		5
GPT Group REIT		1,161		4
GrainCorp Ltd.		1,336		8
Invocare Ltd.		930		10
IOOF Holdings Ltd.		3,470		23
JB Hi-Fi Ltd.		645		14
Macquarie Atlas Roads Group		656		3
Oil Search Ltd.		1,443		8
Perpetual Ltd.		604		22

	Shares		Value (000)
Primary Health Care Ltd.		2,099	$	6
Scentre Group REIT		1,969		7
Shopping Centres Australasia Property Group REIT		8,013		14
Sims Metal Management Ltd.		1,003		7
Spark Infrastructure Group		5,673		10
Stockland REIT		1,377		5
Sydney Airport		1,822		10
Transurban Group		3,403		30
Westfield Corp. REIT		694		5
				299
Austria (0.0%)
Erste Group Bank AG (f)		104		3
Raiffeisen Bank International AG (f)		44		1
				4
Belgium (0.3%)
Anheuser-Busch InBev N.V.		207		27
Cofinimmo SA REIT		43		6
Elia System Operator SA		4		—	@
KBC Group N.V. (f)		202		12
				45
Canada (2.1%)
Alimentation Couche-Tard, Inc.		100		5
ARC Resources Ltd.		100		2
Bank of Montreal		100		7
Bank of Nova Scotia		200		11
Barrick Gold Corp.		100		2
Blackberry Ltd. (f)		100		1
Brookfield Asset Management, Inc., Class A		100		4
Brookfield Business Partners LP		2		—	@
Cameco Corp.		100		1
Canadian Imperial Bank of Commerce		100		8
Canadian National Railway Co.		100		7
Canadian Natural Resources Ltd.		200		6
Cenovus Energy, Inc.		100		1
Cominar Real Estate Investment Trust REIT		400		5
Enbridge Income Fund Holdings, Inc.		200		5
Enbridge, Inc.		1,600		70
Encana Corp.		200		2
First Quantum Minerals Ltd.		100		1
Fortis, Inc.		100		3
Goldcorp, Inc.		200		3
H&R Real Estate Investment Trust REIT		200		3
Husky Energy, Inc.		102		1
Imperial Oil Ltd.		100		3
Inter Pipeline Ltd.		600		13
Keyera Corp.		300		10
Magna International, Inc.		100		4
Manulife Financial Corp.		300		4
Pembina Pipeline Corp.		700		21
Potash Corp. of Saskatchewan, Inc.		100		2
Power Corp. of Canada		100		2
PrairieSky Royalty Ltd.		4		—	@

The accompanying notes are an integral part of the financial statements.
9

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Multi-Asset Income Portfolio

	Shares		Value (000)
Canada (cont'd)
RioCan REIT		200	$	4
Rogers Communications, Inc., Class B		100		4
Royal Bank of Canada		200		12
Shaw Communications, Inc., Class B		100		2
Silver Wheaton Corp.		100		3
Sun Life Financial, Inc.		100		3
Suncor Energy, Inc.		200		6
Teck Resources Ltd., Class B		100		2
Toronto-Dominion Bank (The)		100		4
TransCanada Corp.		1,400		66
Veresen, Inc.		500		5
Westshore Terminals Investment Corp.		100		2
				320
China (0.2%)
Beijing Capital International Airport Co., Ltd. H Shares (g)		2,000		2
Beijing Enterprises Holdings Ltd. (g)		1,000		5
China Merchants Port Holdings Co., Ltd. (g)		2,000		6
Global Logistic Properties Ltd.		1,700		2
Hanergy Thin Film Power Group Ltd. (f)(g)(h)(i)		2,000		—	@
Hutchison Port Holdings Trust (Units) (j)		9,500		4
Jiangsu Expressway Co., Ltd. H Shares (g)		2,000		3
Shenzhen Expressway Co., Ltd. (g)		2,000		2
Zhejiang Expressway Co., Ltd. (g)		2,000		2
				26
Denmark (0.2%)
DSV A/S		263		13
ISS A/S		264		11
				24
Finland (0.2%)
Kone Oyj, Class B		122		6
Nokia Oyj		1,043		6
Sampo Oyj, Class A		167		8
UPM-Kymmene Oyj		235		5
				25
France (4.5%)
Accor SA		804		32
Aeroports de Paris (ADP)		79		8
Air Liquide SA		108		12
Airbus Group SE		156		9
Atos SE		208		22
AXA SA		473		10
BNP Paribas SA		668		34
Bouygues SA		565		19
Cap Gemini SA		445		44
Carrefour SA		182		5
Cie de Saint-Gobain		1,350		58
Cie Generale des Etablissements Michelin		62		7
Credit Agricole SA		727		7
Danone SA		169		12
Engie SA		394		6

	Shares		Value (000)
Essilor International SA		69	$	9
Eutelsat Communications SA		289		6
Gecina SA REIT		30		5
Groupe Eurotunnel SE		1,542		17
Kering		22		4
Klepierre REIT		77		3
L'Oreal SA		64		12
Legrand SA		111		7
LVMH Moet Hennessy Louis Vuitton SE		67		11
Metropole Television SA		87		2
Natixis SA		351		2
Orange SA		515		8
Pernod Ricard SA		69		8
Peugeot SA (f)		3,219		49
Publicis Groupe SA		74		6
Renault SA		133		11
Rexel SA		621		9
Safran SA		114		8
Sanofi		289		22
Schneider Electric SE		149		10
SES SA		676		17
Societe Generale SA		488		17
Sodexo SA		66		8
Television Francaise 1		306		3
Total SA		522		25
Unibail-Rodamco SE REIT		61		16
Valeo SA		97		6
Vinci SA		1,048		80
Vivendi SA		347		7
				673
Germany (2.8%)
Adidas AG		67		12
Allianz SE (Registered)		112		17
BASF SE		224		19
Bayer AG (Registered)		201		20
Bayerische Motoren Werke AG		208		17
Bayerische Motoren Werke AG (Preference)		22		2
Commerzbank AG		781		5
Continental AG		31		6
Daimler AG (Registered)		593		42
Deutsche Bank AG (Registered) (f)		380		5
Deutsche Boerse AG (f)		406		33
Deutsche Euroshop AG		74		3
Deutsche Lufthansa AG (Registered)		2,317		26
Deutsche Post AG (Registered)		274		8
Deutsche Telekom AG (Registered)		776		13
Deutsche Wohnen AG		133		5
E.ON SE		553		4
Fraport AG Frankfurt Airport Services Worldwide		137		7
Fresenius Medical Care AG & Co., KGaA		66		6
Fresenius SE & Co., KGaA		99		8
HeidelbergCement AG		66		6

The accompanying notes are an integral part of the financial statements.
10

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Multi-Asset Income Portfolio

	Shares		Value (000)
Germany (cont'd)
Henkel AG & Co., KGaA		41	$	5
Henkel AG & Co., KGaA (Preference)		55		7
Infineon Technologies AG		427		8
Johnson Electric Holdings Ltd. (g)		1,500		4
Linde AG		51		9
Merck KGaA		61		7
Muenchener Rueckversicherungs AG (Registered)		52		10
Porsche Automobil Holding SE (Preference)		118		6
ProSiebenSat.1 Media SE (Registered)		458		20
RWE AG (f)		164		3
SAP SE		224		20
Siemens AG (Registered)		197		23
Stroeer SE & Co. KGaA		57		2
ThyssenKrupp AG		199		5
Uniper SE (f)		55		1
Volkswagen AG		12		2
Volkswagen AG (Preference)		109		14
Vonovia SE		225		8
				418
Hong Kong (0.4%)
Champion REIT		9,000		5
Great Eagle Holdings Ltd.		2,017		9
Hang Lung Group Ltd.		1,000		4
Hang Lung Properties Ltd.		1,000		2
Hong Kong & China Gas Co., Ltd.		840		2
Hongkong & Shanghai Hotels Ltd. (The)		3,098		3
Hongkong Land Holdings Ltd.		400		3
Hopewell Holdings Ltd.		1,500		5
Kowloon Development Co., Ltd. REIT		6,000		6
Link REIT		1,000		7
New World Development Co., Ltd.		4,235		6
Stella International Holdings Ltd.		1,500		3
				55
Ireland (0.5%)
Bank of Ireland (f)		18,747		4
CRH PLC		681		23
CRH PLC		626		21
Kerry Group PLC, Class A		42		3
Ryanair Holdings PLC		1,692		23
				74
Italy (1.1%)
ACEA SpA		5		—	@
Assicurazioni Generali SpA		359		4
Atlantia SpA		2,053		52
Ei Towers SpA (f)		28		1
Enel SpA		1,896		8
Eni SpA		701		10
Ferrari N.V.		74		4
Infrastrutture Wireless Italiane SpA (c)		355		2
Intesa Sanpaolo SpA		348		1
Intesa Sanpaolo SpA		8,151		18

	Shares		Value (000)
Luxottica Group SpA		72	$	3
Mediaset SpA		5,630		18
Mediobanca SpA		4,083		27
Rizzoli Corriere Della Sera Mediagroup SpA (f)		17		—	@
Snam SpA		1,184		7
Societa Iniziative Autostradali e Servizi SpA		111		1
Telecom Italia SpA (f)		3,594		3
Terna Rete Elettrica Nazionale SpA		172		1
UniCredit SpA		3,140		7
Unione di Banche Italiane SpA		329		1
				168
Japan (0.2%)
Japan Airport Terminal Co., Ltd.		100		4
Japan Real Estate Investment Corp. REIT		1		6
Japan Retail Fund Investment Corp. REIT		2		5
Nippon Building Fund, Inc. REIT		1		6
United Urban Investment Corp. REIT		2		4
				25
Mexico (0.1%)
Grupo Aeroportuario del Pacifico S.A.B. de C.V. ADR		100		10
Netherlands (0.9%)
ABN AMRO Group N.V. (c)		87		2
Aegon N.V.		640		2
Akzo Nobel N.V.		98		7
ArcelorMittal (f)		387		2
ASML Holding N.V.		83		9
Fiat Chrysler Automobiles N.V.		614		4
Heineken N.V.		81		7
ING Groep N.V. CVA		2,401		30
Koninklijke KPN N.V.		1,219		4
Koninklijke Philips N.V.		305		9
Koninklijke Vopak N.V.		109		6
Randstad Holding N.V.		505		23
RELX N.V.		422		8
Unilever N.V. CVA		397		18
Wolters Kluwer N.V.		174		7
				138
New Zealand (0.1%)
Auckland International Airport Ltd.		1,546		8
Portugal (0.0%)
EDP - Energias de Portugal SA		1,402		5
Singapore (0.0%)
CapitaLand Ltd.		1,500		4
City Developments Ltd.		500		3
				7
South Africa (0.1%)
SABMiller PLC		142		8
Spain (1.3%)
Abertis Infraestructuras SA		825		13
Aena SA (c)		121		18
Amadeus IT Group SA, Class A		164		8

The accompanying notes are an integral part of the financial statements.
11

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Multi-Asset Income Portfolio

	Shares		Value (000)
Spain (cont'd)
Banco Bilbao Vizcaya Argentaria SA		4,223	$	26
Banco de Sabadell SA		3,816		5
Banco Popular Espanol SA		1,244		2
Banco Santander SA		8,797		39
Bankia SA		1,716		1
Bankinter SA		251		2
CaixaBank SA		2,016		5
Cellnex Telecom SA (c)		250		4
Enagas SA		28		1
Ferrovial SA		696		15
Iberdrola SA		1,826		12
Industria de Diseno Textil SA		292		11
Mediaset Espana Comunicacion SA		872		10
Obrascon Huarte Lain SA		291		1
Red Electrica Corp., SA		53		1
Repsol SA		455		6
Telefonica SA		1,195		12
				192
Sweden (0.0%)
Castellum AB		206		3
Switzerland (0.3%)
Adecco Group AG (Registered)		630		36
Flughafen Zuerich AG (Registered)		31		6
LafargeHolcim Ltd. (Registered) (f)		145		8
Swiss Prime Site AG (Registered) (f)		38		3
				53
United Kingdom (2.5%)
AstraZeneca PLC		166		11
Aviva PLC		707		4
BAE Systems PLC		932		6
Barclays PLC		2,356		5
BHP Billiton PLC		312		5
BP PLC		2,445		14
British American Tobacco PLC		248		16
British Land Co., PLC REIT		513		4
BT Group PLC		1,276		6
Capital & Counties Properties PLC		569		2
Compass Group PLC		488		9
Diageo PLC		351		10
easyJet PLC		1,586		21
GlaxoSmithKline PLC		633		14
Glencore PLC (f)		1,632		5
Hammerson PLC REIT		564		4
Henderson Group PLC		571		2
HSBC Holdings PLC		2,327		17
HSBC Holdings PLC (g)		1,249		9
Imperial Brands PLC		166		9
International Consolidated Airlines Group SA		12,420		64
Land Securities Group PLC REIT		369		5
Lloyds Banking Group PLC		7,870		6
National Grid PLC		1,263		18
Next PLC		47		3

	Shares		Value (000)
Pennon Group PLC		50	$	1
Prudential PLC		462		8
Reckitt Benckiser Group PLC		103		10
Rio Tinto PLC		186		6
Rolls-Royce Holdings PLC (f)		304		3
Royal Dutch Shell PLC, Class A		957		24
Severn Trent PLC		29		1
Shire PLC		83		5
Taylor Wimpey PLC		1,417		3
Tesco PLC (f)		1,173		3
Unilever PLC		218		10
United Utilities Group PLC		85		1
Vodafone Group PLC		3,442		10
Wolseley PLC		107		6
WPP PLC		379		9
				369
United States (12.0%)
Alexandria Real Estate Equities, Inc. REIT		100		11
Allergan PLC (f)		200		46
American Airlines Group, Inc.		577		21
American Campus Communities, Inc. REIT		100		5
American Capital Agency Corp. REIT		100		2
American Express Co.		150		10
American Tower Corp. REIT		800		91
Annaly Capital Management, Inc. REIT		400		4
Apple, Inc.		100		11
Applied Materials, Inc.		100		3
AT&T, Inc.		100		4
Bank of America Corp.		1,050		16
Bank of New York Mellon Corp. (The)		250		10
BB&T Corp.		250		9
Berkshire Hathaway, Inc., Class B (f)		200		29
Boston Properties, Inc. REIT		300		41
Bristol-Myers Squibb Co.		300		16
Brixmor Property Group, Inc. REIT		300		8
CalAtlantic Group, Inc.		150		5
Capital One Financial Corp.		150		11
Care Capital Properties, Inc. REIT		25		1
CBRE Group, Inc., Class A (f)		300		8
Celgene Corp. (f)		100		10
CenterPoint Energy, Inc.		100		2
Charles Schwab Corp. (The)		200		6
Cheniere Energy, Inc. (f)		400		17
Chevron Corp.		100		10
Cisco Systems, Inc.		100		3
Citigroup, Inc.		300		14
Citizens Financial Group, Inc.		150		4
Colgate-Palmolive Co.		100		7
Comcast Corp., Class A		100		7
ConocoPhillips		100		4
Crown Castle International Corp. REIT		700		66
CSX Corp.		100		3
D.R. Horton, Inc.		250		8

The accompanying notes are an integral part of the financial statements.
12

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Multi-Asset Income Portfolio

	Shares		Value (000)
United States (cont'd)
DDR Corp. REIT		300	$	5
Dell Technologies, Inc. - VMware, Inc., Class V (f)		11		1
Delta Air Lines, Inc.		826		33
Digital Realty Trust, Inc. REIT		300		29
Discover Financial Services		150		8
Dow Chemical Co. (The)		100		5
Duke Realty Corp. REIT		500		14
Eli Lilly & Co.		300		24
Enbridge Energy Management LLC (f)		100		3
Equity Lifestyle Properties, Inc. REIT		100		8
Equity Residential REIT		100		6
Extra Space Storage, Inc. REIT		100		8
Facebook, Inc., Class A (f)		100		13
Fifth Third Bancorp		150		3
First American Financial Corp.		150		6
General Electric Co.		100		3
General Growth Properties, Inc. REIT		500		14
Genworth Financial, Inc., Class A (f)		350		2
Goldman Sachs Group, Inc. (The)		150		24
Halliburton Co.		100		5
HCP, Inc. REIT		500		19
Hewlett Packard Enterprise Co.		100		2
Highwoods Properties, Inc. REIT		100		5
Host Hotels & Resorts, Inc. REIT		700		11
Huntington Bancshares, Inc.		150		1
Invesco Ltd.		150		5
Iron Mountain, Inc. REIT		100		4
JetBlue Airways Corp. (f)		325		6
Johnson & Johnson		300		35
JPMorgan Chase & Co.		450		30
KB Home		150		2
KeyCorp		150		2
Kilroy Realty Corp. REIT		100		7
Kimco Realty Corp. REIT		500		14
Kinder Morgan, Inc.		3,000		69
Koninklijke Ahold Delhaize N.V.		334		8
Kroger Co. (The)		100		3
Lennar Corp., Class A		100		4
Liberty Property Trust REIT		200		8
Louisiana-Pacific Corp. (f)		50		1
Macerich Co. (The) REIT		100		8
Martin Marietta Materials, Inc.		150		27
Masco Corp.		250		9
Merck & Co., Inc.		300		19
MetLife, Inc.		100		4
MGIC Investment Corp. (f)		250		2
Microsoft Corp.		100		6
Mid-America Apartment Communities, Inc. REIT		100		9
Mohawk Industries, Inc. (f)		150		30
Mylan N.V. (f)		200		8
National Health Investors, Inc. REIT		100		8
National Retail Properties, Inc. REIT		100		5

	Shares		Value (000)
NIKE, Inc., Class B		100	$	5
Old Republic International Corp.		100		2
ONEOK, Inc.		300		15
Oracle Corp.		100		4
Owens Corning		150		8
PayPal Holdings, Inc. (f)		100		4
PepsiCo, Inc.		100		11
Pfizer, Inc.		900		31
PG&E Corp.		100		6
PNC Financial Services Group, Inc. (The)		50		5
ProLogis, Inc. REIT		500		27
Public Storage REIT		300		67
Pulte Group, Inc.		250		5
Radian Group, Inc.		100		1
Realogy Holdings Corp.		100		3
Realty Income Corp. REIT		300		20
Regency Centers Corp. REIT		100		8
Regions Financial Corp.		200		2
Rite Aid Corp. (f)		100		1
SBA Communications Corp., Class A (f)		200		22
Schlumberger Ltd.		100		8
Scotts Miracle-Gro Co. (The), Class A		150		13
SemGroup Corp., Class A		100		4
Simon Property Group, Inc. REIT		300		62
Southwest Airlines Co.		754		29
Spectra Energy Corp.		1,100		47
State Street Corp.		150		10
SunTrust Banks, Inc.		150		7
Synchrony Financial		150		4
Targa Resources Corp.		300		15
Texas Instruments, Inc.		100		7
Time Warner, Inc.		100		8
Toll Brothers, Inc. (f)		100		3
UDR, Inc. REIT		100		4
Union Pacific Corp.		100		10
United Continental Holdings, Inc. (f)		325		17
United Technologies Corp.		100		10
UnitedHealth Group, Inc.		100		14
US Bancorp		200		9
Ventas, Inc. REIT		200		14
VEREIT, Inc. REIT		800		8
Visa, Inc., Class A		100		8
Vornado Realty Trust REIT		300		30
Vulcan Materials Co.		50		6
Wells Fargo & Co.		400		18
Welltower, Inc. REIT		200		15
Weyerhaeuser Co. REIT		400		13
Williams Cos., Inc. (The)		1,000		31
WP Carey, Inc. REIT		100		6
Zoetis, Inc.		200		10
				1,795
Total Common Stocks (Cost $4,732)				4,744

The accompanying notes are an integral part of the financial statements.
13

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Multi-Asset Income Portfolio

	Shares			Value (000)
Investment Companies (9.7%)
United Kingdom (0.0%)
HICL Infrastructure Co., Ltd. (United Kingdom)		2,217		$	5
United States (9.7%)
Morgan Stanley Institutional Fund Trust — High Yield Portfolio (See Note G)		69,531			690
Morgan Stanley Institutional Fund, Inc. — Emerging Markets Fixed Income Opportunities Portfolio (See Note G)		76,964			747
					1,437
Total Investment Companies (Cost $1,424)					1,442
	Notional Amount (000)
Put Options Purchased (0.0%)
Germany (0.0%)
Kone Oyj December 2016 @ EUR 50.00, Goldman Sachs International		1			3
Switzerland (0.0%)
Schindler Holding AG December 2016 @ CHF 200.00, Goldman Sachs International		—	@@		2
Total Put Options Purchased (Cost $5)					5
	Shares
Short-Term Investments (11.0%)
Investment Company (7.4%)
Morgan Stanley Institutional Liquidity Funds — Government Portfolio — Institutional Class (See Note G) (Cost $1,103)		1,103,188			1,103
	Face Amount (000)
Sovereign (0.4%)
Argentina (0.4%)
Letras del Banco Central de la Republica Argentina,
25.00%, 1/11/17 - 1/25/17	ARS	815			49
26.00%, 1/11/17		50			3
26.25%, 1/11/17 - 1/18/17		190			12
Total Sovereign (Cost $67)					64
U.S. Treasury Securities (3.2%)
U.S. Treasury Note,
0.63%, 12/31/16	$	100			100
U.S. Treasury Bill,
0.41%, 3/23/17 (k)(l)		382			382
Total U.S. Treasury Securities (Cost $481)					482
Total Short-Term Investments (Cost $1,651)					1,649
Total Investments (102.8%) (Cost $15,015) (m)(n)(o)					15,335
Liabilities in Excess of Other Assets (-2.0%)					(306	)
Total Written Options Outstanding (-0.8%) (Premiums Received $112)					(116	)
Net Assets (100.0%)				$	14,913

(a) Security is subject to delayed delivery.

(b) Variable/Floating Rate Security — Interest rate changes on these instruments are based on changes in a designated base rate. The rates shown are those in effect on September 30, 2016.

(c) 144A security — Certain conditions for public sale may exist. Unless otherwise noted, these securities are deemed to be liquid.

(d) When-issued security.

(e) Multi-step — Coupon rate changes in predetermined increments to maturity. Rate disclosed is as of September 30, 2016. Maturity date disclosed is the ultimate maturity date.

(f) Non-income producing security.

(g) Security trades on the Hong Kong exchange.

(h) Security has been deemed illiquid at September 30, 2016.

(i) At September 30, 2016, the Portfolio held a fair valued security valued at less than $500, representing less than 0.05% of net assets. This security has been fair valued as determined in good faith under procedures established by and under the general supervision of the Fund's Trustees.

(j) Consists of one or more classes of securities traded together as a unit; stocks with attached warrants.

(k) Rate shown is the yield to maturity at September 30, 2016.

(l) All or a portion of the security was pledged to cover margin requirements for swap agreements.

(m) The approximate fair value and percentage of net assets, $2,179,000 and 14.6%, respectively, represent the securities that have been fair valued under the fair valuation policy for international investments as described in Note A-1 within the Notes to the Financial Statements.

(n) Securities are available for collateral in connection with purchase of when-issued security, securities purchased on a forward commitment basis, open call options written, foreign currency forward exchange contracts, futures contracts and swap agreements.

(o) At September 30, 2016, the aggregate cost for federal income tax purposes is approximately $15,116,000. The aggregate gross unrealized appreciation is approximately $522,000 and the aggregate gross unrealized depreciation is approximately $303,000 resulting in net unrealized appreciation of approximately $219,000.

@ Value is less than $500.

@@ Amount is less than 500.

ADR American Depositary Receipt.

CVA Certificaten Van Aandelen.

MTN Medium Term Note.

OAT Obligations Assimilables du Trésor (French Treasury Obligation).

REIT Real Estate Investment Trust.

TBA To Be Announced.

The accompanying notes are an integral part of the financial statements.
14

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Multi-Asset Income Portfolio

Call Options Written:

The Portfolio had the following call options written open at September 30, 2016:

Counterparty		Notional Amount (000)			Description	Strike Price		Expiration Date	Value (000)
	Goldman Sachs International		—	@@	Euro Stoxx 50 Index (Premiums received $26)	EUR	2,950.00	Oct-16	$	(34	)
	Goldman Sachs International		1		iShares MSCI Emerging Markets Index Fund (Premiums received $29)	$	885.00	Oct-16		(35	)
	Goldman Sachs International		7		NIKKEI Index (Premiums received $27)	JPY	16,750.00	Oct-16		(7	)
	Goldman Sachs International*		1		S&P 500 Index (Premiums received $30)	$	2,125.00	Oct-16		(40	)
									$	(116	)

Foreign Currency Forward Exchange Contracts:

The Portfolio had the following foreign currency forward exchange contracts open at September 30, 2016:

Counterparty	Contracts to Deliver (000)			In Exchange For (000)			Delivery Date	Unrealized Appreciation (Depreciation) (000)
Australia and New Zealand Banking Group	AUD	34		$	26		10/5/16	$	(—	@)
Australia and New Zealand Banking Group	CAD	178		$	137		10/5/16		1
Australia and New Zealand Banking Group	EUR	5		GBP	4		10/5/16		(—	@)
Australia and New Zealand Banking Group	EUR	68		NZD	105		10/5/16		(—	@)
Australia and New Zealand Banking Group	KRW	93,150		$	84		10/5/16		(—	@)
Australia and New Zealand Banking Group	MYR	79		$	19		10/5/16		—	@
Australia and New Zealand Banking Group	NZD	105		EUR	68		10/5/16		(—	@)
Australia and New Zealand Banking Group	NZD	63		$	46		10/5/16		—	@
Australia and New Zealand Banking Group	PLN	248		$	65		10/5/16		—	@
Australia and New Zealand Banking Group	RUB	965		$	15		10/5/16		(—	@)
Australia and New Zealand Banking Group	SGD	15		$	11		10/5/16		—	@
Australia and New Zealand Banking Group	THB	625		$	18		10/5/16		—	@
Australia and New Zealand Banking Group	TRY	35		$	12		10/5/16		(—	@)
Australia and New Zealand Banking Group	$	133		BRL	433		10/5/16		—	@
Australia and New Zealand Banking Group	$	5		GBP	4		10/5/16		(—	@)
Australia and New Zealand Banking Group	$	166		JPY	16,816		10/5/16		(—	@)
Australia and New Zealand Banking Group	$	85		KRW	93,150		10/5/16		—	@
Australia and New Zealand Banking Group	$	19		MYR	79		10/5/16		—	@
Australia and New Zealand Banking Group	$	46		NZD	63		10/5/16		—	@
Australia and New Zealand Banking Group	$	18		THB	625		10/5/16		—	@
Australia and New Zealand Banking Group	$	12		TRY	35		10/5/16		(—	@)
Australia and New Zealand Banking Group	ZAR	1,271		$	89		10/5/16		(4	)
Barclays Bank PLC	EUR	17		$	19		10/5/16		—	@
Barclays Bank PLC	$	2		JPY	239		10/5/16		—	@
Barclays Bank PLC	$	43		PLN	166		10/5/16		—	@
Citibank NA	EUR	112		$	126		10/5/16		—	@
Citibank NA	NOK	300		EUR	33		10/5/16		(—	@)
Citibank NA	NOK	369		$	46		10/5/16		—	@
Citibank NA	$	152		CAD	199		10/5/16		(—	@)
HSBC Bank PLC	GBP	146		$	192		10/5/16		3
HSBC Bank PLC	JPY	48		$	—	@	10/5/16		(—	@)
HSBC Bank PLC	SEK	302		$	35		10/5/16		—	@
HSBC Bank PLC	$	—	@	CAD	—	@	10/5/16		(—	@)
HSBC Bank PLC	$	184		GBP	141		10/5/16		(1	)
HSBC Bank PLC	$	44		ZAR	635		10/5/16		3
JPMorgan Chase Bank NA	EUR	32		NOK	300		10/5/16		1
JPMorgan Chase Bank NA	EUR	245		$	275		10/5/16		—	@
JPMorgan Chase Bank NA	EUR	30		$	33		10/5/16		(—	@)
JPMorgan Chase Bank NA	GBP	4		EUR	5		10/5/16		—	@
JPMorgan Chase Bank NA	MYR	79		$	19		10/5/16		(—	@)
JPMorgan Chase Bank NA	$	87		MXN	1,678		10/5/16		(1	)

The accompanying notes are an integral part of the financial statements.
15

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Multi-Asset Income Portfolio

Foreign Currency Forward Exchange Contracts: (cont'd)

Counterparty	Contracts to Deliver (000)		In Exchange For (000)		Delivery Date	Unrealized Appreciation (Depreciation) (000)
JPMorgan Chase Bank NA	$	20	MYR	79	10/5/16	$	(1	)
JPMorgan Chase Bank NA	$	65	NOK	539	10/5/16		2
JPMorgan Chase Bank NA	$	124	PLN	473	10/5/16		—	@
JPMorgan Chase Bank NA	$	15	RUB	965	10/5/16		1
JPMorgan Chase Bank NA	$	36	SEK	302	10/5/16		(—	@)
JPMorgan Chase Bank NA	$	11	SGD	15	10/5/16		(—	@)
JPMorgan Chase Bank NA	$	46	ZAR	656	10/5/16		2
JPMorgan Chase Bank NA	ZAR	20	$	1	10/5/16		—	@
Royal Bank of Canada	CAD	22	$	17	10/5/16		—	@
State Street Bank and Trust Co.	NOK	170	$	21	10/5/16		(—	@)
UBS AG	BRL	433	$	133	10/5/16		(—	@)
UBS AG	CAD	44	MXN	635	10/5/16		(1	)
UBS AG	CHF	52	$	54	10/5/16		—	@
UBS AG	DKK	140	$	21	10/5/16		(—	@)
UBS AG	EUR	54	$	61	10/5/16		(—	@)
UBS AG	JPY	3,510	MXN	670	10/5/16		(—	@)
UBS AG	JPY	17,007	$	168	10/5/16		—	@
UBS AG	KRW	93,150	$	85	10/5/16		(—	@)
UBS AG	MXN	635	CAD	43	10/5/16		—	@
UBS AG	MXN	670	JPY	3,654	10/5/16		1
UBS AG	MXN	1,156	$	62	10/5/16		3
UBS AG	MXN	522	$	27	10/5/16		—	@
UBS AG	PLN	169	$	44	10/5/16		(—	@)
UBS AG	PLN	137	$	35	10/5/16		(1	)
UBS AG	PLN	85	$	22	10/5/16		(—	@)
UBS AG	$	26	AUD	34	10/5/16		—	@
UBS AG	$	54	CHF	52	10/5/16		(—	@)
UBS AG	$	21	DKK	140	10/5/16		(—	@)
UBS AG	$	515	EUR	458	10/5/16		(1	)
UBS AG	$	83	KRW	93,150	10/5/16		1
Bank of America NA	EUR	23	$	25	10/20/16		(—	@)
Bank of America NA	PLN	204	$	53	10/20/16		(—	@)
Bank of America NA	$	47	GBP	36	10/20/16		(—	@)
Bank of America NA	$	11	ILS	40	10/20/16		—	@
Bank of America NA	$	25	PLN	96	10/20/16		—	@
Bank of America NA	$	90	SEK	772	10/20/16		(—	@)
Bank of Montreal	AUD	9	$	6	10/20/16		(—	@)
Bank of Montreal	$	26	CAD	34	10/20/16		(—	@)
Bank of Montreal	$	26	JPY	2,673	10/20/16		—	@
Bank of New York Mellon	$	4	GBP	3	10/20/16		(—	@)
Bank of New York Mellon	$	7	SEK	57	10/20/16		(—	@)
Barclays Bank PLC	AUD	173	$	131	10/20/16		(2	)
Barclays Bank PLC	EUR	312	$	350	10/20/16		(1	)
Barclays Bank PLC	$	191	GBP	146	10/20/16		(2	)
Barclays Bank PLC	$	163	JPY	16,575	10/20/16		—	@
BNP Paribas SA	JPY	3,747	$	37	10/20/16		—	@
BNP Paribas SA	$	101	CAD	133	10/20/16		(—	@)
BNP Paribas SA	$	111	CAD	146	10/20/16		1
BNP Paribas SA	$	3	CHF	3	10/20/16		—	@
BNP Paribas SA	$	1	ILS	5	10/20/16		—	@
Citibank NA	CHF	17	$	18	10/20/16		—	@
Citibank NA	EUR	191	$	214	10/20/16		(1	)
Citibank NA	SEK	942	$	109	10/20/16		(1	)
Citibank NA	$	31	CHF	30	10/20/16		—	@
Citibank NA	$	10	EUR	9	10/20/16		(—	@)
Citibank NA	$	110	EUR	98	10/20/16		—	@
Citibank NA	$	75	GBP	58	10/20/16		(1	)
Citibank NA	$	58	JPY	5,854	10/20/16		—	@
Citibank NA	$	117	SEK	996	10/20/16		(1	)

The accompanying notes are an integral part of the financial statements.
16

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Multi-Asset Income Portfolio

Foreign Currency Forward Exchange Contracts: (cont'd)

Counterparty	Contracts to Deliver (000)		In Exchange For (000)			Delivery Date	Unrealized Appreciation (Depreciation) (000)
Commonwealth Bank of Australia	AUD	106	$	80		10/20/16	$	(1	)
Commonwealth Bank of Australia	$	28	AUD	37		10/20/16		(—	@)
Commonwealth Bank of Australia	$	36	JPY	3,615		10/20/16		—	@
Credit Suisse International	EUR	28	$	32		10/20/16		(—	@)
Credit Suisse International	THB	15	$	—	@	10/20/16		(—	@)
Credit Suisse International	$	28	GBP	22		10/20/16		(—	@)
Credit Suisse International	$	6	ILS	23		10/20/16		—	@
Credit Suisse International	$	2	NZD	2		10/20/16		(—	@)
Credit Suisse International	$	27	SGD	37		10/20/16		(—	@)
Goldman Sachs International	HUF	3,679	$	13		10/20/16		(—	@)
Goldman Sachs International	TRY	330	$	110		10/20/16		1
Goldman Sachs International	$	9	GBP	7		10/20/16		(—	@)
Goldman Sachs International	$	66	HKD	516		10/20/16		—	@
Goldman Sachs International	$	117	JPY	11,910		10/20/16		—	@
JPMorgan Chase Bank NA	AUD	26	$	20		10/20/16		(—	@)
JPMorgan Chase Bank NA	EUR	279	$	312		10/20/16		(1	)
JPMorgan Chase Bank NA	NOK	702	$	85		10/20/16		(3	)
JPMorgan Chase Bank NA	PLN	8	$	2		10/20/16		(—	@)
JPMorgan Chase Bank NA	TRY	49	$	16		10/20/16		—	@
JPMorgan Chase Bank NA	$	7	DKK	45		10/20/16		—	@
JPMorgan Chase Bank NA	$	42	EUR	38		10/20/16		—	@
JPMorgan Chase Bank NA	$	205	JPY	20,838		10/20/16		1
JPMorgan Chase Bank NA	$	65	MXN	1,262		10/20/16		—	@
JPMorgan Chase Bank NA	$	128	MXN	2,525		10/20/16		2
JPMorgan Chase Bank NA	$	101	NOK	810		10/20/16		1
JPMorgan Chase Bank NA	$	21	NOK	171		10/20/16		(—	@)
JPMorgan Chase Bank NA	$	101	NOK	838		10/20/16		4
JPMorgan Chase Bank NA	$	2	NZD	3		10/20/16		(—	@)
JPMorgan Chase Bank NA	$	55	SEK	469		10/20/16		(—	@)
JPMorgan Chase Bank NA	$	25	SGD	34		10/20/16		(—	@)
JPMorgan Chase Bank NA	ZAR	250	$	18		10/20/16		(—	@)
State Street Bank and Trust Co.	BRL	124	$	37		10/20/16		(1	)
State Street Bank and Trust Co.	BRL	155	$	47		10/20/16		(1	)
State Street Bank and Trust Co.	BRL	79	$	24		10/20/16		—	@
State Street Bank and Trust Co.	BRL	32	$	10		10/20/16		—	@
State Street Bank and Trust Co.	IDR	429,685	$	32		10/20/16		(—	@)
State Street Bank and Trust Co.	MYR	27	$	7		10/20/16		—	@
State Street Bank and Trust Co.	RUB	2,877	$	44		10/20/16		(2	)
State Street Bank and Trust Co.	$	61	CHF	60		10/20/16		—	@
State Street Bank and Trust Co.	$	3	HKD	21		10/20/16		—	@
State Street Bank and Trust Co.	$	101	RUB	6,389		10/20/16		1
State Street Bank and Trust Co.	$	157	RUB	10,332		10/20/16		7
UBS AG	AUD	20	$	15		10/20/16		(—	@)
UBS AG	EUR	146	$	164		10/20/16		(1	)
UBS AG	MXN	1,380	$	70		10/20/16		(1	)
UBS AG	$	4	CAD	5		10/20/16		—	@
UBS AG	$	40	CHF	39		10/20/16		—	@
UBS AG	$	20	EUR	18		10/20/16		(—	@)
UBS AG	$	57	GBP	44		10/20/16		(—	@)
UBS AG	$	21	JPY	2,094		10/20/16		—	@
UBS AG	$	6	NOK	50		10/20/16		—	@
UBS AG	ZAR	84	$	6		10/20/16		(—	@)
Australia and New Zealand Banking Group	$	15	RUB	965		11/3/16		—	@
Australia and New Zealand Banking Group	BRL	433	$	132		11/4/16		(—	@)
Australia and New Zealand Banking Group	GBP	4	EUR	5		11/4/16		—	@
Australia and New Zealand Banking Group	NZD	105	EUR	68		11/4/16		—	@
Australia and New Zealand Banking Group	$	26	AUD	34		11/4/16		—	@
Australia and New Zealand Banking Group	$	56	BRL	185		11/4/16		—	@
Australia and New Zealand Banking Group	$	84	KRW	93,150		11/4/16		—	@
Australia and New Zealand Banking Group	$	19	MYR	79		11/4/16		(—	@)

The accompanying notes are an integral part of the financial statements.
17

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Multi-Asset Income Portfolio

Foreign Currency Forward Exchange Contracts: (cont'd)

Counterparty	Contracts to Deliver (000)		In Exchange For (000)		Delivery Date	Unrealized Appreciation (Depreciation) (000)
Australia and New Zealand Banking Group	$	46	NZD	63	11/4/16	$	(—	@)
Australia and New Zealand Banking Group	$	11	SGD	15	11/4/16		(—	@)
Australia and New Zealand Banking Group	$	18	THB	625	11/4/16		(—	@)
Australia and New Zealand Banking Group	$	12	TRY	35	11/4/16		—	@
Citibank NA	CAD	199	$	152	11/4/16		—	@
Citibank NA	EUR	33	NOK	300	11/4/16		—	@
Citibank NA	$	126	EUR	112	11/4/16		(—	@)
Citibank NA	$	46	NOK	369	11/4/16		(—	@)
HSBC Bank PLC	GBP	141	$	184	11/4/16		1
HSBC Bank PLC	$	35	SEK	302	11/4/16		(—	@)
JPMorgan Chase Bank NA	PLN	473	$	124	11/4/16		(—	@)
JPMorgan Chase Bank NA	$	1	ZAR	20	11/4/16		—	@
UBS AG	CAD	43	MXN	635	11/4/16		(—	@)
UBS AG	MXN	670	JPY	3,493	11/4/16		—	@
UBS AG	$	54	CHF	52	11/4/16		(—	@)
UBS AG	$	21	DKK	140	11/4/16		—	@
UBS AG	$	168	JPY	17,007	11/4/16		(—	@)
UBS AG	$	27	MXN	522	11/4/16		(—	@)
Citibank NA	CNH	1,391	$	211	3/16/17		4
Citibank NA	$	209	CNH	1,391	3/16/17		(2	)
Citibank NA	CNH	952	$	140	5/11/17		(1	)
Citibank NA	CNH	955	$	141	5/11/17		(1	)
Citibank NA	CNH	168	$	25	5/11/17		(—	@)
Citibank NA	CNH	391	$	58	5/11/17		(—	@)
Citibank NA	CNH	2,923	$	436	5/11/17		3
Citibank NA	$	287	CNH	1,942	5/11/17		1
Citibank NA	$	216	CNH	1,471	5/11/17		2
JPMorgan Chase Bank NA	CNH	952	$	141	5/11/17		(—	@)
JPMorgan Chase Bank NA	CNH	116	$	17	5/11/17		(—	@)
JPMorgan Chase Bank NA	CNH	362	$	53	5/11/17		(—	@)
JPMorgan Chase Bank NA	CNH	1,472	$	217	5/11/17		(1	)
JPMorgan Chase Bank NA	CNH	1,472	$	216	5/11/17		(2	)
JPMorgan Chase Bank NA	$	154	CNH	1,046	5/11/17		—	@
						$	10

Futures Contracts:

The Portfolio had the following futures contracts open at September 30, 2016:

	Number of Contracts		Value (000)			Expiration Date	Unrealized Appreciation (Depreciation) (000)
Long:
Brent Crude Futures (United Kingdom)		2	$	100		Oct-16	$	6
MSCI Emerging Market E Mini (United States)		12		548		Dec-16		(10	)
NIKKEI 225 Index (Japan)		5		408		Dec-16		(6	)
S&P 500 E Mini Index (United States)		16		1,728		Dec-16		28
U.S. Treasury 10 yr. Note (United States)		3		393		Dec-16		(—	@)
U.S. Treasury 2 yr. Note (United States)		3		656		Dec-16		—	@
U.S. Treasury 5 yr. Note (United States)		2		243		Dec-16		—	@
Short:
Euro Stoxx 50 Index (Germany)		1		(34	)	Dec-16		(—	@)
German Euro Bund (Germany)		6		(1,117	)	Dec-16		(8	)
SPI 200 Index (Australia)		1		(103	)	Dec-16		(2	)
U.S. Treasury 10 yr. Note (United States)		7		(918	)	Dec-16		1
U.S. Treasury 10 yr. Ultra Long Bond (United States)		1		(144	)	Dec-16		—	@
U.S. Treasury Long Bond (United States)		1		(168	)	Dec-16		3
UK Long Gilt Bond (United Kingdom)		2		(338	)	Dec-16		2
							$	14

The accompanying notes are an integral part of the financial statements.
18

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Multi-Asset Income Portfolio

Credit Default Swap Agreements:

The Portfolio had the following credit default swap agreements open at September 30, 2016:

Swap Counterparty and Reference Obligation	Buy/Sell Protection	Notional Amount (000)		Pay/Receive Fixed Rate			Termination Date	Upfront Payment Paid (Received) (000)			Unrealized Appreciation (Depreciation) (000)			Value (000)			Credit Rating of Reference Obligation† (Unaudited)
JPMorgan Chase Bank NA Russian Federation	Sell	$	110		1.00	%	6/20/21	$	(10	)	$	5		$	(5	)	BB+
Morgan Stanley & Co., LLC** CDX.NA.HY.24	Sell		159		5.00		6/20/20		8			4			12		NR
Morgan Stanley & Co., LLC** ITRAXX.XO.23	Sell	EUR	25		5.00		6/20/20		3			(—	@)		3		NR
		$	294					$	1		$	9		$	10

Interest Rate Swap Agreements:

The Portfolio had the following interest rate swap agreements open at September 30, 2016:

Swap Counterparty	Floating Rate Index	Pay/Receive Floating Rate	Fixed Rate			Termination Date	Notional Amount (000)		Unrealized Appreciation (Depreciation) (000)
Bank of America NA	6 Month BBSW	Pay		2.50	%	5/6/26	AUD	121	$	3
Citibank NA	6 Month BBSW	Pay		2.51		5/6/26		120		3
Citibank NA	6 Month BBSW	Pay		2.22		6/29/26		27		—	@
JPMorgan Chase Bank NA	3 Month LIBOR	Receive		1.85		3/21/26	$	147		—	@
JPMorgan Chase Bank NA	6 Month BBSW	Pay		2.55		5/5/26	AUD	120		4
JPMorgan Chase Bank NA	6 Month BBSW	Pay		2.44		5/20/26		207		5
JPMorgan Chase Bank NA	3 Month LIBOR	Receive		1.69		8/5/26	$	450		8
Morgan Stanley & Co., LLC**	3 Month LIBOR	Receive		1.29		3/7/21		250		(1	)
Morgan Stanley & Co., LLC**	3 Month LIBOR	Receive		1.18		8/31/21		20		—	@
Morgan Stanley & Co., LLC**	3 Month LIBOR	Receive		1.80		3/14/26		320		(10	)
Morgan Stanley & Co., LLC**	3 Month LIBOR	Receive		1.68		4/4/26		30		(1	)
Morgan Stanley & Co., LLC**	3 Month LIBOR	Receive		1.66		4/6/26		240		(6	)
Morgan Stanley & Co., LLC**	3 Month LIBOR	Pay		1.61		4/13/26		660		18
Morgan Stanley & Co., LLC**	3 Month LIBOR	Receive		1.62		5/13/26		330		(6	)
Morgan Stanley & Co., LLC**	3 Month LIBOR	Receive		1.50		6/16/26		70		—	@
Morgan Stanley & Co., LLC**	6 Month LIBOR	Receive		0.08		7/15/26	JPY	10,555		1
Morgan Stanley & Co., LLC**	3 Month LIBOR	Receive		1.51		7/28/26	$	20		—	@
									$	18

The accompanying notes are an integral part of the financial statements.
19

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Multi-Asset Income Portfolio

Total Return Swap Agreements:

The Portfolio had the following total return swap agreements open at September 30, 2016:

Swap Counterparty

Index

Notional
Amount
(000)

Floating
Rate

Pay/Receive
Total Return
of Referenced
Index

Maturity
Date

Upfront
Payment
(Received)
(000)

Unrealized
Appreciation
(Depreciation)
(000)

Bank of America NA

U.S. Apartment REITs††

3 Month USD LIBOR minus
0.24%

Pay

4/20/17

—

Bank of America NA

U.S. Apartment REITs††

244

3 Month USD LIBOR minus
0.24%

Pay

4/20/17

—

Bank of America NA

U.S. Apartment REITs††

3 Month USD LIBOR minus
0.24%

Pay

4/20/17

—

Bank of America NA

U.S. Apartment REITs††

3 Month USD LIBOR minus
0.24%

Pay

4/20/17

—

Citibank NA

U.S. Media Index††

309

3 Month USD LIBOR minus
0.15%

Pay

2/8/17

—

Goldman Sachs
International

USD Liquid High Yield Index

220

3 Month USD LIBOR plus
0.64%

Receive

12/23/16

(—

Goldman Sachs
International

U.S. Consumer Staples Index††

3 Month USD LIBOR minus
0.14%

Pay

3/2/17

—

Goldman Sachs
International

U.S. Consumer Staples Index††

168

3 Month USD LIBOR minus
0.14%

Pay

3/2/17

—

Goldman Sachs
International

U.S. Consumer Staples Index††

3 Month USD LIBOR minus
0.15%

Pay

3/2/17

—

Goldman Sachs
International

Global Aerospace Index††

168

3 Month USD LIBOR minus
0.25%

Pay

4/6/17

—

)

Goldman Sachs
International

Global Aerospace Index††

221

3 Month USD LIBOR minus
0.25%

Pay

4/6/17

—

)

Goldman Sachs
International

Global Aerospace Index††

3 Month USD LIBOR minus
0.25%

Pay

4/6/17

—

)

JPMorgan Chase
Bank NA

Short European Staples Index††

140

3 Month USD LIBOR plus
0.03%

Pay

8/11/17

—

)

JPMorgan Chase
Bank NA

JPM Short Luxury Index††

230

3 Month USD LIBOR minus
0.05%

Pay

9/6/17

—

)

†† See tables below for details of the equity basket holdings underlying the swap.

The accompanying notes are an integral part of the financial statements.
20

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Multi-Asset Income Portfolio

The following table represents the equity basket holdings underlying the total return swap with U.S. Apartment REITs as of September 30, 2016.

Security Description	Index Weight
U.S. Apartment REITs
Apartment Investment & Management Co.		7.26	%
AvalonBay Communities, Inc.		24.44
Camden Property Trust		7.29
Equity Residential		23.53
Essex Property Trust, Inc.		14.71
Independence Realty Trust, Inc.		0.36
Mid-America Apartment Communities, Inc.		7.12
Monogram Residential Trust, Inc.		1.38
Post Properties, Inc.		4.23
UDR, Inc.		9.68
		100.00	%

The following table represents the equity basket holdings underlying the total return swap with U.S. Media Index as of September 30, 2016.

Security Description	Index Weight
U.S. Media Index
CBS Corp.		3.81	%
Charter Communications, Inc.		9.18
Comcast Corp.		25.69
Discovery Communications, Inc.		1.78
DISH Network Corp.		1.92
Interpublic Group of Cos, Inc. (The)		1.44
Liberty Global PLC		4.59
Liberty Global PLC LiLAC		0.48
Liberty Media Corporation-Liberty Braves		0.08
Liberty Media Corporation-Liberty Media		0.32
Liberty Media Corporation-Liberty SiriusXM		1.56
News Corp.		0.84
Omnicom Group, Inc.		3.25
Scripps Networks Interactive, Inc.		0.75
Sirius XM Holdings, Inc.		1.59
TEGNA, Inc.		0.74
Time Warner, Inc.		10.21
Twenty-First Century Fox, Inc.		6.36
Viacom, Inc.		2.08
Walt Disney Co. (The)		23.33
		100.00	%

The following table represents the equity basket holdings underlying the total return swap with U.S. Consumer Staples Index as of September 30, 2016.

Security Description	Index Weight
U.S. Consumer Staples Index
Altria Group, Inc.		6.57	%
Archer-Daniels-Midland Co.		1.33
Brown-Forman Corp.		0.51
Campbell Soup Co.		0.52
Church & Dwight Co., Inc.		0.67
Clorox Co. (The)		0.86
Coca-Cola Co. (The)		8.78
Coca-Cola European Partners PLC		0.44
Colgate-Palmolive Co.		3.52
ConAgra Foods, Inc.		1.08
Constellation Brands, Inc.		1.53
Costco Wholesale Corp.		3.54

Security Description	Index Weight
CVS Health Corp.		5.22	%
Dr. Pepper Snapple Group, Inc.		0.91
Estee Lauder Cos, Inc. (The)		1.04
General Mills, Inc.		2.02
Hershey Co. (The)		0.73
Hormel Foods Corp.		0.54
JM Smucker Co. (The)		0.86
Kellogg Co.		1.05
Kimberly-Clark Corp.		2.43
Kraft Heinz Co. (The)		2.82
Kroger Co. (The)		1.53
McCormick & Co., Inc.		0.62
Mead Johnson Nutrition Co.		0.78
Molson Coors Brewing Co.		1.06
Mondelez International, Inc.		3.70
Monster Beverage Corp.		1.17
PepsiCo, Inc.		8.40
Philip Morris International, Inc.		7.99
Procter & Gamble Co. (The)		12.95
Reynolds American, Inc.		2.07
Sysco Corp.		1.36
Tyson Foods, Inc.		1.17
Walgreens Boots Alliance, Inc.		3.72
Wal-Mart Stores, Inc.		6.00
Whole Foods Market, Inc.		0.51
		100.00	%

The following table represents the equity basket holdings underlying the total return swap with Global Aerospace Index as of September 30, 2016.

Security Description	Index Weight
Global Aerospace Index
Airbus Group SE		19.71	%
B/E Aerospace, Inc.		2.23
Boeing Co. (The)		36.77
KLX, Inc.		0.80
Rolls-Royce Holdings PLC		7.05
Safran SA		12.52
Spirit AeroSystems Holdings, Inc.		4.64
Thales SA		3.97
TransDigm Group, Inc.		6.52
Zodiac Aerospace		5.79
		100.00	%

The following table represents the equity basket holdings underlying the total return swap with Short European Staples Index as of September 30, 2016.

Security Description	Index Weight
Short European Staples Index
Anheuser-Busch InBev N.V.		8.81	%
Aryzta AG		0.32
Associated British Foods PLC		1.01
Barry Callebaut AG		0.24
Beiersdorf AG		0.80
British American Tobacco PLC		9.98
Carlsberg A/S		0.85
Carrefour SA		1.20
Casino Guichard Perrachon SA		0.23
Chocoladefabriken Lindt & Spruengli AG		1.06
Coca-Cola European Partners PLC		0.72

The accompanying notes are an integral part of the financial statements.
21

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Multi-Asset Income Portfolio

Security Description	Index Weight
Short European Staples Index (cont'd)
Coca-Cola HBC AG		0.35	%
Colruyt SA		0.31
Danone SA		3.66
Diageo PLC		6.04
Distribuidora Internacional de Alimentac		0.32
Heineken Holding N.V.		0.68
Heineken N.V.		1.70
Henkel AG & Co. KGaA		3.04
ICA Gruppen AB		0.22
Imperial Brands PLC		4.14
J Sainsbury PLC		0.36
Jeronimo Martins SGPS SA		0.37
Kerry Group PLC		1.10
Koninklijke Ahold Delhaize N.V.		2.44
L'Oreal SA		4.00
Marine Harvest ASA		0.57
METRO AG		0.44
Nestle SA		21.02
Orkla ASA		0.71
Pernod Ricard SA		2.10
Reckitt Benckiser Group PLC		5.02
Remy Cointreau SA		0.16
Svenska Cellulosa AB SCA		1.51
Swedish Match AB		0.61
Tate & Lyle PLC		0.38
Tesco PLC		1.62
Unilever N.V.		6.29
Unilever PLC		5.09
WM Morrison Supermarkets PLC		0.53
		100.00	%

The following table represents the equity basket holdings underlying the total return swap with JPM Short Luxury Index as of September 30, 2016.

Security Description	Index Weight
JPM Short Luxury Index
Brunello Cucinelli SpA		0.13	%
Burberry Group PLC		5.87
Christian Dior SE		2.43
Cie Financiere Richemont SA		20.39
Coach, Inc.		5.83
Hermes International		3.51
Hugo Boss AG		2.88
Kering		9.07
LVMH Moet Hennessy Louis Vuitton SE		28.91
Moncler SpA		2.29
Salvatore Ferragamo SpA		2.97
Swatch Group AG (The)		15.28
Tod's SpA		0.44
		100.00	%

@ Value is less than $500.

@@ Amount is less than 500.

* Cleared option, the broker is Goldman Sachs International.

** Cleared swap agreement, the broker is Morgan Stanley & Co., LLC.

† Credit rating as issued by Standard & Poor's.

BBSW Australia's Bank Bill Swap

LIBOR London Interbank Offered Rate.

STIBOR Stockholm Interbank Offered Rate.

NR Not rated.

ARS — Argentine Peso

AUD — Australian Dollar

BRL — Brazilian Real

CAD — Canadian Dollar

CHF — Swiss Franc

CNH — Chinese Yuan Renminbi

DKK — Danish Krone

EUR — Euro

GBP — British Pound

HKD — Hong Kong Dollar

HUF — Hungarian Forint

IDR — Indonesian Rupiah

ILS — Israeli Shekel

JPY — Japanese Yen

KRW — South Korean Won

MXN — Mexican Peso

MYR — Malaysian Ringgit

NOK — Norwegian Krone

NZD — New Zealand Dollar

PLN — Polish Zloty

RUB — Russian Ruble

SEK — Swedish Krona

SGD — Singapore Dollar

THB — Thai Baht

TRY — Turkish Lira

USD — United States Dollar

ZAR — South African Rand

Portfolio Composition

Classification	Percentage of Total Investments
Fixed Income Securities		48.9	%
Other***		25.2
Short-Term Investments		10.8
Investment Companies		9.4
Real Estate Investment Trusts (REITs)		5.7
Total Investments		100.0	%****

*** Industries and/or investment types representing less than 5% of total investments.

**** Does not include open call options written with a value of approximately $116,000. Does not include open long/short futures contracts with an underlying face amount of approximately $6,898,000 with net unrealized appreciation of approximately $14,000. Does not include open foreign currency forward exchange contracts with net unrealized appreciation of approximately $10,000 and does not include open swap agreements with net unrealized appreciation of approximately $36,000.

The accompanying notes are an integral part of the financial statements.
22

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Global Multi-Asset Income Portfolio

Statement of Assets and Liabilities	September 30, 2016 (000)
Assets:
Investments in Securities of Unaffiliated Issuers, at Value (Cost $12,492)	$	12,795
Investment in Securities of Affiliated Issuer, at Value (Cost $2,523)		2,540
Total Investments in Securities, at Value (Cost $15,015)		15,335
Foreign Currency, at Value (Cost $13)		13
Restricted Cash		39
Receivable for Investments Sold		321
Receivable for Variation Margin on Futures Contracts		217
Due from Adviser		69
Unrealized Appreciation on Swap Agreements		59
Interest Receivable		54
Unrealized Appreciation on Foreign Currency Forward Exchange Contracts		47
Dividends Receivable		6
Tax Reclaim Receivable		3
Receivable for Variation Margin on Swap Agreements		3
Receivable from Affiliate		—	@
Other Assets		26
Total Assets		16,192
Liabilities:
Payable for Investments Purchased		956
Due to Broker		39
Options Written, at Value (Premiums received $112)		116
Payable for Custodian Fees		52
Unrealized Depreciation on Foreign Currency Forward Exchange Contracts		37
Unrealized Depreciation on Swap Agreements		22
Payable for Professional Fees		18
Premium Received on Open Swap Agreements		10
Payable for Transfer Agency Fees — Class I		1
Payable for Transfer Agency Fees — Class A		—	@
Payable for Transfer Agency Fees — Class C		1
Payable for Transfer Agency Fees — Class IS		—	@
Payable for Organizational Costs (Note K)		2
Payable for Administration Fees		1
Payable for Shareholder Services Fees — Class A		—	@
Payable for Distribution and Shareholder Services Fees — Class C		—	@
Payable for Sub Transfer Agency Fees — Class A		—	@
Other Liabilities		24
Total Liabilities		1,279
Net Assets	$	14,913
Net Assets Consist Of:
Paid-in-Capital	$	15,062
Distributions in Excess of Net Investment Income		(29	)
Accumulated Net Realized Loss		(496	)
Unrealized Appreciation (Depreciation) on:
Investments		303
Investments in Affiliates		17
Futures Contracts		14
Options Written		(4	)
Swap Agreements		36
Foreign Currency Forward Exchange Contracts		10
Foreign Currency Translations		(—	@)
Net Assets	$	14,913

The accompanying notes are an integral part of the financial statements.
23

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Global Multi-Asset Income Portfolio

Statement of Assets and Liabilities (cont'd)	September 30, 2016 (000)
CLASS I:
Net Assets	$	10
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		1,000
Net Asset Value, Offering and Redemption Price Per Share	$	9.90
CLASS A:
Net Assets	$	73
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		7,406
Net Asset Value, Redemption Price Per Share	$	9.88
Maximum Sales Load		5.25	%
Maximum Sales Charge	$	0.55
Maximum Offering Price Per Share	$	10.43
CLASS C:
Net Assets	$	10
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		1,000
Net Asset Value, Offering and Redemption Price Per Share	$	9.84
CLASS IS:
Net Assets	$	14,820
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		1,497,000
Net Asset Value, Offering and Redemption Price Per Share	$	9.90

@ Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
24

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Global Multi-Asset Income Portfolio

Statement of Operations	Year Ended September 30, 2016 (000)
Investment Income:
Interest from Securities of Unaffiliated Issuers	$	158
Dividends from Securities of Unaffiliated Issuers (Net of $11 of Foreign Taxes Withheld)		123
Dividends from Securities of Affiliated Issuer (Note G)		84
Total Investment Income		365
Expenses:
Custodian Fees (Note F)		186
Professional Fees		131
Advisory Fees (Note B)		93
Offering Costs		75
Registration Fees		29
Shareholder Reporting Fees		14
Administration Fees (Note C)		11
Pricing Fees		8
Transfer Agency Fees — Class I (Note E)		—	@
Transfer Agency Fees — Class A (Note E)		—	@
Transfer Agency Fees — Class C (Note E)		1
Transfer Agency Fees — Class IS (Note E)		2
Trustees' Fees and Expenses		2
Organizational Costs (Note K)		2
Shareholder Services Fees — Class A (Note D)		—	@
Distribution and Shareholder Services Fees — Class C (Note D)		—	@
Sub Transfer Agency Fees — Class A		—	@
Other Expenses		19
Total Expenses		573
Expenses Reimbursed by Adviser (Note B)		(332	)
Waiver of Advisory Fees (Note B)		(93	)
Rebate from Morgan Stanley Affiliate (Note G)		(5	)
Reimbursement of Class Specific Expenses — Class I (Note B)		(—	@)
Reimbursement of Class Specific Expenses — Class A (Note B)		(—	@)
Reimbursement of Class Specific Expenses — Class C (Note B)		(1	)
Reimbursement of Class Specific Expenses — Class IS (Note B)		(2	)
Reimbursement of Custodian Fees (Note F)		(15	)
Net Expenses		125
Net Investment Income		240
Realized Gain (Loss):
Investments Sold		(300	)
Investments in Affiliates		(4	)
Foreign Currency Forward Exchange Contracts		3
Foreign Currency Transactions		(1	)
Futures Contracts		215
Options Written		38
Swap Agreements		(192	)
Net Realized Loss		(241	)
Change in Unrealized Appreciation (Depreciation):
Investments		1,031
Investments in Affiliates		89
Foreign Currency Forward Exchange Contracts		5
Foreign Currency Translations		1
Futures Contracts		59
Swap Agreements		13
Options Written		(33	)
Net Change in Unrealized Appreciation (Depreciation)		1,165
Net Realized Loss and Change in Unrealized Appreciation (Depreciation)		924
Net Increase in Net Assets Resulting from Operations	$	1,164

@ Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
25

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Global Multi-Asset Income Portfolio

Statements of Changes in Net Assets	Year Ended September 30, 2016 (000)			Period from April 30, 2015^ to September 30, 2015 (000)
Increase (Decrease) in Net Assets:
Operations:
Net Investment Income	$	240		$	108
Net Realized Loss		(241	)		(279	)
Net Change in Unrealized Appreciation (Depreciation)		1,165			(789	)
Net Increase (Decrease) in Net Assets Resulting from Operations		1,164			(960	)
Distributions from and/or in Excess of:
Class I:
Net Investment Income		(—	@)		(—	@)
Class A:
Net Investment Income		(1	)		(—	@)
Class C:
Net Investment Income		(—	@)		(—	@)*
Class IS:
Net Investment Income		(307	)		(45	)
Total Distributions		(308	)		(45	)
Capital Share Transactions:⁽¹⁾
Class I:
Subscribed		—			10
Class A:
Subscribed		25			46
Distributions Reinvested		1			—	@
Class C:
Subscribed		—			10	*
Class IS:
Subscribed		—			14,970
Net Increase in Net Assets Resulting from Capital Share Transactions		26			15,036
Total Increase in Net Assets		882			14,031
Net Assets:
Beginning of Period		14,031			—
End of Period (Including Distributions in Excess of Net Investment Income and Accumulated Undistributed Net Investment Income of $(29) and $56, respectively)	$	14,913		$	14,031
(1) Capital Share Transactions:
Class I:
Shares Subscribed		—			1
Class A:
Shares Subscribed		3			5
Shares Issued on Distributions Reinvested		—	@@		—	@@
Net Increase in Class A Shares Outstanding		3			5
Class C:
Shares Subscribed		—			1	*
Class IS:
Shares Subscribed		—			1,497

^ Commencement of Operations.

* For the period May 8, 2015 through September 30, 2015.

@ Amount is less than $500.

@@ Amount is less than 500 shares.

The accompanying notes are an integral part of the financial statements.
26

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Global Multi-Asset Income Portfolio

	Class I
Selected Per Share Data and Ratios	Year Ended September 30, 2016††			Period from April 30, 2015^ to September 30, 2015
Net Asset Value, Beginning of Period	$	9.33		$	10.00
Income (Loss) from Investment Operations:
Net Investment Income†		0.15			0.07
Net Realized and Unrealized Gain (Loss)		0.62			(0.71	)
Total from Investment Operations		0.77			(0.64	)
Distributions from and/or in Excess of:
Net Investment Income		(0.20	)		(0.03	)
Net Asset Value, End of Period	$	9.90		$	9.33
Total Return++		8.39	%		(6.42	)%#
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	10		$	9
Ratio of Expenses to Average Net Assets ⁽¹⁾		0.92	%+		0.93	%+*
Ratio of Net Investment Income to Average Net Assets ⁽¹⁾		1.62	%+		1.72	%+*
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.03	%		0.01	%*
Portfolio Turnover Rate		236	%		139	%#
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		6.73	%		20.20	%*
Net Investment Loss to Average Net Assets		(4.19	)%		(17.55	)%*

^ Commencement of Operations.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value as of the last business day of the period.

# Not Annualized.

* Annualized.

The accompanying notes are an integral part of the financial statements.
27

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Global Multi-Asset Income Portfolio

	Class A
Selected Per Share Data and Ratios	Year Ended September 30, 2016††			Period from April 30, 2015^ to September 30, 2015
Net Asset Value, Beginning of Period	$	9.32		$	10.00
Income (Loss) from Investment Operations:
Net Investment Income†		0.12			0.04
Net Realized and Unrealized Gain (Loss)		0.61			(0.69	)
Total from Investment Operations		0.73			(0.65	)
Distributions from and/or in Excess of:
Net Investment Income		(0.17	)		(0.03	)
Net Asset Value, End of Period	$	9.88		$	9.32
Total Return++		8.10	%		(6.64	)%#
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	73		$	44
Ratio of Expenses to Average Net Assets ⁽¹⁾		1.26	%+		1.27	%+*
Ratio of Net Investment Income to Average Net Assets ⁽¹⁾		1.27	%+		1.02	%+*
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.04	%		0.01	%*
Portfolio Turnover Rate		236	%		139	%#
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		4.74	%		12.75	%*
Net Investment Loss to Average Net Assets		(2.21	)%		(10.46	)%*

†† Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class A shares. The Ratio of Expenses to Average Net Assets and the Ratio of Net Investment Income to Average Net Assets would be unchanged as the change to current period custodian fees was offset against current period expense waivers/reimbursements with no impact to net expenses or net investment income.

^ Commencement of Operations.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

# Not Annualized.

* Annualized.

The accompanying notes are an integral part of the financial statements.
28

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Global Multi-Asset Income Portfolio

	Class C
Selected Per Share Data and Ratios	Year Ended September 30, 2016††			Period from May 8, 2015^ to September 30, 2015
Net Asset Value, Beginning of Period	$	9.30		$	10.00
Income (Loss) from Investment Operations:
Net Investment Income†		0.04			0.02
Net Realized and Unrealized Gain (Loss)		0.61			(0.71	)
Total from Investment Operations		0.65			(0.69	)
Distributions from and/or in Excess of:
Net Investment Income		(0.11	)		(0.01	)
Net Asset Value, End of Period	$	9.84		$	9.30
Total Return++		7.11	%		(6.86	)%#
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	10		$	9
Ratio of Expenses to Average Net Assets ⁽¹⁾		2.02	%+		2.03	%+*
Ratio of Net Investment Income to Average Net Assets ⁽¹⁾		0.41	%+		0.56	%+*
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.03	%		0.01	%*
Portfolio Turnover Rate		236	%		139	%#
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		14.16	%		21.28	%*
Net Investment Loss to Average Net Assets		(11.73	)%		(18.68	)%*

†† Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class C shares. The Ratio of Expenses to Average Net Assets and the Ratio of Net Investment Income to Average Net Assets would be unchanged as the change to current period custodian fees was offset against current period expense waivers/reimbursements with no impact to net expenses or net investment income.

^ Commencement of Offering.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

# Not Annualized.

* Annualized.

The accompanying notes are an integral part of the financial statements.
29

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Global Multi-Asset Income Portfolio

	Class IS
Selected Per Share Data and Ratios	Year Ended September 30, 2016††			Period from April 30, 2015^ to September 30, 2015
Net Asset Value, Beginning of Period	$	9.33		$	10.00
Income (Loss) from Investment Operations:
Net Investment Income†		0.16			0.07
Net Realized and Unrealized Gain (Loss)		0.61			(0.71	)
Total from Investment Operations		0.77			(0.64	)
Distributions from and/or in Excess of:
Net Investment Income		(0.20	)		(0.03	)
Net Asset Value, End of Period	$	9.90		$	9.33
Total Return++		8.44	%		(6.41	)%#
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	14,820		$	13,969
Ratio of Expenses to Average Net Assets ⁽¹⁾		0.86	%+		0.87	%+*
Ratio of Net Investment Income to Average Net Assets ⁽¹⁾		1.68	%+		1.76	%+*
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.04	%		0.01	%*
Portfolio Turnover Rate		236	%		139	%#
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		3.99	%		5.97	%*
Net Investment Loss to Average Net Assets		(1.45	)%		(3.34	)%*

†† Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class IS shares. The Ratio of Expenses to Average Net Assets and the Ratio of Net Investment Income to Average Net Assets would be unchanged as the change to current period custodian fees was offset against current period expense waivers/reimbursements with no impact to net expenses or net investment income.

^ Commencement of Operations.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value as of the last business day of the period.

# Not Annualized.

* Annualized.

The accompanying notes are an integral part of the financial statements.
30

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements

The accompanying financial statements relate to the Global Multi-Asset Income Portfolio. The Portfolio seeks to maximize current income and to seek capital appreciation over time. The Portfolio offers four classes of shares — Class I, Class A, Class C and Class IS.

readily available are valued at the latest reported sales price (or at the market official closing price if such market reports an official closing price), and if there was no trading in the security on a given day and if there is no official closing price from relevant markets for that day, the security is valued at the mean between the last reported bid and asked prices if such bid and asked prices are available on the relevant markets. Listed equity securities not traded on the valuation date with no reported bid and asked prices available on the exchange are valued at the mean between the current bid and asked prices obtained from one or more reputable brokers or dealers. An unlisted equity security that does not trade on the valuation date and for which bid and asked prices from the relevant markets are unavailable is valued at the mean between the current bid and asked prices obtained from one or more reputable brokers or dealers. In cases where a security is traded on more than one exchange, the security is valued on the exchange designated as the primary market; (4) futures are valued at the latest price published by the commodities exchange on which they trade; (5) swaps are marked-to-market daily based upon quotations from market makers; (6) listed options are valued at the last reported sales price on the exchange on which they are listed (or at the exchange official closing price if such exchange reports an official closing price). If an official closing price or last reported sales price is unavailable, the listed option should be fair valued at the mean between their latest bid and asked price. Unlisted options and swaps are valued by an outside pricing service approved by the Trustees or quotes from a broker or dealer; (7) when market quotations are not readily available, including circumstances under which Morgan Stanley Investment Management Inc. (the "Adviser") determines that the closing price, last sale price or the mean between the last reported bid and asked prices are not reflective of a security's market value, portfolio securities are valued at their fair value as determined in good faith under procedures established by and under the general supervision of the Trustees. Occasionally, developments affecting the closing prices of securities and other assets may occur between the times at which valuations of such securities are determined (that is, close of the foreign market on which the securities trade) and the close of business of the New York Stock Exchange ("NYSE"). If developments occur during such periods that are expected to materially affect the value of such securities, such valuations may be adjusted to reflect the estimated fair value of such securities as of the close of the NYSE, as

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

determined in good faith by the Trustees or by the Adviser using a pricing service and/or procedures approved by the Trustees; (8) quotations of foreign portfolio securities, other assets and liabilities and forward contracts stated in foreign currency are translated into U.S. dollar equivalents at the prevailing market rates prior to the close of the NYSE; and (9) investments in mutual funds, including the Morgan Stanley Institutional Liquidity Funds, are valued at the net asset value ("NAV") as of the close of each business day.

The Fund has procedures to determine the fair value of securities and other financial instruments for which market prices are not readily available. Under these procedures, the Valuation Committee convenes on a regular and ad hoc basis to review such securities and considers a number of factors, including valuation methodologies and significant unobservable valuation inputs, when arriving at fair value. The Valuation Committee may employ a market-based approach which may use related or comparable assets or liabilities, recent transactions, market multiples, book values, and other relevant information for the investment to determine the fair value of the investment. An income-based valuation approach may also be used in which the anticipated future cash flows of the investment are discounted to calculate fair value. Discounts may also be applied due to the nature or duration of any restrictions on the disposition of the investments. Due to the inherent uncertainty of valuations of such investments, the fair values may differ significantly from the values that would have been used had an

active market existed. The Valuation Committee employs various methods for calibrating these valuation approaches including a regular review of valuation methodologies, key inputs and assumptions, transactional back-testing or disposition analysis, and reviews of any related market activity.

• Level 1 – unadjusted quoted prices in active markets for identical investments

• Level 2 – other significant observable inputs (including quoted prices for similar investments, interest rates, prepayment speeds, credit risk, etc.)

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

The following is a summary of the inputs used to value the Portfolio's investments as of September 30, 2016.

Investment Type	Level 1 Unadjusted quoted prices (000)		Level 2 Other significant observable inputs (000)		Level 3 Significant unobservable inputs (000)		Total (000)
Assets:
Fixed Income Securities
Agency Fixed Rate Mortgages	$	—	$	786	$	—	$	786
Commercial Mortgage-Backed Securities		—		176		—		176
Corporate Bonds		—		1,577		—		1,577
Sovereign		—		4,169		—		4,169
U.S. Treasury Securities		—		787		—		787
Total Fixed Income Securities		—		7,495		—		7,495
Common Stocks
Aerospace & Defense		10		26		—		36
Air Freight & Logistics		—		8		—		8
Airlines		106		134		—		240
Auto Components		4		36		—		40
Automobiles		11		140		—		151
Banks		255		195		—		450
Beverages		11		60		—		71
Biotechnology		10		5		—		15
Building Products		17		58		—		75
Capital Markets		59		85		—		144
Chemicals		20		47		—		67
Commercial Services & Supplies		—		22		��		22
Communications Equipment		3		7		—		10
Construction & Engineering		20		95		—		115
Construction Materials		56		35		—		91
Consumer Finance		33		—		—		33
Diversified Consumer Services		—		10		—		10
Diversified Financial Services		29		18		—		47
Diversified Telecommunication Services		38		40		—		78
Electric Utilities		14		32		—		46
Electrical Equipment		—		21		—		21
Energy Equipment & Services		13		—		—		13
Equity Real Estate Investment Trusts (REITs)		714		103		—		817
Food & Staples Retailing		9		16		—		25
Food Products		—		23		—		23

Investment Type	Level 1 Unadjusted quoted prices (000)		Level 2 Other significant observable inputs (000)		Level 3 Significant unobservable inputs (000)			Total (000)
Common Stocks (cont'd)
Gas Utilities	$	—	$	11	$	—		$	11
Health Care Equipment & Supplies		—		17		—			17
Health Care Providers & Services		14		20		—			34
Hotels, Restaurants & Leisure		32		20		—			52
Household Durables		57		3		—			60
Household Products		7		22		—			29
Independent Power and Renewable Electricity Producers		1		—		—			1
Industrial Conglomerates		3		42		—			45
Information Technology Services		78		8		—			86
Insurance		35		51		—			86
Internet Software & Services		13		—		—			13
Machinery		—		6		—			6
Media		61		56		—			117
Metals & Mining		11		48		—			59
Multi-Utilities		8		37		—			45
Multi-line Retail		—		3		—			3
Oil, Gas & Consumable Fuels		427		93		—			520
Paper & Forest Products		1		5		—			6
Personal Products		—		40		—			40
Pharmaceuticals		189		74		—			263
Professional Services		30		44		—			74
Real Estate Management & Development		24		58		—			82
Road & Rail		20		13		—			33
Semiconductors & Semiconductor Equipment		10		17		—	@		27
Software		11		20		—			31
Specialty Retail		11		25		—			36
Tech Hardware, Storage & Peripherals		14		—		—			14
Textiles, Apparel & Luxury Goods		17		21		—			38
Thrifts & Mortgage Finance		3		—		—			3
Tobacco		—		25		—			25
Trading Companies & Distributors		—		15		—			15
Transportation Infrastructure		51		157		—			208
Water Utilities		1		2		—			3
Wireless Telecommunication Services		4		10		—			14
Total Common Stocks		2,565		2,179		—	@		4,744
Investment Companies		1,437		5		—			1,442
Put Options Purchased		—		5		—			5
Short-Term Investments
Investment Company		1,103		—		—			1,103
Sovereign		—		64		—			64
U.S. Treasury Securities		—		482		—			482
Total Short-Term Investments		1,103		546		—			1,649

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

Investment Type	Level 1 Unadjusted quoted prices (000)			Level 2 Other significant observable inputs (000)			Level 3 Significant unobservable inputs (000)			Total (000)
Foreign Currency Forward Exchange Contracts	$	—		$	47		$	—		$	47
Futures Contracts		40			—			—			40
Credit Default Swap Agreements		—			9			—			9
Interest Rate Swap Agreements		—			42			—			42
Total Return Swap Agreements		—			31			—			31
Total Assets		5,145			10,359			—			15,504
Liabilities:
Call Options Written		(40	)		(76	)		—			(116	)
Foreign Currency Forward Exchange Contracts		—			(37	)		—			(37	)
Futures Contracts		(26	)		—			—			(26	)
Credit Default Swap Agreement		—			(—	@)		—			(—	@)
Interest Rate Swap Agreements		—			(24	)		—			(24	)
Total Return Swap Agreements		—			(22	)		—			(22	)
Total Liabilities		(66	)		(159	)		—			(225	)
Total	$	5,079		$	10,200		$	—	@	$	15,279

@ Value is less than $500.

Transfers between investment levels may occur as the markets fluctuate and/or the availability of data used in an investment's valuation changes. The Portfolio recognizes transfers between the levels as of the end of the period. As of September 30, 2016, securities with a total value of approximately $385,000 transferred from Level 2 to Level 1. Securities that were valued using other significant observable inputs at September 30, 2015 were valued using unadjusted quoted prices at September 30, 2016. At September 30, 2016, the fair value of certain securities were adjusted due to developments which occurred between the time of the close of the foreign markets on which they trade and the close of business on the NYSE which resulted in their Level 2 classification.

Following is a reconciliation of investments in which significant unobservable inputs (Level 3) were used in determining fair value.

	Common Stock (000)
Beginning Balance	$	—	@
Purchases		—
Sales		—
Amortization of discount		—
Transfers in		—
Transfers out		—
Corporate actions		—
Change in unrealized appreciation (depreciation)		(—	@)
Realized gains (losses)		—
Ending Balance	$	—	@
Net change in unrealized appreciation (depreciation) from investments still held as of September 30, 2016	$	(—	@)

@ Value is less than $500.

– investments, other assets and liabilities at the prevailing rate of exchange on the valuation date;

– investment transactions and investment income at the prevailing rates of exchange on the dates of such transactions.

Although the net assets of the Portfolio are presented at the foreign exchange rates and market values at the close of the period, the Portfolio does not isolate that portion of the results of operations arising as a result of changes in the foreign exchange rates from the fluctuations arising from changes in the market prices of securities held at period end. Similarly, the Portfolio does not isolate the effect of changes in foreign exchange rates from the fluctuations arising from changes in the market prices of securities sold during the period. Accordingly, realized and unrealized foreign currency gains (losses) on investments in securities are included in the reported net realized and unrealized gains (losses) on investment transactions and balances. However, pursuant to U.S. federal income tax regulations, gains and losses from certain foreign currency transactions and the foreign currency portion of gains and losses realized on sales and maturities of foreign denominated debt

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

securities are treated as ordinary income for U.S. federal income tax purposes.

underlying asset, interest rate, index or financial instrument. Prevailing interest rates and volatility levels, among other things, also affect the value of derivative instruments. A derivative instrument often has risks similar to its underlying asset and may have additional risks, including imperfect correlation between the value of the derivative and the underlying asset, risks of default by the counterparty to certain transactions, magnification of losses incurred due to changes in the market value of the securities, instruments, indices or interest rates to which the derivative instrument relates, risks that the transactions may not be liquid and risks arising from margin requirements. The use of derivatives involves risks that are different from, and possibly greater than, the risks associated with other portfolio investments. Derivatives may involve the use of highly specialized instruments that require investment techniques and risk analyses different from those associated with other portfolio investments. All of the Portfolio's holdings, including derivative instruments, are marked-to-market each day with the change in value reflected in unrealized appreciation (depreciation). Upon disposition, a realized gain or loss is recognized.

Following is a description of the derivative instruments and techniques that the Portfolio used during the period and their associated risks:

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

instrument on the settlement date or by payment of a cash settlement amount on the settlement date. During the period the futures contract is open, payments are received from or made to the broker based upon changes in the value of the contract (the variation margin). A decision as to whether, when and how to use futures contracts involves the exercise of skill and judgment and even a well-conceived futures transaction may be unsuccessful because of market behavior or unexpected events. In addition to the derivatives risks discussed above, the prices of futures contracts can be highly volatile, using futures contracts can lower total return, and the potential loss from futures contracts can exceed the Portfolio's initial investment in such contracts. No assurance can be given that a liquid market will exist for any particular futures contract at any particular time. There is also the risk of loss by the Portfolio of margin deposits in the event of bankruptcy of a broker with which the Portfolio has open positions in the futures contract.

Swaps: The Portfolio may enter into OTC swap contracts or cleared swap transactions. A swap contract is an agreement between two parties pursuant to which the parties exchange payments at specified dates on the basis of a specified notional amount, with the payments calculated by reference to specified securities, indices, reference rates, currencies or other instruments. Typically swap agreements provide that when the period payment dates for both parties are the same, the payments are made on a net basis (i.e., the two payment streams are netted out, with only the net amount paid by one party to the other). The Portfolio's obligations or rights under a swap contract entered into on a net basis will generally be equal only to the net amount to be paid or received under the agreement, based on the relative values of the positions held by each party. Cleared swap transactions may help reduce counterparty credit risk. In a cleared swap, the Portfolio's ultimate counterparty is a clearinghouse rather than a swap dealer, bank or other financial institution. OTC swap agreements are not entered into or traded on exchanges and often there is no central clearing or guaranty function for OTC swaps. These OTC swaps are often subject to credit risk or the risk of default or non-performance by the counterparty. Both OTC and cleared swaps could result in losses if interest rates, foreign currency exchange rates or other factors are not correctly anticipated by the Portfolio or if the reference index, security or investments do not perform

as expected. During the period swap agreements are open, payments are received from or made to the clearinghouse or counterparty based upon changes in the value of the contract (variation margin). The Dodd-Frank Wall Street Reform and Consumer Protection Act and related regulatory developments require the clearing and exchange-trading of certain standardized swap transactions. Mandatory exchange-trading and clearing is occurring on a phased-in basis.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

deliver the referenced obligation, other deliverable obligations or underlying securities comprising the referenced index or (ii) receive a net settlement amount in the form of cash or securities equal to the notional amount of the swap agreement less the recovery value of the referenced obligation or underlying securities comprising the referenced index. Recovery values are estimated by market makers considering either industry standard recovery rates or entity specific factors and considerations until a credit event occurs. If a credit event has occurred, the recovery value is determined by a facilitated auction whereby a minimum number of allowable broker bids, together with a specified valuation method, are used to calculate the settlement value. The Portfolio's maximum risk of loss from counterparty risk, either as the protection seller or as the protection buyer, is the fair value of the swap agreement.

Upfront payments paid or received by the Portfolio will be reflected as an asset or liability, respectively, in the Statement of Assets and Liabilities.

amount of currency at a specified future time at a specified rate. The rate can be higher or lower than the spot rate between the currencies that are the subject of the contract. Currency contracts may be used to protect against uncertainty in the level of future foreign currency exchange rates or to gain or modify exposure to a particular currency. In addition, the Portfolio may use cross currency hedging or proxy hedging with respect to currencies in which the Portfolio has or expects to have portfolio or currency exposure. Cross currency hedges involve the sale of one currency against the positive exposure to a different currency and may be used for hedging purposes or to establish an active exposure to the exchange rate between any two currencies. To the extent hedged by the use of currency contracts, the precise matching of the currency contract amounts and the value of the securities involved will not generally be possible because the future value of such securities in foreign currencies will change as a consequence of market movements in the value of those securities between the date on which the contract is entered into and the date it matures. Furthermore, such transactions may reduce or preclude the opportunity for gain if the value of the currency should move in the direction opposite to the position taken. There is additional risk to the extent that currency contracts create exposure to currencies in which the Portfolio's securities are not denominated. Unanticipated changes in currency prices may result in poorer overall performance for the Portfolio than if it had not entered into such contracts. The use of currency contracts involves the risk of loss from the insolvency or bankruptcy of the counterparty to the contract or the failure of the counterparty to make payments or otherwise comply with the terms of the contract. A currency contract is marked-to-market daily and the change in market value is recorded by the Portfolio as unrealized gain or loss. The Portfolio records realized gains (losses) when the currency contract is closed equal to the difference between the value of the currency contract at the time it was opened and the value at the time it was closed.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

typically in exchange for a premium paid by the Portfolio. The Portfolio may purchase and/or sell put and call options. Purchasing call options tends to increase the Portfolio's exposure to the underlying (or similar) instrument. Purchasing put options tends to decrease the Portfolio's exposure to the underlying (or similar) instrument. When entering into purchased option contracts, the Portfolio bears the risk of interest or exchange rates or securities prices moving unexpectedly, in which case, the Portfolio may not achieve the anticipated benefits of the purchased option contracts; however the risk of loss is limited to the premium paid. Purchased options are reported as part of "Total Investments in Securities" in the Statement of Assets and Liabilities. Premium paid for purchasing options which expired are treated as realized losses. If the Portfolio sells an option, it sells to another party the right to buy from or sell to the Portfolio a specific amount of the underlying instrument or foreign currency, or futures contract on the underlying instrument or foreign currency, at an agreed-upon price typically in exchange for a premium received by the Portfolio. The Portfolio may write call and put options on stock indexes, futures, securities or currencies it owns or in which it may invest. Writing put options tend to increase the Portfolio's exposure to the underlying instrument. Writing call options tend to decrease the Portfolio's exposure to the underlying instruments. When the Portfolio writes a call or put option, an amount equal to the premium received is recorded as a liability. Any liability recorded is subsequently adjusted to reflect the current value of the options written. Premiums received from writing options which expire are treated as realized gains. Premiums received from writing options which are exercised or are closed are added to or offset against the proceeds or amount paid on the transaction to determine the net realized gain or loss. The Portfolio as a writer of an option has no control over whether the underlying future, security or currency may be sold (call) or purchased (put) and as a result bears the market risk of an unfavorable change in the price of the future, security or currency underlying the written option. When options are purchased OTC, the Portfolio bears the risk that the counterparty that wrote the option will be unable or unwilling to perform its obligations under the option contract. Options may also be illiquid and the Portfolio may have difficulty closing out its position. A decision

as to whether, when and how to use options involves the exercise of skill and judgment and even a well-conceived option transaction may be unsuccessful because of market behavior or unexpected events. The prices of options can be highly volatile and the use of options can lower total returns.

Transactions in written options for the year ended September 30, 2016 were as follows:

Written Options	Notional Amount (000)			Premiums Received (000)
Options outstanding at September 30, 2015		3		$	41
Options written		1,022			819
Options closed		(950	)		(17	)
Options exercised		(29	)		(442	)
Options expired		(37	)		(289	)
Options outstanding at September 30, 2016		9		$	112

The following tables set forth the fair value of the Portfolio's derivative contracts by primary risk exposure as of September 30, 2016.

Asset Derivatives
Statement of Assets and
Liabilities Location

Primary Risk
Exposure

Value
(000)

Options Purchased

Investments, at Value
(Options Purchased)

Equity Risk

(a)

Foreign Currency
Forward Exchange
Contracts

Unrealized Appreciation on
Foreign Currency Forward
Exchange Contracts

Currency Risk

Futures Contract

Variation Margin on
Futures Contract

Commodity Risk

(b)

Futures Contract

Variation Margin on
Futures Contract

Equity Risk

(b)

Futures Contracts

Variation Margin on
Futures Contracts

Interest Rate Risk

(b)

Swap Agreement

Unrealized Appreciation on
Swap Agreement

Credit Risk

Swap Agreement

Variation Margin on
Swap Agreement

Credit Risk

(b)

Swap Agreements

Unrealized Appreciation on
Swap Agreements

Equity Risk

Swap Agreements

Unrealized Appreciation on
Swap Agreements

Interest Rate Risk

Swap Agreements

Variation Margin on
Swap Agreements

Interest Rate Risk

(b)

Total

174

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

Liability Derivatives
Statement of Assets and
Liabilities Location

Primary Risk
Exposure

Value
(000)

Options Written

Options Written, at
Value

Equity Risk

(116

)

Foreign Currency
Forward Exchange
Contracts

Unrealized Depreciation on
Foreign Currency Forward
Exchange Contracts

Currency Risk

(37

)

Futures Contracts

Variation Margin on
Futures Contracts

Equity Risk

(18

)(b)

Futures Contracts

Variation Margin on
Futures Contracts

Interest Rate Risk

)(b)

Swap Agreement

Variation Margin on
Swap Agreement

Credit Risk

(—

@)(b)

Swap Agreements

Unrealized Depreciation on
Swap Agreements

Equity Risk

(22

)

Swap Agreements

Variation Margin on
Swap Agreements

Interest Rate Risk

(24

)(b)

Total

(225

)

(a) Amounts are included in Investments in Securities in the Statement of Assets and Liabilities.

(b) This amount represents the cumulative appreciation (depreciation) as reported in the Portfolio of Investments. The Statement of Assets and Liabilities only reflects the current day's net variation margin.

@ Amount is less than $500.

Realized Gain (Loss)
Primary Risk Exposure	Derivative Type	Value (000)
Currency Risk	Options Purchased	$	(9	)(c)
Currency Risk	Options Written		6
Equity Risk	Options Written		32
Currency Risk	Foreign Currency Forward Exchange Contracts		3
Commodity Risk	Futures Contracts		(16	)
Equity Risk	Futures Contracts		355
Interest Rate Risk	Futures Contracts		(124	)
Credit Risk	Swap Agreements		11
Equity Risk	Swap Agreements		(19	)
Interest Rate Risk	Swap Agreements		(184	)
Total		$	55
Change in Unrealized Appreciation (Depreciation)
Primary Risk Exposure	Derivative Type	Value (000)
Currency Risk	Options Written	$	(29	)
Equity Risk	Options Written		(4	)
Currency Risk	Foreign Currency Forward Exchange Contracts		5
Commodity Risk	Futures Contracts		13
Equity Risk	Futures Contracts		37
Interest Rate Risk	Futures Contracts		9
Credit Risk	Swap Agreements		8
Equity Risk	Swap Agreements		(15	)
Interest Rate Risk	Swap Agreements		20
Total		$	44

At September 30, 2016, the Portfolio's derivative assets and liabilities are as follows:

Gross Amounts of Assets and Liabilities Presented in the Statement of Assets and Liabilities
Derivatives(d)	Assets(e) (000)			Liabilities(e) (000)
Options Purchased	$	5	(a)	$	—
Options Written		—			(76	)
Foreign Currency Forward Exchange Contracts		47			(37	)
Swap Agreements		59			(22	)
Total	$	111		$	(135	)

(a) Amounts are included in Investments in Securities in the Statement of Assets and Liabilities.

(d) Excludes exchange traded derivatives.

(e) Absent an event of default or early termination, OTC derivative assets and liabilities are presented gross and not offset in the Statement of Assets and Liabilities.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

in the Master Agreement, the return of collateral with market value in excess of the Portfolio's net liability may be delayed or denied.

The following tables present derivative financial instruments that are subject to enforceable netting arrangements as of September 30, 2016.

Gross Amounts Not Offset in the Statement of Assets and Liabilities
Counterparty	Gross Asset Derivatives Presented in Statement of Assets and Liabilities (000)			Financial Instrument (000)			Collateral Received (000)			Net Amount (not less than $0) (000)
Australia and New Zealand Banking Group	$	1		$	(1	)	$	—		$	0
Bank of America NA		14			(—	@)		—			14
Bank of Montreal		—	@		(—	@)		—			0
Barclays Bank PLC		—	@		(—	@)		—			0
BNP Paribas SA		1			(—	@)		—			1
Citibank NA		14			(8	)		—			6
Commonwealth Bank of Australia		—	@		(—	@)		—			0
Credit Suisse International		—	@		(—	@)		—			0
Goldman Sachs International		25			(22	)		—			3
HSBC Bank PLC		7			(1	)		—			6
JPMorgan Chase Bank NA		36			(14	)		—			22
Royal Bank of Canada		—	@		—			—			—	@
State Street Bank and Trust Co.		8			(4	)		—			4
UBS AG		5			(5	)		—			0
Total	$	111		$	(55	)	$	—		$	56
Gross Amounts Not Offset in the Statement of Assets and Liabilities
Counterparty	Gross Liability Derivatives Presented in Statement of Assets and Liabilities (000)			Financial Instrument (000)			Collateral Pledged (000)(f)			Net Amount (not less than $0) (000)
Australia and New Zealand Banking Group	$	4		$	(1	)	$	—		$	3
Bank of America NA		—	@		(—	@)		—			0
Bank of Montreal		—	@		(—	@)		—			0
Bank of New York Mellon		—	@		—			—			—	@
Barclays Bank PLC		5			(—	@)		—			5
BNP Paribas SA		—	@		(—	@)		—			0
Citibank NA		8			(8	)		—			0
Commonwealth Bank of Australia		1			(—	@)		—			1
Credit Suisse International		—	@		(—	@)		—			0
Goldman Sachs International		93			(22	)		(71	)		0
HSBC Bank PLC		1			(1	)		—			0
JPMorgan Chase Bank NA		14			(14	)		—			0
State Street Bank and Trust Co.		4			(4	)		—			0
UBS AG		5			(5	)		—			0
Total	$	135		$	(55	)	$	(71	)	$	9

@ Amount is less than $500.

(f) In some instances, the actual collateral pledged may be more than the amount shown here due to overcollateralization.

For the year ended September 30, 2016, the approximate average monthly amount outstanding for each derivative type is as follows:

Foreign Currency Forward Exchange Contracts:
Average monthly principal amount	$	10,657,000
Futures Contracts:
Average monthly original value	$	11,532,000
Swap Agreements:
Average monthly notional amount	$	4,463,000
Options Purchased:
Average monthly notional amount		529,000
Options Written:
Average monthly notional amount		534,000

5. When-Issued/Delayed Delivery Securities: The Portfolio purchases and sells when-issued and delayed delivery securities. Securities purchased on a when-issued or delayed delivery basis are purchased for delivery beyond the normal settlement date at a stated price and yield, and no income accrues to the Portfolio on such securities prior to delivery date. Payment and delivery for when-issued and delayed delivery securities can take place a month or more after the date of the transaction. When the Portfolio enters into a purchase transaction on a when-issued or delayed delivery basis, securities are available for collateral in an amount at least equal in value to the Portfolio's commitments to purchase such securities. Purchasing securities on a when-issued or delayed delivery basis may involve a risk that the market price at the time of delivery may be lower than the agreed upon purchase price, in which case there could be an unrealized loss at the time of delivery. Purchasing investments on a when-issued or delayed delivery basis may be considered a form of leverage which may increase the impact that gains (losses) may have on the Portfolio.

6. Indemnifications: The Fund enters into contracts that contain a variety of indemnifications. The Fund's maximum exposure under these arrangements is unknown. However, the Fund has not had prior claims or losses pursuant to these contracts and expects the risk of loss to be remote.

7. Dividends and Distributions to Shareholders: Dividend income and distributions to shareholders are recorded on the ex-dividend date. Dividends from net investment income, if any, are declared and paid quarterly. Net realized capital gains, if any, are distributed at least annually.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

8. Security Transactions, Income and Expenses: Security transactions are accounted for on the trade date (date the order to buy or sell is executed). Realized gains and losses on the sale of investment securities are determined on the specific identified cost method. Dividend income and other distributions are recorded on the ex-dividend date (except for certain foreign dividends which may be recorded as soon as the Portfolio is informed of such dividends) net of applicable withholding taxes. Interest income is recognized on the accrual basis except where collection is in doubt. Discounts are accreted and premiums are amortized over the life of the respective securities. Most expenses of the Fund can be directly attributed to a particular Portfolio. Expenses which cannot be directly attributed are apportioned among the Portfolios based upon relative net assets or other appropriate methods. Income, expenses (other than class specific expenses — distribution and shareholder services, transfer agency and sub transfer agency fees) and realized and unrealized gains or losses are allocated to each class of shares based upon their relative net assets.

The Portfolio owns shares of real estate investment trusts ("REITs") which report information on the source of their distributions annually in the following calendar year. A portion of distributions received from REITs during the year is estimated to be a return of capital and is recorded as a reduction of their cost.

The Adviser has agreed to reduce its advisory fee and/or reimburse the Portfolio so that total annual portfolio operating expenses, excluding certain investment related expenses, taxes, interest and other extraordinary expenses (including litigation), will not exceed 0.95% for Class I shares, 1.30% for Class A shares, 2.05% for Class C shares and 0.90% for Class IS shares. The fee waivers and/or expense reimbursements will continue for at least one year from the date of the Portfolio's prospectus or until such time as the Trustees act to discontinue all or a portion of such waivers and/or reimbursements when they deem such action is appropriate. For the year ended September 30, 2016, approximately $93,000 of advisory fees were waived and approximately $335,000 of other expenses were reimbursed by the Adviser pursuant to this arrangement.

C. Administration Fees: The Adviser also serves as Administrator to the Fund and provides administrative services pursuant to an Administration Agreement for an annual fee, accrued daily and paid monthly, of 0.08% of the Portfolio's average daily net assets. Under a Sub-Administration Agreement between the Administrator and State Street Bank and Trust Company ("State Street"), State Street provides certain administrative services to the Fund. For such services, the Administrator pays State Street a portion of the fee the Administrator receives from the Portfolio.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

and sales activity and account maintenance fees, plus reimbursement for certain out-of-pocket expenses.

In December 2015, the Fund's Custodian announced that it had identified inconsistencies in the way in which clients were invoiced for out-of-pocket expenses from 1998 until November 2015. The dollar amount difference between what was charged and what should have been charged, plus interest, was paid back to the Portfolio in September 2016 as a reimbursement. State Street reimbursed the Portfolio directly, which was recognized as a change in accounting estimate and was reflected as "Reimbursement of Custodian Fees" in the Statement of Operations. Pursuant to the expense limitations described in Note B, the Portfolio has experienced expenses reimbursed by the Adviser during the current period. Accordingly, the reimbursement of out-of-pocket expenses in the current period resulted in the reduction in the current period expenses reimbursed by Adviser.

G. Security Transactions and Transactions with Affiliates: For the year ended September 30, 2016, purchases and sales of investment securities for the Portfolio, other than long-term U.S. Government securities and short-term investments, were approximately $12,833,000 and $12,203,000, respectively. For the year ended September 30, 2016, purchases and sales of long-term U.S. Government securities were approximately $18,225,000 and $18,340,000, respectively.

The Portfolio invests in the Institutional Class of the Morgan Stanley Institutional Liquidity Funds (the "Liquidity Funds"), an open-end management investment company managed by the Adviser. Advisory fees paid by the Portfolio are reduced by an amount equal to its pro-rata share of the advisory and administration fees paid by the Portfolio due to its investment in the Liquidity Funds. For the year ended September 30, 2016, advisory fees paid were reduced by approximately $2,000 relating to the Portfolio's investment in the Liquidity Funds.

A summary of the Portfolio's transactions in shares of the Liquidity Funds during the year ended September 30, 2016 is as follows:

Value September 30, 2015 (000)				Purchases at Cost (000)				Sales (000)				Dividend Income (000)				Value September 30, 2016 (000)
$	1,742			$	9,307			$	9,946			$	5			$	1,103

The Portfolio invests in Morgan Stanley Institutional Fund, Inc. — Emerging Markets Fixed Income Opportunities Portfolio ("Emerging Markets Fixed Income Opportunities Portfolio"), an open-end management investment company advised

by an affiliate of the Adviser. Advisory fees paid by the Portfolio are reduced by an amount equal to its pro-rata share of the advisory and administration fees paid by the Emerging Markets Fixed Income Opportunities Portfolio. For the year ended September 30, 2016, advisory fees paid were reduced by approximately $2,000 relating to the Portfolio's investment in the Emerging Markets Fixed Income Opportunities Portfolio. The Emerging Markets Fixed Income Opportunities Portfolio has a cost basis of approximately $712,000 at September 30, 2016.

A summary of the Portfolio's transactions in shares of the Emerging Markets Fixed Income Opportunities Portfolio during the year ended September 30, 2016 is as follows:

Value September 30, 2015 (000)				Purchases at Cost (000)				Sales (000)				Realized Loss (000)				Dividend Income (000)				Value September 30, 2016 (000)
$	417			$	318			$	57			$	(4	)		$	36			$	747

The Portfolio invests in Morgan Stanley Institutional Fund Trust — High Yield Portfolio ("High Yield Portfolio"), an open-end management investment company advised by an affiliate of the Adviser. Advisory fees paid by the Portfolio are reduced by an amount equal to its pro-rata share of the advisory and administration fees paid by the High Yield Portfolio. For the year ended September 30, 2016, advisory fees paid were reduced by approximately $1,000 relating to the Portfolio's investment in the High Yield Portfolio. The High Yield Portfolio has a cost basis of approximately $708,000 at September 30, 2016.

A summary of the Portfolio's transactions in shares of the High Yield Portfolio during the year ended September 30, 2016 is as follows:

Value September 30, 2015 (000)				Purchases at Cost (000)				Sales (000)				Dividend Income (000)				Value September 30, 2016 (000)
$	565			$	108			$	—			$	43			$	690

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

FASB ASC 740-10, "Income Taxes — Overall", sets forth a minimum threshold for financial statement recognition of the benefit of a tax position taken or expected to be taken in a tax return. Management has concluded there are no significant uncertain tax positions that would require recognition in the financial statements. If applicable, the Portfolio recognizes interest accrued related to unrecognized tax benefits in "Interest Expense" and penalties in "Other Expenses" in the Statement of Operations. The Portfolio files tax returns with the U.S. Internal Revenue Service, New York and various states. Each of the tax years in the two-year period ended September 30, 2016, remains subject to examination by taxing authorities.

The tax character of distributions paid may differ from the character of distributions shown in the Statements of Changes in Net Assets due to short-term capital gains being treated as

ordinary income for tax purposes. The tax character of distributions paid during fiscal years 2016 and 2015 was as follows:

2016 Distributions Paid From:		2015 Distributions Paid From:
Ordinary Income (000)		Ordinary Income (000)
$	308		45

Permanent differences, primarily due to differing treatments of gains (losses) related to foreign currency transactions, basis adjustments for swap transactions, paydown adjustments and tax adjustments on passive foreign investment companies sold by the Portfolio, resulted in the following reclassifications among the components of net assets at September 30, 2016:

Distributions in Excess of Net Investment Income (000)				Accumulated Net Realized Loss (000)				Paid-in- Capital (000)
$	(17	)		$	17			$	—

At September 30, 2016, the components of distributable earnings for the Portfolio on a tax basis were as follows:

Undistributed Ordinary Income (000)				Undistributed Long-Term Capital Gain (000)
$	148			$	—

At September 30, 2016, the Portfolio had available for federal income tax purposes unused short term capital losses of approximately $390,000 that do not have an expiration date.

I. Credit Facility: As of April 4, 2016, the Fund and other Morgan Stanley funds participate in a $150,000,000 committed, unsecured revolving line of credit facility (the "facility")

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

with State Street. This facility is to be used for temporary emergency purposes or funding of shareholder redemption requests. The interest rate on borrowings is based on the federal funds rate or one month libor rate plus a spread. The facility also has a commitment fee of 0.25% per annum based on the unused portion of the facility. During the year ended September 30, 2016, the Portfolio did not have any borrowings under the facility.

J. Other: At September 30, 2016, the Portfolio did not have record owners of 10% or greater.

K. Subsequent Event: Effective October 3, 2016, the Portfolio may, consistent with its principal investment strategies, invest up to 25% of its total assets in a wholly-owned subsidiary of the Portfolio organized as a company under the laws of the Cayman Islands (the "Subsidiary"). The Subsidiary may invest, directly or indirectly through the use of derivatives, in securities, commodities, commodity-related instruments and other investments, primarily futures, swaps and notes. The initial startup cost, including legal and other costs associated with the creation of the Subsidiary, was approximately $2,000 and is reflected as "Organizational Costs" in the Statement of Operations. The Subsidiary is advised by the Adviser.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Report of Independent Registered Public Accounting Firm

To the Shareholders and Board of Trustees of
Morgan Stanley Institutional Fund Trust —
Global Multi-Asset Income Portfolio

We have audited the accompanying statement of assets and liabilities, including the portfolio of investments, of Global Multi-Asset Income Portfolio (one of the portfolios constituting Morgan Stanley Institutional Fund Trust) (the "Portfolio") as of September 30, 2016, the related statement of operations for the year then ended and the statements of changes in net assets and the financial highlights for each of the years or periods indicated therein. These financial statements and financial highlights are the responsibility of the Portfolio's management. Our responsibility is to express an opinion on these financial statements and financial highlights based on our audits.

In our opinion, the financial statements and financial highlights referred to above present fairly, in all material respects, the financial position of Global Multi-Asset Income Portfolio (one of the portfolios constituting Morgan Stanley Institutional Fund Trust) at September 30, 2016, the results of its operations for the year then ended and the changes in its net assets and the financial highlights for each of the years or periods indicated therein, in conformity with U.S. generally accepted accounting principles.

Boston, Massachusetts
November 22, 2016

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Advisory Agreement Approval (unaudited)

Nature, Extent and Quality of Services

Performance, Fees and Expenses of the Portfolio

The Board reviewed the performance, fees and expenses of the Portfolio compared to its peers, as determined by Broadridge, and to appropriate benchmarks where applicable. The Board discussed with the Adviser the performance goals and the actual results achieved in managing the Portfolio. When considering a fund's performance, the Board and the Adviser place emphasis on trends and longer-term returns (focusing on one-year, three-year and five-year performance, as of December 31, 2015, or since inception, as applicable). When a fund underperforms its benchmark and/or its peer group average, the Board and the Adviser discuss the causes of such underperformance and, where necessary, they discuss specific changes to investment strategy or investment personnel. The Board noted that the Portfolio's performance was better than its peer group average for the period since the end of April 2015, the month of the Portfolio's inception. The Board discussed with the Adviser the level of the advisory and administration fees (together, the "management fee") for this Portfolio relative to comparable funds and/or other accounts advised by the Adviser and/or compared to its peers as determined by Broadridge. In addition to the management fee, the Board also reviewed the Portfolio's total expense ratio. The Board noted that the Portfolio's management fee and total expense ratio were lower than its peer group averages. After discussion, the Board concluded that the Portfolio's (i) performance was competitive with its peer group average; and (ii) management fee and total expense ratio were competitive with its peer group averages.

Economies of Scale

The Board considered the size and growth prospects of the Portfolio and how that relates to the Portfolio's total expense ratio and particularly the Portfolio's management fee rate, which does not include breakpoints. In conjunction with its review of the Adviser's profitability, the Board discussed with the Adviser how a change in assets can affect the efficiency or effectiveness of managing the Portfolio and whether the management fee level is appropriate relative to current and projected asset levels and/or whether the management fee structure reflects economies of scale as asset levels change. The Board has determined that its review of the actual and/or potential economies of scale of the Portfolio supports its decision to approve the Management Agreement.

Profitability of the Adviser and Affiliates

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Advisory Agreement Approval (unaudited) (cont'd)

Other Benefits of the Relationship

Resources of the Adviser and Historical Relationship Between the Portfolio and the Adviser

Other Factors and Current Trends

General Conclusion

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Federal Tax Notice (unaudited)

For federal income tax purposes, the following information is furnished with respect to the distributions paid by the Portfolio during its taxable year ended September 30, 2016. For corporate shareholders 4.92% of the dividends qualified for the dividends received deduction.

For federal income tax purposes, the following information is furnished with respect to the Portfolio's earnings for its taxable year ended September 30, 2016. When distributed, certain earnings may be subject to a maximum tax rate of 15% as provided for by the Jobs and Growth Tax Relief Reconciliation Act of 2003. The Portfolio designated up to a maximum of approximately $109,000 as taxable at this lower rate.

In January, the Portfolio provides tax information to shareholders for the preceding calendar year.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Privacy Notice (unaudited)

MORGAN STANLEY INVESTMENT MANAGEMENT INC.
AN IMPORTANT NOTICE CONCERNING OUR U.S. PRIVACY POLICY

WE RESPECT YOUR PRIVACY

1. WHAT PERSONAL INFORMATION DO WE COLLECT ABOUT YOU?

For example:

• We may obtain information about your creditworthiness and credit history from consumer reporting agencies.

• We may collect background information from and through third-party vendors to verify representations you have made and to comply with various regulatory requirements.

2. WHEN DO WE DISCLOSE PERSONAL INFORMATION WE COLLECT ABOUT YOU?

We may disclose personal information we collect about you to other Morgan Stanley companies and to non-affiliated third parties.

a. Information We Disclose to Other Morgan Stanley Companies.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Privacy Notice (unaudited) (cont'd)

b. Information We Disclose to Non-affiliated Third Parties.

3. HOW DO WE PROTECT THE SECURITY AND CONFIDENTIALITY OF PERSONAL INFORMATION WE COLLECT ABOUT YOU?

4. HOW CAN YOU LIMIT THE SHARING OF CERTAIN TYPES OF PERSONAL INFORMATION WITH OTHER MORGAN STANLEY COMPANIES?

5. HOW CAN YOU LIMIT THE USE OF CERTAIN TYPES OF PERSONAL INFORMATION BY OTHER MORGAN STANLEY COMPANIES FOR MARKETING?

6. HOW CAN YOU SEND US AN OPT-OUT INSTRUCTION?

• Calling us at (800) 548-7786
Monday–Friday between 8a.m. and 6p.m.(EST)

• Writing to us at the following address:

Boston Financial Data Services, Inc.
c/o Privacy Coordinator
P.O. Box 219804
Kansas City, Missouri 64121

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Privacy Notice (unaudited) (cont'd)

7. WHAT IF AN AFFILIATED COMPANY BECOMES A NON-AFFILIATED THIRD PARTY?

SPECIAL NOTICE TO RESIDENTS OF VERMONT

If you wish to receive offers for investment products and services offered by or through other Morgan Stanley companies, please notify us in writing at the following address:

Boston Financial Data Services, Inc.
c/o Privacy Coordinator
P.O. Box 219804
Kansas City, Missouri 64121

SPECIAL NOTICE TO RESIDENTS OF CALIFORNIA

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited)

Independent Trustees:

Name, Age and Address of
Independent Trustee

Position(s)
Held with
Registrant

Length of Time
Served*

Principal Occupation(s) During Past 5 Years
and Other Relevant Professional Experience

Number of
Portfolios in
Fund Complex
Overseen by
Independent
Trustee**

Other Directorships
Held by Independent
Trustee***

Frank L. Bowman (71)
c/o Perkins Coie LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
August
2006

Kathleen A. Dennis (63)
c/o Perkins Coie LLP
Counsel to the Independent Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
August
2006

Director of various non-profit organizations.

Nancy C. Everett (61)
c/o Perkins Coie LLP
Counsel to the Independent Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
January
2015

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Age and Address of
Independent Trustee

Position(s)
Held with
Registrant

Length of Time
Served*

Principal Occupation(s) During Past 5 Years
and Other Relevant Professional Experience

Number of
Portfolios in
Fund Complex
Overseen by
Independent
Trustee**

Other Directorships
Held by Independent
Trustee***

Jakki L. Haussler (59)
c/o Perkins Coie LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
January
2015

Dr. Manuel H. Johnson (67)
c/o Johnson Smick International, Inc.
220 I Street, N.E. — Suite 200
Washington, D.C. 20002

Trustee

Since
July
1991

100

Director of NVR, Inc. (home construction).

Joseph J. Kearns (74)
c/o Kearns & Associates LLC
23823 Malibu Road
S-50-440
Malibu, CA 90265

Trustee

Since
August
1994

101

Director of Electro Rent Corporation (equipment leasing). Prior to December 31, 2013, Director of The Ford Family Foundation.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Age and Address of
Independent Trustee

Position(s)
Held with
Registrant

Length of Time
Served*

Principal Occupation(s) During Past 5 Years
and Other Relevant Professional Experience

Number of
Portfolios in
Fund Complex
Overseen by
Independent
Trustee**

Other Directorships
Held by Independent
Trustee***

Michael F. Klein (57)
c/o Perkins Coie LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
August
2006

Director of certain investment funds managed or sponsored by Aetos Capital, LLC; Director of Sanitized AG and Sanitized Marketing AG (specialty chemicals).

Michael E. Nugent (80)
522 Fifth Avenue
New York, NY 10036

Chair of the
Board and
Trustee

Chair of the Boards since
July 2006 and Trustee since
July 1991

100

None.

W. Allen Reed (69)
c/o Perkins Coie LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
August
2006

Director of Legg Mason, Inc.; formerly, Director of the Auburn University Foundation (2010-2015).

Fergus Reid (84)
c/o Joe Pietryka, Inc.
85 Charles Colman Blvd.
Pawling, NY 12564

Trustee

Since
June
1992

Chairman, Joe Pietryka, Inc.; Chairperson of the Governance Committee and Director or Trustee of various Morgan Stanley Funds (since June 1992).

100

Formerly, Trustee and Director of certain investment companies in the JP Morgan Fund Complex managed by JP Morgan Investment Management Inc. (1987-2012).

* This is the earliest date the Trustee began serving the Morgan Stanley Funds. Each Trustee serves an indefinite term, until his or her successor is elected.

*** This includes any directorships at public companies and registered investment companies held by the Trustee at any time during the past five years.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited) (cont'd)

Executive Officers:

Name, Age and Address of Executive Officer

Position(s) Held
with
Registrant

Length of
Time Served*

Principal Occupation(s) During Past 5 Years

John H. Gernon (53)
522 Fifth Avenue
New York, NY 10036

President and
Principal
Executive
Officer

Since
September
2013

Stefanie V. Chang Yu (49)
522 Fifth Avenue
New York, NY 10036

Chief
Compliance
Officer

Since
December
1997

Joseph C. Benedetti (51)
522 Fifth Avenue
New York, NY 10036

Vice President

Since
January
2014

Francis J. Smith (51)
522 Fifth Avenue
New York, NY 10036

Treasurer and
Principal
Financial
Officer

Treasurer
since July
2003 and
Principal
Financial
Officer since
September
2002

Executive Director of the Adviser and various entities affiliated with the Adviser; Treasurer (since July 2003) and Principal Financial Officer of various Morgan Stanley Funds (since September 2002).

Mary E. Mullin (49)
522 Fifth Avenue
New York, NY 10036

Secretary

Since
June
1999

Executive Director of the Adviser; Secretary of various Morgan Stanley Funds (since June 1999).

* This is the earliest date the officer began serving the Morgan Stanley Funds. Each officer serves a one-year term, until his or her successor is elected and has qualified.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Adviser and Administrator

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

Distributor

Morgan Stanley Distribution, Inc.
522 Fifth Avenue
New York, New York 10036

Dividend Disbursing and Transfer Agent

Boston Financial Data Services, Inc.
2000 Crown Colony Drive
Quincy, Massachusetts 02169

Custodian

State Street Bank and Trust Company
One Lincoln Street
Boston, Massachusetts 02111

Legal Counsel

Dechert LLP
1095 Avenue of the Americas
New York, New York 10036

Counsel to the Independent Trustees

Perkins Coie LLP
30 Rockefeller Plaza
New York, New York 10112

Independent Registered Public Accounting Firm

Ernst & Young LLP
200 Clarendon Street
Boston, Massachusetts 02116

Reporting to Shareholders

Proxy Voting Policies and Procedures and Proxy Voting Record

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable Portfolio of Morgan Stanley Institutional Funds Trust, which describes in detail the Portfolio's investment policies, risks, fees and expenses. Please read the prospectus carefully before you invest or send money. For additional information, including information regarding the investments comprising the Portfolio, please visit our website at www.morganstanley.com/im or call toll free 1 (800) 548-7786.

Printed in U.S.A.
This Report has been prepared for shareholders and may be distributed to others only if preceded or accompanied by a current prospectus.

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

IFGMAPANN
1627400 EXP. 11.30.17

INVESTMENT MANAGEMENT

Morgan Stanley Institutional Fund Trust

Global Strategist Portfolio

Annual Report

September 30, 2016

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Table of Contents

Shareholders' Letter					2
Expense Example					3
Investment Overview					4
Portfolio of Investments					8
Statement of Assets and Liabilities					34
Statement of Operations					36
Statements of Changes in Net Assets					37
Financial Highlights					39
Notes to Financial Statements					44
Report of Independent Registered Public Accounting Firm					58
Investment Advisory Agreement Approval					59
Federal Tax Notice					61
Privacy Notice					62
Trustee and Officer Information					65

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Shareholders' Letter (unaudited)

Dear Shareholders,

We are pleased to provide this Annual report, in which you will learn how your investment in Global Strategist Portfolio (the "Portfolio") performed during the latest twelve-month period.

As always, we thank you for selecting Morgan Stanley Investment Management, and look forward to working with you in the months and years ahead.

Sincerely,

John H. Gernon
President and Principal Executive Officer

October 2016

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Expense Example (unaudited)

Global Strategist Portfolio

This example is based on an investment of $1,000 invested at the beginning of the six-month period ended September 30, 2016 and held for the entire six-month period (unless otherwise noted).

Actual Expenses

Hypothetical Example for Comparison Purposes

	Beginning Account Value 4/1/16		Actual Ending Account Value 9/30/16		Hypothetical Ending Account Value		Actual Expenses Paid During Period*		Hypothetical Expenses Paid During Period*		Net Expense Ratio During Period**
Global Strategist Portfolio Class I	$	1,000.00	$	1,039.50	$	1,021.90	$	3.16	$	3.13		0.62	%***
Global Strategist Portfolio Class A		1,000.00		1,037.80		1,020.55		4.53		4.50		0.89	***
Global Strategist Portfolio Class L		1,000.00		1,034.80		1,017.75		7.38		7.31		1.45	***
Global Strategist Portfolio Class C		1,000.00		1,033.50		1,016.05		9.10		9.02		1.79	***
Global Strategist Portfolio Class IS		1,000.00		1,038.80		1,021.45		3.62		3.59		0.71	***

** Annualized.

*** Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Overview (unaudited)

Global Strategist Portfolio

The Portfolio seeks above-average total return over a market cycle of three to five years.

Performance

For the fiscal year ended September 30, 2016, the Portfolio's Class I shares had a total return based on net asset value and reinvestment of distributions per share of 8.42%, net of fees. The Portfolio's Class I shares underperformed against the Portfolio's benchmarks, the MSCI All Country World Index, which returned 11.96%, and the Customized MSIM Global Allocation Index (the "Customized Index", which is comprised of 60% MSCI All Country World Index, 30% Bloomberg Barclays Global Aggregate Index, 5% S&P GSCI Light Energy Index, and 5% Bank of America/Merrill Lynch U.S. Dollar 1-Month LIBID Average Index), which returned 9.59%.

During calendar year 2016, the Portfolio received monies related to certain nonrecurring litigation settlements. If these monies were not received, any period returns which include these settlement monies would have been lower. For example, the 2016 fiscal year total return would have been 8.21% for Class I Shares as of September 30, 2016. The returns on the other Share Classes would also have been similarly impacted. These were one-time settlements, and as a result, the impact on the net asset value and consequently the performance will not likely be repeated in the future. Please call 1-800-548-7786 for additional information.

Factors Affecting Performance⁽ⁱ⁾

• In the 12 months ended September 30, 2016, global equities outperformed bonds and commodities, with the MSCI All Country World Index up +12.0%, the Bloomberg Barclays Global Aggregate Index up +8.8%, and the S&P GSCI Index, a broad index of commodity prices, falling –12.2%.⁽ⁱⁱ⁾ (Except where noted, equity market returns are represented by the MSCI regional or country index and are calculated in U.S. dollars [USD].)

equities underperformed (+2.5% USD, +7.0% local), driven by generally disappointing monetary policy from the European Central Bank (ECB), comparatively greater exposure to emerging market growth and the threat of knock-on effects from Brexit. Japan (+12.1% USD, –5.2% local) was the regional laggard in local currency terms, as growth resumed slowing (though narrowly avoided slipping back into recession), but outperformed in USD terms as the effectiveness of Bank of Japan (BOJ) monetary policy appeared to reach a limit, contributing to a strong rally in the yen (+18.3% versus USD). Emerging markets (EM) were the top performer (+16.8% USD, +13.0% local), as massive credit easing by the People's Bank of China (PBOC) stabilized Chinese growth. Within emerging markets, Brazil rose +57.6% in USD, as growth and inflation began to improve, while the impeachment of President Dilma Rousseff ushered in a new administration and the hope of meaningful economic reforms.

• Within bonds, global government yields fell to all-time lows in July and sentiment indicators reached extreme bearishness, as the U.K.'s vote to exit the European Union added to uncertainty in the already sluggish global growth outlook, extending expectations for extremely low rates almost indefinitely. In the U.S., the 10-year yield fell –44 basis points (bps) to 1.59%, while the 2-year yield rose +13 bps to 0.76%, helped by a 25 bps hike in the policy rate. U.S. credit spreads tightened on resilient domestic activity and stabilization in the oil price (which returned to $52 per barrel by the end of the period after bottoming at $28 in January). U.S. investment grade credit spreads fell –31 bps to 1.38%, and U.S. high yield spreads fell –150 bps to 4.80%. Elsewhere in developed markets, deflationary fears coupled with negative policy rates contributed to the German 10-year yield falling –71 bps to –0.12%, and the Japanese 10-year yield falling –45 bps to –0.09%. The UK 10-year yield fell –102 bps to 0.75%, as the market prepared for a hard Brexit. Emerging sovereign spreads fell –114 bps to 3.60%, as emerging market growth and commodity prices stabilized.

• Within currencies, the U.S. dollar fell –0.9% on a trade-weighted basis, as rate hike expectations were pushed out further. Relative to the U.S. dollar, the

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Overview (unaudited) (cont'd)

Global Strategist Portfolio

British pound fell –14.2% following Brexit, the Mexican peso fell –12.4% on fears of a Trump presidency in the U.S., and the Chinese renminbi fell –4.7% as the government attempted to regain control of its monetary policy amid record capital outflows. The top-performing currencies were the Brazilian real, which rose +22.6% versus USD as economic and political risks subsided, and the Japanese yen, which rose +18.3% as the market appeared to accept that "Abenomics" had failed.

• Regarding the Portfolio's overall performance relative to the Customized Index, the Portfolio's asset allocation mix of an average underweight in fixed income and commodities and an average overweight in equities and cash had a positive impact on performance. The underweight position in commodities and the overweight position in equities (the Portfolio was underweight equities until February, then shifted to an overweight position) were strong contributors.

• Active positions within commodities (implemented via commodity futures) had a neutral impact on performance, as gains from an overweight position in Brent crude oil were offset by losses from overweight positions in sugar and gold.

• Active currency positions (implemented via currency forwards and futures) negatively impacted

performance. Overweight positions in the Swedish krona (versus the Australian dollar, Swiss franc, Chinese renminbi, euro) and the Mexican peso, as well as underweight positions in China-sensitive currencies (Australian dollar, New Zealand dollar, South Korean won, Thai baht) versus G-3 currencies (U.S. dollar, euro, yen) detracted from performance. Positive contributors included an underweight in the Chinese renminbi and overweight positions in oil-sensitive currencies (Norwegian kroner, Canadian dollar, Russian ruble).

Management Strategies

• We are overweight eurozone domestic equities. Despite post-Brexit expectations for a slowdown in

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Overview (unaudited) (cont'd)

Global Strategist Portfolio

eurozone growth, domestically-led (or non-export related) growth is back above trend, inflation is turning up, and the fiscal impulse is no longer contractionary. We expect 8% earnings growth for domestically-exposed eurozone stocks versus 5% U.S. earnings growth. We believe eurozone versus U.S. relative valuations have meaningful upside potential, while sentiment is extremely bearish.

(i) Certain of the Portfolio's investment themes may, in whole or part, be implemented through the use of derivatives, including the purchase and sale of futures, options, swaps, structured investments (including commodity-linked notes) and other related instruments and techniques. The Portfolio may also invest in foreign currency forward exchange contracts, which are also derivatives, in connection with its investments in foreign securities. The Portfolio may use derivative instruments for a variety of purposes, including hedging, risk management, portfolio management or to earn income. As a result, the use of derivatives had a material effect on the Portfolio's performance during the period.

(ii) Data sources used in preparation of this commentary include FactSet and Bloomberg LP. Data as of September 30, 2016.

* Minimum Investment

In accordance with SEC regulations, the Portfolio's performance shown assumes that all recurring fees (including management fees) were deducted and all dividends and distributions were reinvested. The performance of Class A, Class L, Class C and Class IS shares will vary from the performance of Class I shares based upon their different inception dates and will be negatively impacted by additional fees assessed to those classes (where applicable).

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Overview (unaudited) (cont'd)

Global Strategist Portfolio

Performance Compared to the MSCI All Country World Index⁽¹⁾, the Customized MSIM Global Allocation Index⁽²⁾ and the Lipper Flexible Portfolio Funds Index⁽³⁾

	Period Ended September 30, 2016 Total Returns⁽⁴⁾
				Average Annual
	One Year			Five Years			Ten Years			Since Inception⁽¹⁰⁾
Portfolio — Class I Shares w/o sales charges⁽⁵⁾		8.42	%		8.36	%		5.37	%		7.20	%
Portfolio — Class A Shares w/o sales charges⁽⁶⁾		7.98			8.01			5.06			6.04
Portfolio — Class A Shares with maximum 5.25% sales charges⁽⁶⁾		2.33			6.86			4.49			5.75
Portfolio — Class L Shares w/o sales charges⁽⁷⁾		7.47			—			—			4.79
Portfolio — Class C Shares w/o sales charges⁽⁸⁾		7.13			—			—			–2.62
Portfolio — Class C Shares with maximum 1.00% deferred sales charges⁽⁸⁾		6.13			—			—			–2.62
Portfolio — Class IS Shares w/o sales charges⁽⁹⁾		8.42			—			—			–0.76
MSCI All Country World Index		11.96			10.63			4.34			7.30
Customized MSIM Global Allocation Index		9.59			6.46			3.96			—
Lipper Flexible Portfolio Funds Index		9.79			8.64			5.25			6.71

⁽¹⁾ The MSCI All Country World Index (ACWI) is a free float-adjusted market capitalization weighted index designed to measure the equity market performance of developed and emerging markets. The term "free float" represents the portion of shares outstanding that are deemed to be available for purchase in the public equity markets by investors. The performance of the Index is listed in U.S. dollars and assumes reinvestment of net dividends. "Net dividends" reflects a reduction in dividends after taking into account withholding of taxes by any foreign countries represented in the Index. Returns, including periods prior to January 1, 2001, are calculated using the return data of the MSCI All Country World Index (gross dividends) through December 31, 2000 and the return data of the MSCI All Country World Index (net dividends) after December 31, 2000. The Index is unmanaged and its returns do not include any sales charges or fees. Such costs would lower performance. It is not possible to invest directly in an index.

⁽²⁾ The Customized MSIM Global Allocation Index is comprised of 60% MSCI All Country World Index (benchmark that measures the equity market performance of developed and emerging markets), 30% Bloomberg Barclays Global Aggregate Index (benchmark that provides a broadbased measure of the global investment grade fixed-rate debt markets), 5% S&P GSCI Light Energy Index (benchmark for investment performance in the energy commodity market) and 5% Bank of America/Merrill Lynch U.S. Dollar 1-Month LIBID Average Index (benchmark that tracks the performance of a basket of synthetic assets paying LIBID to a stated maturity). The Customized MSIM Global Allocation Index was added as the Portfolio benchmark on October 2, 2013 and is provided for comparative purposes only. The Index is unmanaged and its returns do not include any sales charges or fees. Such costs would lower performance. It is not possible to invest directly in an index.

⁽⁴⁾ Total returns for the Portfolio reflect expenses waived and/or reimbursed, if applicable, by the Adviser. Without such waivers and/or reimbursements, total returns would have been lower.

⁽⁵⁾ Commenced operations on December 31, 1992.

⁽⁶⁾ Commenced operations on November 1, 1996.

⁽⁷⁾ Commenced operations on April 27, 2012.

⁽⁸⁾ Commenced operations on April 30, 2015.

⁽⁹⁾ Commenced operations on May 29, 2015.

⁽¹⁰⁾ For comparative purposes, average annual since inception returns listed for the Indexes refer to the inception date of the Class I of the Portfolio, not the inception of the Indexes.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments

Global Strategist Portfolio

	Face Amount (000)		Value (000)
Fixed Income Securiy (39.4%)
Agency Adjustable Rate Mortgage (0.1%)
United States (0.1%)
Federal Home Loan Mortgage Corporation, Conventional Pool:
2.55%, 7/1/45	$	309	$	319
Agency Fixed Rate Mortgages (3.2%)
United States (3.2%)
Federal Home Loan Mortgage Corporation,
Gold Pools:
3.50%, 1/1/44 - 6/1/45		1,553		1,656
6.50%, 5/1/32 - 7/1/32		59		68
7.50%, 5/1/35		7		8
October TBA:
4.00%, 10/1/46 (a)		980		1,051
Federal National Mortgage Association,
Conventional Pools:
3.00%, 3/1/30 - 5/1/30		398		419
3.50%, 4/1/29		376		396
4.00%, 4/1/45 - 9/1/45		1,689		1,832
4.50%, 3/1/41 - 11/1/44		415		459
5.00%, 1/1/41 - 3/1/41		1,184		1,325
6.00%, 1/1/38		11		13
6.50%, 12/1/29		21		25
7.00%, 12/1/17 - 2/1/31		241		262
7.50%, 8/1/37		13		16
October TBA:
2.50%, 10/1/31 (a)		460		476
3.00%, 10/1/46 (a)		1,520		1,580
3.50%, 10/1/46 (a)		463		489
4.00%, 10/1/46 (a)		140		150
Government National Mortgage Association,
Various Pools:
3.50%, 12/15/43		516		555
4.00%, 8/20/41 - 11/20/42		592		637
5.50%, 8/15/39		88		99
				11,516
Asset-Backed Security (0.1%)
United States (0.1%)
CVS Pass-Through Trust,
6.04%, 12/10/28		333		387
Collateralized Mortgage Obligations — Agency Collateral Series (0.5%)
United States (0.5%)
Federal Home Loan Mortgage Corporation,
2.40%, 6/25/22		1,625		1,692
2.79%, 1/25/22		75		79
2.97%, 10/25/21		90		96
IO REMIC
5.53%, 4/15/39 (b)		106		10
				1,877

	Face Amount (000)		Value (000)
Commercial Mortgage-Backed Securities (0.8%)
United States (0.8%)
COMM Mortgage Trust,
3.28%, 1/10/46	$	305	$	319
4.90%, 7/15/47 (b)(c)		152		125
Commercial Mortgage Pass-Through Certificates,
2.82%, 10/15/45		376		392
JP Morgan Chase Commercial Mortgage Securities Trust,
4.39%, 7/15/46 (c)		100		109
4.72%, 7/15/47 (b)(c)		745		595
JPMBB Commercial Mortgage Securities Trust,
4.11%, 9/15/47 (b)(c)		205		171
4.71%, 9/15/47 (b)(c)		263		216
4.82%, 8/15/47 (b)(c)		361		307
UBS-Barclays Commercial Mortgage Trust,
3.53%, 5/10/63		255		275
WF-RBS Commercial Mortgage Trust,
4.14%, 10/15/57 (b)(c)		362		305
				2,814
Corporate Bonds (8.8%)
Australia (0.5%)
Australia & New Zealand Banking Group Ltd.,
5.13%, 9/10/19	EUR	400		516
BHP Billiton Finance USA Ltd.,
3.85%, 9/30/23	$	170		186
Macquarie Bank Ltd.,
6.63%, 4/7/21 (c)		270		311
Origin Energy Finance Ltd.,
3.50%, 10/9/18 (c)		200		204
QBE Insurance Group Ltd.,
2.40%, 5/1/18 (c)		200		201
Telstra Corp., Ltd.,
3.13%, 4/7/25 (c)		135		142
Transurban Finance Co., Pty Ltd.,
4.13%, 2/2/26 (c)		170		182
				1,742
Belgium (0.1%)
Anheuser-Busch InBev Finance, Inc.,
3.70%, 2/1/24		300		325
4.70%, 2/1/36		225		259
				584
Canada (0.2%)
Brookfield Asset Management, Inc.,
5.80%, 4/25/17		295		301
Goldcorp, Inc.,
3.70%, 3/15/23		198		206
Royal Bank of Canada,
1.50%, 7/29/19		325		325
				832

The accompanying notes are an integral part of the financial statements.
8

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Face Amount (000)		Value (000)
Chile (0.1%)
Empresa Nacional de Telecomunicaciones SA,
4.75%, 8/1/26 (c)	$	250	$	254
China (0.2%)
Baidu, Inc.,
3.25%, 8/6/18		225		231
Sinopec Group Overseas Development 2013 Ltd.,
2.63%, 10/17/20 (d)	EUR	300		365
Want Want China Finance Ltd.,
1.88%, 5/14/18 (c)	$	200		200
				796
Colombia (0.1%)
Ecopetrol SA,
5.88%, 9/18/23		270		292
France (0.9%)
Air Liquide Finance SA,
1.75%, 9/27/21 (c)		200		200
AXA SA,
3.94%, 11/7/24 (b)(e)	EUR	500		581
Banque Federative du Credit Mutuel SA,
2.00%, 9/19/19		500		596
BNP Paribas SA,
4.38%, 5/12/26 (c)	$	200		207
5.00%, 1/15/21		95		106
BPCE SA,
5.15%, 7/21/24 (c)		450		474
Credit Agricole Assurances SA,
4.25%, 1/13/25 (b)(e)	EUR	500		554
Electricite de France SA,
5.00%, 1/22/26 (b)(e)		300		335
TOTAL SA,
2.25%, 2/26/21 (b)(e)		200		223
				3,276
Germany (0.5%)
Bayer AG,
3.75%, 7/1/74 (b)		300		345
Daimler Finance North America LLC,
1.50%, 7/5/19 (c)	$	300		298
Muenchener Rueckversicherungs- Gesellschaft AG in Muenchen,
6.00%, 5/26/41 (b)	EUR	400		537
Siemens Financieringsmaatschappij N.V.,
1.30%, 9/13/19 (c)	$	250		249
3.25%, 5/27/25 (c)		250		267
Vier Gas Transport GmbH,
3.13%, 7/10/23	EUR	100		135
				1,831
Hong Kong (0.1%)
CK Hutchison International 16 Ltd.,
1.88%, 10/3/21 (c)(d)(f)	$	200		198

	Face Amount (000)		Value (000)
Israel (0.1%)
Teva Pharmaceutical Finance Netherlands III BV,
2.20%, 7/21/21	$	315	$	314
Italy (0.3%)
Assicurazioni Generali SpA,
10.13%, 7/10/42 (b)	EUR	400		581
FCA Capital Ireland PLC,
1.38%, 4/17/20		250		289
Telecom Italia Finance SA,
7.75%, 1/24/33		80		120
				990
Korea, Republic of (0.1%)
SK Telecom Co., Ltd.,
2.13%, 5/1/18 (c)	$	200		202
Malaysia (0.1%)
Petronas Capital Ltd.,
3.50%, 3/18/25 (c)		375		405
Netherlands (0.6%)
ABN Amro Bank N.V.,
2.50%, 10/30/18 (c)		300		306
2.88%, 6/30/25 (b)	EUR	250		294
ASR Nederland N.V.,
5.00%, 9/30/24 (b)(e)		500		584
Cooperatieve Rabobank UA,
3.95%, 11/9/22	$	250		262
Series G
3.75%, 11/9/20	EUR	300		383
ING Bank N.V.,
5.80%, 9/25/23 (c)	$	240		269
				2,098
Spain (0.3%)
Santander Issuances SAU,
5.18%, 11/19/25		600		613
Telefonica Emisiones SAU,
4.71%, 1/20/20	EUR	300		388
				1,001
Sweden (0.1%)
Skandinaviska Enskilda Banken AB,
1.75%, 3/19/18 (c)	$	200		201
Swedbank AB,
1.75%, 3/12/18 (c)		270		271
				472
Switzerland (0.4%)
Aquarius and Investments PLC for Zurich Insurance Co., Ltd.,
4.25%, 10/2/43 (b)	EUR	450		563
Credit Suisse AG,
0.63%, 11/20/18		550		626
6.00%, 2/15/18	$	90		95
Novartis Capital Corp.,
4.40%, 5/6/44		150		178
				1,462

The accompanying notes are an integral part of the financial statements.
9

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Face Amount (000)		Value (000)
United Kingdom (0.8%)
Diageo Capital PLC,
1.50%, 5/11/17	$	215	$	216
Experian Finance PLC,
2.38%, 6/15/17 (c)		400		402
GlaxoSmithKline Capital, Inc.,
6.38%, 5/15/38		100		144
Heathrow Funding Ltd.,
4.60%, 2/15/18	EUR	300		358
Lloyds Bank PLC,
6.50%, 3/24/20		450		597
Nationwide Building Society,
3.90%, 7/21/25 (c)	$	200		216
6.25%, 2/25/20 (c)		300		341
NGG Finance PLC,
5.63%, 6/18/73 (b)	GBP	200		292
Santander UK PLC,
4.00%, 3/13/24	$	120		131
Standard Chartered PLC,
2.10%, 8/19/19 (c)		300		300
				2,997
United States (3.3%)
Air Lease Corp.,
2.13%, 1/15/20 (f)		400		399
Altria Group, Inc.,
2.85%, 8/9/22		25		26
5.38%, 1/31/44		155		196
Apple, Inc.,
1.55%, 8/4/21		225		225
AT&T, Inc.,
4.50%, 3/9/48 (c)		191		193
5.15%, 3/15/42		25		27
Bank of America Corp.,
MTN
4.00%, 4/1/24		250		270
4.20%, 8/26/24		100		106
4.25%, 10/22/26		45		48
5.00%, 1/21/44		250		295
Baxalta, Inc.,
4.00%, 6/23/25		300		321
Boston Properties LP,
3.85%, 2/1/23		25		27
Burlington Northern Santa Fe LLC,
4.55%, 9/1/44		195		226
Capital One Bank USA NA,
3.38%, 2/15/23		546		562
Capital One NA,
1.85%, 9/13/19		400		400
Charter Communications Operating LLC/ Charter Communications Operating Capital,
4.91%, 7/23/25 (c)		300		331
6.48%, 10/23/45 (c)		150		182

	Face Amount (000)		Value (000)
Citigroup, Inc.,
2.65%, 10/26/20	$	50	$	51
5.50%, 9/13/25		250		286
6.68%, 9/13/43		20		26
8.13%, 7/15/39		175		276
Coca-Cola Co.,
3.20%, 11/1/23		250		269
Comcast Corp.,
4.60%, 8/15/45		130		151
Discover Bank,
2.00%, 2/21/18		345		346
Enterprise Products Operating LLC,
3.35%, 3/15/23		275		282
Five Corners Funding Trust,
4.42%, 11/15/23 (c)		350		379
General Motors Financial Co., Inc.,
4.30%, 7/13/25		250		258
Gilead Sciences, Inc.,
3.65%, 3/1/26		175		189
4.80%, 4/1/44		75		84
Goldman Sachs Group, Inc. (The), MTN
4.80%, 7/8/44		275		311
Hartford Financial Services Group, Inc. (The),
5.50%, 3/30/20		25		28
Home Depot, Inc.,
5.88%, 12/16/36		100		137
HSBC USA, Inc.,
3.50%, 6/23/24		100		104
JPMorgan Chase & Co.,
3.20%, 6/15/26		500		514
Liberty Mutual Group, Inc.,
4.85%, 8/1/44 (c)		100		105
McDonald's Corp., MTN
3.38%, 5/26/25		275		290
Medtronic, Inc.,
3.63%, 3/15/24		250		272
4.63%, 3/15/45		50		59
Merck & Co., Inc.,
2.80%, 5/18/23		250		262
Microsoft Corp.,
1.55%, 8/8/21		300		299
Monongahela Power Co.,
5.40%, 12/15/43 (c)		100		127
NBC Universal Media LLC,
4.38%, 4/1/21		175		195
Omnicom Group, Inc.,
3.63%, 5/1/22		60		64
3.65%, 11/1/24		84		89
Oracle Corp.,
3.40%, 7/8/24		175		187
Pacific LifeCorp,
6.00%, 2/10/20 (c)		25		28

The accompanying notes are an integral part of the financial statements.
10

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Face Amount (000)		Value (000)
United States (cont'd)
PepsiCo, Inc.,
3.60%, 3/1/24	$	250	$	274
Prudential Financial, Inc., MTN
6.63%, 12/1/37		150		194
Tyco International Finance SA,
3.90%, 2/14/26		175		191
UnitedHealth Group, Inc.,
3.75%, 7/15/25		75		82
4.25%, 3/15/43		150		166
Verizon Communications, Inc.,
4.67%, 3/15/55		231		244
5.01%, 8/21/54		120		133
Visa, Inc.,
3.15%, 12/14/25		325		344
Wal-Mart Stores, Inc.,
2.55%, 4/11/23		475		494
Wells Fargo & Co., MTN
4.10%, 6/3/26		275		292
				11,916
				31,662
Mortgages — Other (0.7%)
United Kingdom (0.2%)
Holmes Master Issuer PLC,
2.08%, 10/15/54 (b)(c)	GBP	514		672
United States (0.5%)
Banc of America Alternative Loan Trust,
5.86%, 10/25/36	$	40		26
6.00%, 4/25/36		15		15
ChaseFlex Trust,
6.00%, 2/25/37		38		31
First Horizon Alternative Mortgage Securities Trust,
6.25%, 8/25/36		18		14
Freddie Mac Whole Loan Securities Trust,
3.00%, 9/25/45 - 7/25/46		646		659
3.50%, 5/25/45 - 7/25/46		952		983
4.00%, 5/25/45		78		82
GSR Mortgage Loan Trust,
5.75%, 1/25/37		28		27
Lehman Mortgage Trust,
5.50%, 11/25/35		10		9
6.50%, 9/25/37		37		28
				1,874
				2,546
Sovereign (18.6%)
Argentina (0.4%)
Argentine Republic Government International Bond,
7.50%, 4/22/26 (c)		1,430		1,617

	Face Amount (000)		Value (000)
Australia (0.3%)
Australia Government Bond,
3.25%, 4/21/25	AUD	1,300	$	1,102
Austria (0.2%)
Austria Government Bond,
1.20%, 10/20/25 (c)	EUR	500		626
Belgium (1.0%)
Belgium Government Bond,
0.80%, 6/22/25 (c)		2,900		3,488
Bermuda (0.1%)
Bermuda Government International Bond,
4.85%, 2/6/24 (c)	$	390		433
Brazil (1.1%)
Brazil Notas do Tesouro Nacional, Series F,
10.00%, 1/1/21 - 1/1/25	BRL	13,787		4,032
Canada (1.3%)
Canadian Government Bond,
1.50%, 6/1/23	CAD	3,025		2,419
3.25%, 6/1/21		2,600		2,227
				4,646
China (0.1%)
Sinopec Group Overseas Development 2015 Ltd.,
2.50%, 4/28/20 (c)	$	375		382
Colombia (0.2%)
Colombia Government International Bond,
4.50%, 1/28/26		600		664
France (1.8%)
France Government Bond OAT,
0.00%, 5/25/21	EUR	1,400		1,606
1.00%, 11/25/25		500		611
1.75%, 5/25/23		1,990		2,542
3.25%, 5/25/45		685		1,206
5.50%, 4/25/29		300		555
				6,520
Germany (0.4%)
Bundesrepublik Deutschland,
4.25%, 7/4/39		420		881
4.75%, 7/4/34		220		448
				1,329
Greece (0.3%)
Hellenic Republic Government Bond,
3.00%, 2/24/23 - 2/24/42 (g)		1,580		1,139
Hungary (0.3%)
Hungary Government International Bond,
5.38%, 3/25/24	$	250		291
5.75%, 11/22/23		800		944
				1,235
Indonesia (0.4%)
Indonesia Government International Bond,
5.88%, 1/15/24 (c)		1,090		1,288

The accompanying notes are an integral part of the financial statements.
11

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Face Amount (000)		Value (000)
Ireland (0.1%)
Ireland Government Bond,
5.40%, 3/13/25	EUR	200	$	322
Italy (0.9%)
Italy Buoni Poliennali Del Tesoro,
1.50%, 6/1/25		330		385
1.65%, 3/1/32 (c)		540		616
2.35%, 9/15/24 (c)		1,345		1,773
5.00%, 9/1/40		250		436
				3,210
Japan (5.6%)
Japan Finance Organization for Municipalities,
1.90%, 6/22/18	JPY	70,000		714
Japan Government Ten Year Bond,
0.10%, 6/20/26		146,000		1,468
0.50%, 9/20/24		327,000		3,405
1.10%, 3/20/21 - 6/20/21		370,000		3,878
1.70%, 6/20/18		300,000		3,060
Japan Government Thirty Year Bond,
1.70%, 6/20/33		347,000		4,270
2.00%, 9/20/40		239,000		3,221
				20,016
Korea, Republic of (0.3%)
Korea Development Bank (The),
3.88%, 5/4/17	$	400		406
4.63%, 11/16/21		630		719
				1,125
Mexico (0.2%)
Mexican Bonos,
6.50%, 6/10/21	MXN	10,000		532
Petroleos Mexicanos,
6.38%, 1/23/45	$	140		134
				666
Netherlands (0.3%)
Netherlands Government Bond,
0.25%, 7/15/25 (c)	EUR	800		928
New Zealand (0.2%)
New Zealand Government Bond,
4.50%, 4/15/27	NZD	800		704
5.50%, 4/15/23		200		176
				880
Peru (0.1%)
Peruvian Government International Bond,
4.13%, 8/25/27	$	340		390
Poland (0.7%)
Poland Government Bond,
2.50%, 7/25/26	PLN	9,100		2,299
4.00%, 10/25/23		600		171
				2,470
South Africa (0.1%)
South Africa Government Bond,
8.00%, 1/31/30	ZAR	3,800		255

	Face Amount (000)		Value (000)
Spain (0.5%)
Spain Government Bond,
1.15%, 7/30/20	EUR	290	$	341
2.15%, 10/31/25 (c)		390		489
Spain Government Inflation Linked Bond,
1.00%, 11/30/30 (c)		778		956
1.80%, 11/30/24 (c)		130		169
				1,955
United Kingdom (1.7%)
United Kingdom Gilt,
2.00%, 9/7/25	GBP	110		159
2.75%, 9/7/24		1,550		2,354
4.25%, 6/7/32 - 9/7/39		1,810		3,555
				6,068
				66,786
U.S. Treasury Securities (6.6%)
United States (6.6%)
U.S. Treasury Bonds,
2.50%, 2/15/45	$	630		651
3.88%, 8/15/40		2,800		3,654
U.S. Treasury Inflation Indexed Bonds,
0.25%, 1/15/25		3,048		3,107
0.63%, 1/15/26		14,142		14,881
U.S. Treasury Note,
1.38%, 1/31/21		1,520		1,537
				23,830
Total Fixed Income Securities (Cost $135,976)				141,737
	Shares
Common Stocks (56.0%)
Australia (2.0%)
AGL Energy Ltd.		4,451		65
Alumina Ltd.		30,244		34
Amcor Ltd.		11,036		128
AMP Ltd.		31,080		126
Arrium Ltd. (h)(i)		14,100		—	@
ASX Ltd.		1,539		57
Australia & New Zealand Banking Group Ltd.		31,497		669
BHP Billiton Ltd.		28,547		494
BlueScope Steel Ltd.		3,657		22
Brambles Ltd.		13,410		123
CIMIC Group Ltd.		1,366		30
Coca-Cola Amatil Ltd.		4,624		36
Cochlear Ltd.		499		54
Commonwealth Bank of Australia		12,195		678
Computershare Ltd.		4,195		33
Crown Resorts Ltd.		5,745		58
CSL Ltd.		4,783		393
CYBG PLC CDI (h)		6,450		22
Dexus Property Group REIT		7,020		49
DuluxGroup Ltd.		5,515		28
Fairfax Media Ltd.		32,187		23

The accompanying notes are an integral part of the financial statements.
12

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Shares		Value (000)
Australia (cont'd)
Fortescue Metals Group Ltd.		10,837	$	41
Goodman Group REIT		11,464		64
GPT Group REIT		17,813		69
Incitec Pivot Ltd.		14,433		31
Insurance Australia Group Ltd.		19,798		83
Iron Mountain, Inc. CDI		449		17
Lend Lease Group REIT		5,862		63
Macquarie Group Ltd.		2,760		174
Mirvac Group REIT		25,584		44
National Australia Bank Ltd.		26,739		573
Newcrest Mining Ltd.		4,209		70
Orica Ltd.		3,553		42
Origin Energy Ltd.		9,394		39
Orora Ltd.		11,036		27
QBE Insurance Group Ltd.		14,661		105
Rio Tinto Ltd.		3,744		149
Santos Ltd.		9,133		26
Scentre Group REIT		41,036		148
Shopping Centres Australasia Property Group REIT		2,465		4
Sonic Healthcare Ltd.		3,284		56
South32 Ltd.		20,867		40
South32 Ltd.		28,547		53
Star Entertainment Grp Ltd. (The)		7,295		34
Stockland REIT		26,970		98
Suncorp Group Ltd.		11,119		103
Sydney Airport		2,922		16
Tabcorp Holdings Ltd.		7,097		27
Telstra Corp., Ltd.		41,748		166
Transurban Group		12,301		107
Treasury Wine Estates Ltd.		7,395		63
Wesfarmers Ltd.		10,023		339
Westfield Corp. REIT		18,583		139
Westpac Banking Corp.		24,560		558
Woodside Petroleum Ltd.		5,328		117
Woolworths Ltd.		11,047		197
WorleyParsons Ltd.		1,584		10
				7,014
Austria (0.0%)
BUWOG AG (h)		183		5
Erste Group Bank AG (h)		2,494		74
Immofinanz AG (h)		3,664		8
Raiffeisen Bank International AG (h)		1,043		16
Voestalpine AG		1,329		46
				149
Belgium (0.4%)
Ageas		3,005		110
Anheuser-Busch InBev N.V.		6,748		886
Colruyt SA		905		50
Groupe Bruxelles Lambert SA		1,457		129
KBC Group N.V. (h)		5,265		307
Umicore SA		1,567		98
				1,580

	Shares		Value (000)
Canada (2.4%)
Agnico-Eagle Mines Ltd.		1,600	$	87
Agrium, Inc.		1,500		136
Bank of Montreal		5,100		334
Bank of Nova Scotia		8,800		466
Barrick Gold Corp.		9,400		166
BCE, Inc.		5,300		245
Blackberry Ltd. (h)		4,200		34
Bombardier, Inc. (h)		12,800		18
Brookfield Asset Management, Inc., Class A		8,250		290
Brookfield Business Partners LP		165		4
Cameco Corp.		4,100		35
Canadian Imperial Bank of Commerce		3,700		287
Canadian National Railway Co.		8,600		562
Canadian Natural Resources Ltd.		10,300		329
Canadian Pacific Railway Ltd.		1,600		244
Cenovus Energy, Inc.		7,100		102
Crescent Point Energy Corp.		2,100		28
Eldorado Gold Corp.		5,400		21
Enbridge, Inc.		8,200		360
Encana Corp.		7,600		79
Fairfax Financial Holdings Ltd.		300		176
First Quantum Minerals Ltd.		5,100		42
Fortis, Inc.		1,300		42
Goldcorp, Inc.		7,100		117
Great-West Lifeco, Inc.		4,100		101
Husky Energy, Inc.		2,655		33
IGM Financial, Inc.		1,800		49
Imperial Oil Ltd.		2,600		81
Intact Financial Corp.		1,500		108
Kinross Gold Corp. (h)		8,900		38
Kinross Gold Corp. (h)		1,200		5
Lightstream Resources Ltd. (h)		1,136		—	@
Loblaw Cos., Ltd.		673		35
Magna International, Inc.		5,200		223
Manulife Financial Corp.		18,100		255
National Bank of Canada		3,000		106
Pembina Pipeline Corp.		400		12
Penn West Petroleum Ltd.		3,700		7
Potash Corp. of Saskatchewan, Inc.		8,200		134
Power Corp. of Canada		4,100		87
Power Financial Corp.		3,400		79
PrairieSky Royalty Ltd.		206		4
Rogers Communications, Inc., Class B		3,800		161
Royal Bank of Canada		12,300		762
Shaw Communications, Inc., Class B		3,700		76
Silver Wheaton Corp.		3,500		95
SNC-Lavalin Group, Inc.		1,800		71
Sun Life Financial, Inc.		5,900		192
Suncor Energy, Inc.		14,856		412
Teck Resources Ltd., Class B		4,700		85
Thomson Reuters Corp.		3,700		153
Toronto-Dominion Bank (The)		16,200		719

The accompanying notes are an integral part of the financial statements.
13

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Shares		Value (000)
Canada (cont'd)
Touchstone Exploration, Inc. (h)		650	$	—	@
TransAlta Corp.		2,300		10
TransCanada Corp.		6,300		299
Valeant Pharmaceuticals International, Inc. (h)		300		7
Yamana Gold, Inc.		7,200		31
				8,634
Chile (0.0%)
Antofagasta PLC		2,484		17
China (0.1%)
Hanergy Thin Film Power Group Ltd. (d)(h)(i)(j)		42,000		—	@
Yum! Brands, Inc.		1,759		160
				160
Colombia (0.0%)
Millicom International Cellular SA SDR		1,326		69
Denmark (0.6%)
AP Moeller — Maersk A/S Series A		30		42
AP Moeller — Maersk A/S Series B		55		81
Carlsberg A/S Series B		98		9
Coloplast A/S Series B		120		9
Danske Bank A/S		6,044		177
DSV A/S		9,728		486
ISS A/S		6,325		263
Novo Nordisk A/S Series B		19,475		812
Novozymes A/S Series B		2,771		122
TDC A/S		537		3
Vestas Wind Systems A/S		3,486		288
				2,292
Finland (0.3%)
Fortum Oyj		6,094		98
Kone Oyj, Class B		5,074		258
Nokia Oyj		34,796		202
Nokian Renkaat Oyj		1,401		51
Sampo Oyj, Class A		3,582		159
UPM-Kymmene Oyj		11,663		246
				1,014
France (4.9%)
Accor SA		18,604		738
Aeroports de Paris (ADP)		1,177		117
Air Liquide SA		3,070		329
Alstom SA (h)		4,118		109
Atos SE		4,975		536
AXA SA		16,884		359
BNP Paribas SA		19,440		1,000
Bouygues SA		16,204		537
Bureau Veritas SA		2,324		50
Cap Gemini SA		11,078		1,085
Carrefour SA		5,540		143
CGG SA (h)		63		2
Christian Dior SE		710		127
Cie de Saint-Gobain		31,116		1,343

	Shares		Value (000)
Cie Generale des Etablissements Michelin		1,855	$	205
Credit Agricole SA		17,523		173
Danone SA		6,671		495
Edenred		1,823		43
Electricite de France SA		3,256		40
Engie SA		12,237		190
Essilor International SA		1,528		197
Eutelsat Communications SA		799		17
Groupe Eurotunnel SE		23,247		251
Hermes International		150		61
ICADE REIT		86		7
JCDecaux SA		651		21
Kering		1,357		273
L'Oreal SA		2,407		454
LVMH Moet Hennessy Louis Vuitton SE		2,297		392
Metropole Television SA		2,324		42
Natixis SA		8,382		39
Orange SA		19,419		304
Pernod Ricard SA		1,855		219
Peugeot SA (h)		78,588		1,200
Publicis Groupe SA		1,047		79
Renault SA		3,778		310
Rexel SA		14,839		227
Sanofi		11,589		883
SES SA		2,416		59
Societe Generale SA		13,749		475
Sodexo SA		1,223		146
Suez		4,193		69
Technip SA		933		57
Television Francaise 1		9,424		91
Thales SA		1,262		116
Total SA		20,957		993
Unibail-Rodamco SE REIT		1,616		436
Vallourec SA (h)		2,417		11
Veolia Environnement SA		5,613		129
Vinci SA		26,362		2,016
Vivendi SA		16,236		327
				17,522
Germany (3.3%)
Adidas AG		1,738		302
Allianz SE (Registered)		4,059		602
Axel Springer SE		168		9
BASF SE		10,277		879
Bayer AG (Registered)		6,754		678
Bayerische Motoren Werke AG		6,035		507
Bayerische Motoren Werke AG (Preference)		538		40
Beiersdorf AG		851		80
Commerzbank AG		13,376		86
Continental AG		533		112
Daimler AG (Registered)		15,553		1,096
Deutsche Bank AG (Registered) (h)		11,761		153
Deutsche Boerse AG (h)		9,005		729

The accompanying notes are an integral part of the financial statements.
14

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Shares		Value (000)
Germany (cont'd)
Deutsche Lufthansa AG (Registered)		59,071	$	657
Deutsche Post AG (Registered)		5,009		156
Deutsche Telekom AG (Registered)		25,997		436
E.ON SE		15,975		113
Esprit Holdings Ltd. (d)(h)		12,583		10
Fraport AG Frankfurt Airport Services Worldwide		2,300		126
Fresenius Medical Care AG & Co., KGaA		1,557		136
Fresenius SE & Co., KGaA		3,141		251
Henkel AG & Co., KGaA		1,420		165
Henkel AG & Co., KGaA (Preference)		2,044		278
Infineon Technologies AG		10,693		191
K&S AG (Registered)		1,306		25
Lanxess AG		827		51
Linde AG		1,359		231
Merck KGaA		1,048		113
Metro AG		1,062		32
Muenchener Rueckversicherungs AG (Registered)		1,719		321
Osram Licht AG		765		45
Porsche Automobil Holding SE (Preference)		2,264		116
ProSiebenSat.1 Media SE (Registered)		9,118		390
QIAGEN N.V. (h)		2,514		69
RWE AG (h)		3,402		59
SAP SE		9,219		839
Siemens AG (Registered)		7,650		895
Stroeer SE & Co. KGaA		1,518		66
Suedzucker AG		410		11
ThyssenKrupp AG		4,900		117
TUI AG		3,051		43
Uniper SE (h)		1,597		20
Volkswagen AG		607		88
Volkswagen AG (Preference)		3,234		425
				11,748
Greece (0.0%)
National Bank of Greece SA (h)		95		—	@
Hong Kong (0.9%)
AIA Group Ltd.		67,200		450
Bank of East Asia Ltd. (The)		18,617		76
BOC Hong Kong Holdings Ltd.		36,500		124
Cheung Kong Property Holdings Ltd.		28,364		209
CK Hutchison Holdings Ltd.		28,364		362
CLP Holdings Ltd.		19,000		197
Global Brands Group Holding Ltd. (h)		40,000		4
Hang Lung Group Ltd.		8,000		31
Hang Lung Properties Ltd.		22,000		50
Hang Seng Bank Ltd.		11,500		207
Henderson Land Development Co., Ltd.		17,901		107
Hong Kong & China Gas Co., Ltd.		63,774		121
Hong Kong Exchanges and Clearing Ltd.		11,421		301
Kerry Logistics Network Ltd.		3,500		5
Kerry Properties Ltd.		7,000		23
Link REIT		21,033		155

	Shares		Value (000)
MTR Corp., Ltd.		16,531	$	92
New World Development Co., Ltd.		43,980		58
Power Assets Holdings Ltd.		14,500		142
Sands China Ltd.		28,400		124
Sino Land Co., Ltd.		24,339		44
Sun Hung Kai Properties Ltd.		15,504		236
Swire Pacific Ltd., Class A		6,500		70
Swire Properties Ltd.		4,550		13
Wharf Holdings Ltd. (The)		13,200		97
Wheelock & Co., Ltd.		10,000		59
				3,357
Ireland (0.3%)
Bank of Ireland (h)		249,626		52
CRH PLC		16,297		545
DCC PLC		548		50
Ryanair Holdings PLC		40,764		563
				1,210
Italy (1.1%)
Assicurazioni Generali SpA		11,606		142
Atlantia SpA		31,904		810
Banco Popolare SC		2,037		5
Enel SpA		63,716		284
Eni SpA		22,322		322
Ferrari N.V.		2,197		114
Intesa Sanpaolo SpA		209,045		462
Leonardo-Finmeccanica SpA (h)		1,205		14
Luxottica Group SpA		1,123		54
Mediaset SpA		134,874		423
Mediobanca SpA		97,794		637
Prysmian SpA		1,210		32
Rizzoli Corriere Della Sera Mediagroup SpA (h)		677		1
Saipem SpA (h)		2,154		1
Snam SpA		20,778		115
Telecom Italia SpA (h)		155,330		119
Terna Rete Elettrica Nazionale SpA		9,469		49
UniCredit SpA		74,066		172
Unione di Banche Italiane SpA		13,067		30
				3,786
Japan (5.0%)
Advantest Corp.		1,200		16
Aeon Co., Ltd.		6,300		93
Aisin Seiki Co., Ltd.		2,100		96
Ajinomoto Co., Inc.		8,300		185
Asahi Glass Co., Ltd.		9,000		58
Asahi Group Holdings Ltd.		2,800		102
Asahi Kasei Corp.		14,000		112
Astellas Pharma, Inc.		14,400		225
Bridgestone Corp.		5,000		184
Canon, Inc.		7,900		229
Central Japan Railway Co.		1,300		222
Chiba Bank Ltd. (The)		8,000		45
Chubu Electric Power Co., Inc.		4,400		64

The accompanying notes are an integral part of the financial statements.
15

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Shares		Value (000)
Japan (cont'd)
Chugai Pharmaceutical Co., Ltd.		2,600	$	94
Chugoku Electric Power Co., Inc. (The)		2,000		25
Concordia Financial Group Ltd.		11,300		49
Dai Nippon Printing Co., Ltd.		6,000		59
Dai-ichi Life Insurance Co., Ltd. (The)		800		11
Daiichi Sankyo Co., Ltd.		5,100		122
Daikin Industries Ltd.		2,100		196
Daito Trust Construction Co., Ltd.		800		128
Daiwa House Industry Co., Ltd.		6,000		164
Daiwa Securities Group, Inc.		16,000		90
Denso Corp.		4,600		184
Dentsu, Inc.		1,700		86
East Japan Railway Co.		2,700		243
Eisai Co., Ltd.		2,100		131
Electric Power Development Co., Ltd.		1,400		34
FANUC Corp.		1,400		237
Fast Retailing Co., Ltd.		400		129
FUJIFILM Holdings Corp.		4,300		159
Fujitsu Ltd.		14,000		76
Hankyu Hanshin Holdings, Inc.		3,600		124
Hitachi Ltd.		36,000		168
Hokkaido Electric Power Co., Inc.		2,200		19
Hokuriku Electric Power Co.		2,000		24
Honda Motor Co., Ltd.		800		23
Honda Motor Co., Ltd. ADR		10,395		301
Hoya Corp.		3,200		128
Ibiden Co., Ltd.		1,100		15
Inpex Corp.		3,200		29
Isetan Mitsukoshi Holdings Ltd.		2,800		28
Isuzu Motors Ltd.		400		5
ITOCHU Corp.		11,700		147
Japan Real Estate Investment Corp. REIT		9		54
Japan Steel Works Ltd. (The)		400		9
Japan Tobacco, Inc.		8,700		355
JFE Holdings, Inc.		3,500		51
JGC Corp.		2,000		35
JSR Corp.		1,600		25
JX Holdings, Inc.		2,100		8
Kansai Electric Power Co., Inc. (The) (h)		3,700		34
Kao Corp.		4,500		253
Kawasaki Heavy Industries Ltd.		20,000		62
KDDI Corp.		17,000		523
Keikyu Corp.		5,000		52
Keio Corp.		5,000		44
Keyence Corp.		400		291
Kintetsu Group Holdings Co., Ltd.		22,000		92
Kirin Holdings Co., Ltd.		7,600		126
Kobe Steel Ltd. (h)		3,700		33
Komatsu Ltd.		7,400		170
Konica Minolta, Inc.		2,600		22
Kubota Corp.		9,800		148
Kuraray Co., Ltd.		2,600		39

	Shares		Value (000)
Kyocera Corp.		2,400	$	115
Kyushu Electric Power Co., Inc.		2,000		19
LIXIL Group Corp.		2,900		62
Makita Corp.		800		57
Marubeni Corp.		15,900		82
Mazda Motor Corp.		2,600		40
Mitsubishi Chemical Holdings Corp.		11,700		74
Mitsubishi Corp.		9,700		220
Mitsubishi Electric Corp.		14,000		179
Mitsubishi Estate Co., Ltd.		9,000		169
Mitsubishi Heavy Industries Ltd.		28,000		117
Mitsubishi Motors Corp.		4,800		22
Mitsui & Co., Ltd.		14,600		202
Mitsui Fudosan Co., Ltd.		7,000		149
Mitsui OSK Lines Ltd.		9,000		21
Mizuho Financial Group, Inc.		109,300		183
MS&AD Insurance Group Holdings, Inc.		3,000		84
Murata Manufacturing Co., Ltd.		1,700		222
NGK Insulators Ltd.		2,000		41
Nidec Corp.		1,700		156
Nikon Corp.		2,600		39
Nintendo Co., Ltd.		800		212
Nippon Building Fund, Inc. REIT		9		57
Nippon Electric Glass Co., Ltd.		3,000		16
Nippon Express Co., Ltd.		11,000		51
Nippon Steel Sumitomo Metal Corp.		6,000		123
Nippon Telegraph & Telephone Corp.		8,500		388
Nippon Yusen KK		18,000		34
Nissan Motor Co., Ltd.		18,100		177
Nitto Denko Corp.		1,300		84
Nomura Holdings, Inc.		27,300		122
NSK Ltd.		5,300		54
NTT Data Corp.		1,600		80
NTT DoCoMo, Inc.		11,100		281
Odakyu Electric Railway Co., Ltd.		4,500		100
Oji Holdings Corp.		7,000		28
Olympus Corp.		1,800		63
Omron Corp.		1,400		50
Ono Pharmaceutical Co., Ltd.		3,800		105
Oriental Land Co., Ltd.		300		18
ORIX Corp.		7,900		117
Osaka Gas Co., Ltd.		22,000		92
Otsuka Holdings Co., Ltd.		300		14
Panasonic Corp.		14,100		141
Rakuten, Inc.		7,600		99
Resona Holdings, Inc.		5,500		23
Ricoh Co., Ltd.		6,000		54
Rohm Co., Ltd.		600		32
Secom Co., Ltd.		1,600		119
Sekisui House Ltd.		6,000		102
Seven & I Holdings Co., Ltd.		6,300		298
Sharp Corp. (h)		8,000		11
Shikoku Electric Power Co., Inc.		2,900		29

The accompanying notes are an integral part of the financial statements.
16

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Shares		Value (000)
Japan (cont'd)
Shin-Etsu Chemical Co., Ltd.		2,500	$	175
Shionogi & Co., Ltd.		3,300		169
Shiseido Co., Ltd.		3,400		90
Shizuoka Bank Ltd. (The)		8,000		64
SMC Corp.		500		144
SoftBank Group Corp.		5,600		363
Sompo Japan Nipponkoa Holdings, Inc.		300		9
Sony Corp.		700		23
Sony Corp. ADR		6,835		227
Sumitomo Chemical Co., Ltd.		11,000		49
Sumitomo Corp.		8,800		98
Sumitomo Electric Industries Ltd.		12,500		177
Sumitomo Metal Mining Co., Ltd.		5,000		69
Sumitomo Mitsui Financial Group, Inc.		9,800		330
Sumitomo Mitsui Trust Holdings, Inc.		2,300		75
Sumitomo Realty & Development Co., Ltd.		5,000		130
Suzuki Motor Corp.		3,200		107
T&D Holdings, Inc.		4,400		50
Takeda Pharmaceutical Co., Ltd.		5,600		268
TDK Corp.		800		53
Terumo Corp.		3,500		134
Tobu Railway Co., Ltd.		17,000		87
Tohoku Electric Power Co., Inc.		3,500		46
Tokio Marine Holdings, Inc.		3,700		142
Tokyo Electric Power Co. Holdings Inc, (h)		7,200		31
Tokyo Electron Ltd.		1,100		97
Tokyo Gas Co., Ltd.		20,000		89
Tokyu Corp.		9,000		69
Toppan Printing Co., Ltd.		6,000		54
Toray Industries, Inc.		14,000		136
Toshiba Corp. (h)		32,000		107
Toyota Industries Corp.		1,900		88
Toyota Motor Corp.		20,600		1,195
Trend Micro, Inc.		900		31
Unicharm Corp.		4,100		106
West Japan Railway Co.		1,700		105
Yahoo! Japan Corp.		14,400		57
Yamada Denki Co., Ltd.		7,200		36
Yamato Holdings Co., Ltd.		5,000		116
				18,108
Mexico (0.0%)
Fresnillo PLC		1,382		33
Netherlands (1.2%)
ABN AMRO Group N.V. (c)		2,100		43
Akzo Nobel N.V.		4,136		280
ArcelorMittal (h)		12,177		74
ASML Holding N.V.		2,380		261
CNH Industrial N.V.		6,659		48
Fiat Chrysler Automobiles N.V.		18,785		119
Fugro N.V. CVA (h)		657		11
Heineken N.V.		3,516		309

	Shares		Value (000)
ING Groep N.V.		80,222	$	989
Koninklijke DSM N.V.		3,186		215
Koninklijke KPN N.V.		6,177		21
Koninklijke Philips N.V.		11,422		338
Koninklijke Vopak N.V.		1,006		53
PostNL N.V. (h)		4,654		21
Priceline Group, Inc. (The) (h)		238		350
Randstad Holding N.V.		13,264		604
TNT Express N.V. (h)		4,151		37
Unilever N.V. CVA		14,384		664
				4,437
Norway (0.3%)
Akastor ASA (h)		1,833		2
Aker Solutions ASA (h)		1,833		8
DNB ASA		11,838		155
Kvaerner ASA		1,677		2
Norsk Hydro ASA		13,781		59
Orkla ASA		10,248		106
REC Silicon ASA (h)		6,482		1
Seadrill Ltd. (h)		328		1
Statoil ASA		13,168		221
Subsea 7 SA (h)		3,127		34
Telenor ASA		16,272		280
Yara International ASA		2,039		68
				937
Poland (0.0%)
Jeronimo Martins SGPS SA		3,072		53
Portugal (0.0%)
Banco Espirito Santo SA (Registered) (h)(i)(j)		192,146		—
Galp Energia SGPS SA		2,866		39
Pharol SGPS SA (Registered)		11,841		3
				42
South Africa (0.1%)
Mondi PLC		2,267		48
SABMiller PLC		6,076		354
				402
Spain (1.0%)
Abertis Infraestructuras SA		4,633		72
ACS Actividades de Construccion y Servicios SA		1,316		40
Amadeus IT Group SA, Class A		2,024		101
Banco Bilbao Vizcaya Argentaria SA		107,614		651
Banco de Sabadell SA		65,418		84
Banco Popular Espanol SA		32,507		40
Banco Santander SA		219,205		969
Bankia SA		41,059		34
Bankinter SA		6,014		43
CaixaBank SA		33,792		85
Distribuidora Internacional de Alimentacion SA		6,935		43
Enagas SA		1,672		50
Ferrovial SA		2,579		55
Gas Natural SDG SA		2,230		46
Iberdrola SA		38,662		263

The accompanying notes are an integral part of the financial statements.
17

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Shares		Value (000)
Spain (cont'd)
Industria de Diseno Textil SA		10,358	$	384
Mediaset Espana Comunicacion SA		20,880		247
Red Electrica Corp., SA		4,824		104
Repsol SA		6,203		84
Telefonica SA		26,738		270
				3,665
Sweden (1.0%)
Assa Abloy AB, Class B		9,837		200
Atlas Copco AB, Class A		9,926		299
Atlas Copco AB, Class B		7,174		196
Electrolux AB, Class B		2,950		74
Hennes & Mauritz AB, Class B		10,362		292
Husqvarna AB, Class B		5,449		47
Investor AB, Class B		11,790		431
Modern Times Group MTG AB, Class B		443		11
Nordea Bank AB		26,050		258
Sandvik AB		15,296		168
Skandinaviska Enskilda Banken AB, Class A		14,182		142
Skanska AB, Class B		3,281		77
SKF AB, Class B		6,298		109
Svenska Cellulosa AB SCA, Class B		8,585		255
Svenska Handelsbanken AB, Class A		16,437		226
Swedbank AB, Class A		4,898		115
Swedish Match AB		4,201		154
Telefonaktiebolaget LM Ericsson, Class B		25,830		186
Telia Co AB		31,426		141
Volvo AB, Class B		8,272		94
				3,475
Switzerland (3.5%)
ABB Ltd. (Registered) (h)		37,474		841
Actelion Ltd. (Registered) (h)		1,056		183
Adecco Group AG (Registered)		16,474		928
Cie Financiere Richemont SA (Registered)		5,331		325
Coca-Cola HBC AG (h)		1,136		26
Credit Suisse Group AG (Registered) (h)		16,331		214
Geberit AG (Registered)		894		391
Givaudan SA (Registered)		99		201
Julius Baer Group Ltd. (h)		2,309		94
Kuehne & Nagel International AG (Registered)		732		106
LafargeHolcim Ltd. (Registered) (h)		343		18
LafargeHolcim Ltd. (Registered) (h)		4,228		228
Lonza Group AG (Registered) (h)		523		100
Nestle SA (Registered)		38,089		3,001
Novartis AG (Registered)		23,572		1,854
Roche Holding AG (Genusschein)		6,415		1,589
SGS SA (Registered)		60		134
Sonova Holding AG (Registered)		957		135
Swatch Group AG (The)		353		100
Swiss Re AG		1,336		121
Swisscom AG (Registered)		745		354
Syngenta AG (Registered)		914		400

	Shares		Value (000)
Transocean Ltd. (h)		3,245	$	34
UBS Group AG (Registered)		30,443		413
Zurich Insurance Group AG (h)		2,528		651
				12,441
United Arab Emirates (0.0%)
Mediclinic International PLC		2,256		27
United Kingdom (4.4%)
3i Group PLC		5,910		50
Aberdeen Asset Management PLC		5,530		23
Admiral Group PLC		1,303		35
Aggreko PLC		1,584		20
Anglo American PLC (h)		8,504		107
Ashtead Group PLC		3,127		51
Associated British Foods PLC		2,284		77
AstraZeneca PLC		7,819		506
Auto Trader Group PLC (c)		6,244		33
Aviva PLC		24,622		141
Babcock International Group PLC		1,542		21
BAE Systems PLC		19,375		131
Barclays PLC		103,082		225
Barratt Developments PLC		6,174		40
Berkeley Group Holdings PLC		799		27
BHP Billiton PLC		12,962		195
BP PLC		114,221		665
British American Tobacco PLC		11,552		739
British Land Co., PLC REIT		6,046		50
BT Group PLC		52,122		263
Bunzl PLC		2,063		61
Burberry Group PLC		2,739		49
Capita PLC		4,106		36
Carnival PLC		1,180		58
Centrica PLC		33,666		100
Cobham PLC		10,431		23
Compass Group PLC		10,247		199
Croda International PLC		814		37
Diageo PLC		15,437		443
Direct Line Insurance Group PLC		8,358		39
Dixons Carphone PLC		6,003		29
easyJet PLC		39,203		512
Experian PLC		5,973		120
G4S PLC		9,585		28
GKN PLC		10,593		44
GlaxoSmithKline PLC		30,162		643
Glencore PLC (h)		73,910		203
Hammerson PLC REIT		4,859		37
Hargreaves Lansdown PLC		1,560		26
Hikma Pharmaceuticals PLC		884		23
HSBC Holdings PLC		120,820		907
ICAP PLC		3,395		20
Imperial Brands PLC		6,007		310
Inmarsat PLC		2,806		26
InterContinental Hotels Group PLC		1,160		48

The accompanying notes are an integral part of the financial statements.
18

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Shares		Value (000)
United Kingdom (cont'd)
International Consolidated Airlines Group SA		5,222	$	27
International Consolidated Airlines Group SA		298,646		1,546
Intertek Group PLC		1,003		45
Intu Properties PLC REIT		5,786		22
Investec PLC		3,807		23
ITV PLC		22,190		54
J Sainsbury PLC		8,399		27
Johnson Matthey PLC		1,189		51
Kingfisher PLC		14,172		69
Land Securities Group PLC REIT		4,898		67
Legal & General Group PLC		36,205		103
Liberty Global PLC LiLAC, Class A (h)		251		7
Liberty Global PLC LiLAC Series C (h)		630		18
Lloyds Banking Group PLC		397,262		281
London Stock Exchange Group PLC		1,917		70
Marks & Spencer Group PLC		10,173		44
Meggitt PLC		4,791		28
Merlin Entertainments PLC (c)		4,353		25
National Grid PLC		23,220		328
Next PLC		890		55
Old Mutual PLC		29,605		78
Pearson PLC		5,042		49
Persimmon PLC		1,880		44
Petrofac Ltd.		1,629		19
Provident Financial PLC		884		35
Prudential PLC		15,774		280
Randgold Resources Ltd.		589		59
Reckitt Benckiser Group PLC		3,954		373
RELX PLC		6,883		131
Rio Tinto PLC		7,533		251
Rolls-Royce Holdings PLC (h)		11,289		105
Royal Bank of Scotland Group PLC (h)		21,188		49
Royal Dutch Shell PLC, Class A		26,097		648
Royal Dutch Shell PLC, Class B		23,234		603
Royal Mail PLC		5,509		35
RSA Insurance Group PLC		6,182		44
Sage Group PLC (The)		6,619		63
Schroders PLC		828		29
Segro PLC REIT		4,725		28
Severn Trent PLC		1,454		47
Shire PLC		5,483		354
Shire PLC ADR		320		62
Sky PLC		6,356		74
Smith & Nephew PLC		5,518		89
Smiths Group PLC		2,488		47
SSE PLC		6,284		127
St. James's Place PLC		3,179		39
Standard Chartered PLC (h)		19,817		161
Standard Life PLC		11,912		53
Tate & Lyle PLC		2,921		28
Taylor Wimpey PLC		19,983		40
Tesco PLC (h)		49,850		118

	Shares		Value (000)
Travis Perkins PLC		1,534	$	31
Unilever PLC		7,963		377
United Utilities Group PLC		4,213		55
Vodafone Group PLC		163,272		468
Weir Group PLC (The)		1,326		29
Whitbread PLC		1,145		58
William Hill PLC		5,408		21
WM Morrison Supermarkets PLC		13,647		38
Wolseley PLC		1,589		89
Worldpay Group PLC (c)		8,630		33
WPP PLC		7,968		187
				15,858
United States (23.2%)
3M Co.		1,011		178
Abbott Laboratories		3,082		130
AbbVie, Inc.		3,082		194
Abercrombie & Fitch Co., Class A		229		4
Accenture PLC, Class A		1,985		243
ACCO Brands Corp. (h)		104		1
Adobe Systems, Inc. (h)		2,013		218
Advance Auto Parts, Inc.		229		34
Advanced Micro Devices, Inc. (h)		1,860		13
AES Corp.		473		6
Aetna, Inc.		1,446		167
Affiliated Managers Group, Inc. (h)		200		29
Aflac, Inc.		281		20
Agilent Technologies, Inc.		1,099		52
Air Products & Chemicals, Inc.		257		39
Akamai Technologies, Inc. (h)		762		40
Alcoa, Inc.		2,030		21
Alexandria Real Estate Equities, Inc. REIT		900		98
Alexion Pharmaceuticals, Inc. (h)		751		92
Allegheny Technologies, Inc.		415		7
Allegion PLC		232		16
Allergan PLC (h)		2,249		518
Allstate Corp. (The)		423		29
Alphabet, Inc., Class A (h)		913		734
Alphabet, Inc., Class C (h)		917		713
Altria Group, Inc.		4,966		314
Amazon.com, Inc. (h)		910		762
AMC Networks, Inc., Class A (h)		21		1
Ameren Corp.		1,202		59
American Airlines Group, Inc.		14,362		526
American Capital Agency Corp. REIT		4,500		88
American Electric Power Co., Inc.		2,224		143
American Express Co.		4,351		279
American Tower Corp. REIT		7,520		852
Ameriprise Financial, Inc.		1,639		164
AmerisourceBergen Corp.		1,831		148
AMETEK, Inc.		476		23
Amgen, Inc.		2,897		483
Amphenol Corp., Class A		292		19

The accompanying notes are an integral part of the financial statements.
19

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Shares		Value (000)
United States (cont'd)
Anadarko Petroleum Corp.		1,521	$	96
Analog Devices, Inc.		2,107		136
Annaly Capital Management, Inc. REIT		13,278		139
Anthem, Inc.		917		115
Aon PLC		200		22
Apache Corp.		1,474		94
Apollo Education Group, Inc., Class A (h)		416		3
Apple, Inc.		27,673		3,128
Applied Materials, Inc.		3,859		116
Archer-Daniels-Midland Co.		1,623		68
AT&T, Inc.		22,963		933
Automatic Data Processing, Inc.		910		80
AutoZone, Inc. (h)		237		182
AvalonBay Communities, Inc. REIT		807		144
Avery Dennison Corp.		888		69
Avon Products, Inc.		3,795		21
Baker Hughes, Inc.		2,055		104
Ball Corp.		479		39
Bank of America Corp.		73,880		1,156
Bank of New York Mellon Corp. (The)		8,564		342
Baxter International, Inc.		2,160		103
BB&T Corp.		5,570		210
Becton Dickinson and Co.		1,042		187
Bed Bath & Beyond, Inc.		820		35
Berkshire Hathaway, Inc., Class B (h)		5,834		843
Best Buy Co., Inc.		786		30
Biogen, Inc. (h)		864		270
Blackhawk Network Holdings, Inc. (h)		53		2
BlackRock, Inc.		947		343
Boeing Co. (The)		1,779		234
Boston Properties, Inc. REIT		2,766		377
Boston Scientific Corp. (h)		5,667		135
Bristol-Myers Squibb Co.		11,619		626
Brixmor Property Group, Inc. REIT		2,800		78
Broadcom Ltd.		909		157
Brookfield Property Partners LP		2,480		57
Brown-Forman Corp., Class B		62		3
Bunge Ltd.		426		25
C.H. Robinson Worldwide, Inc.		687		48
CA, Inc.		995		33
CalAtlantic Group, Inc.		2,600		87
California Resources Corp.		221		3
Campbell Soup Co.		222		12
Capital One Financial Corp.		3,437		247
Cardinal Health, Inc.		1,701		132
Care Capital Properties, Inc. REIT		161		5
CarMax, Inc. (h)		457		24
Carnival Corp.		1,129		55
Caterpillar, Inc.		2,307		205
CBRE Group, Inc., Class A (h)		6,969		195
CBS Corp., Class B		3,071		168
CDK Global, Inc.		370		21

	Shares		Value (000)
Celanese Corp. Series A		220	$	15
Celgene Corp. (h)		2,812		294
CenterPoint Energy, Inc.		2,396		56
CenturyLink, Inc.		1,970		54
Cerner Corp. (h)		1,132		70
CF Industries Holdings, Inc.		1,660		40
Charles Schwab Corp. (The)		6,973		220
Charter Communications, Inc. (h)		796		215
Chemours Co. (The)		294		5
Chesapeake Energy Corp. (h)		2,464		15
Chevron Corp.		4,895		504
Chipotle Mexican Grill, Inc. (h)		223		94
Chubb Ltd.		158		20
Cigna Corp.		1,186		155
Cintas Corp.		754		85
Cisco Systems, Inc.		22,272		706
CIT Group, Inc.		895		32
Citigroup, Inc.		15,962		754
Citizens Financial Group, Inc.		1,450		36
Citrix Systems, Inc. (h)		909		77
Cliffs Natural Resources, Inc. (h)		437		3
Clorox Co. (The)		719		90
CME Group, Inc.		1,211		127
Coach, Inc.		893		33
Coca-Cola Co.		15,151		641
Coca-Cola European Partners PLC		945		38
Cognizant Technology Solutions Corp., Class A (h)		2,808		134
Colgate-Palmolive Co.		4,554		338
Comcast Corp., Class A		8,419		559
Comerica, Inc.		672		32
ConAgra Foods, Inc.		1,543		73
Concho Resources, Inc. (h)		360		49
ConocoPhillips		3,685		160
CONSOL Energy, Inc.		909		17
Consolidated Edison, Inc.		1,106		83
Constellation Brands, Inc., Class A		233		39
Corning, Inc.		2,304		54
Costco Wholesale Corp.		2,931		447
CR Bard, Inc.		431		97
Crimson Wine Group Ltd. (h)		181		2
Crown Castle International Corp. REIT		5,796		546
Crown Holdings, Inc. (h)		380		22
CST Brands, Inc.		219		11
CSX Corp.		3,358		102
Cummins, Inc.		961		123
CVS Health Corp.		821		73
D.R. Horton, Inc.		8,050		243
Danaher Corp.		397		31
Darden Restaurants, Inc.		404		25
DaVita, Inc. (h)		752		50
Deere & Co.		1,518		130

The accompanying notes are an integral part of the financial statements.
20

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Shares		Value (000)
United States (cont'd)
Dell Technologies, Inc. — VMware, Inc., Class V (h)		952	$	46
Delta Air Lines, Inc.		19,543		769
Deltic Timber Corp.		250		17
Denbury Resources, Inc.		504		2
Devon Energy Corp.		1,142		50
DeVry Education Group, Inc.		21		—	@
Diamond Offshore Drilling, Inc.		43		1
Digital Realty Trust, Inc. REIT		2,000		194
Discover Financial Services		2,989		169
Discovery Communications, Inc., Class A (h)		882		24
Discovery Communications, Inc., Class C (h)		2,088		55
Dollar General Corp.		186		13
Dollar Tree, Inc. (h)		433		34
Dominion Resources, Inc.		2,903		216
Dover Corp.		226		17
Dow Chemical Co. (The)		1,100		57
Dr. Pepper Snapple Group, Inc.		471		43
DTE Energy Co.		830		78
Duke Energy Corp.		2,282		183
Duke Realty Corp. REIT		4,500		123
Dun & Bradstreet Corp. (The)		406		55
E*Trade Financial Corp. (h)		800		23
Eagle Materials, Inc.		1,000		77
Eastman Chemical Co.		262		18
Eaton Corp., PLC		1,168		77
eBay, Inc. (h)		3,967		131
Ecolab, Inc.		808		98
Edison International		1,987		144
Edwards Lifesciences Corp. (h)		342		41
EI du Pont de Nemours & Co.		912		61
Eli Lilly & Co.		6,453		518
Emerson Electric Co.		2,385		130
Endo International PLC (h)		800		16
Engility Holdings, Inc. (h)		18		1
Entergy Corp.		750		58
EOG Resources, Inc.		2,192		212
EQT Corp.		419		30
Equifax, Inc.		801		108
Equinix, Inc. REIT		800		288
Equity Residential REIT		1,533		99
ESC Seventy Seven (j)		275		—
Estee Lauder Cos., Inc. (The), Class A		1,539		136
Exelon Corp.		3,750		125
Expedia, Inc.		232		27
Expeditors International of Washington, Inc.		436		22
Express Scripts Holding Co. (h)		3,376		238
Extra Space Storage, Inc. REIT		1,600		127
Exxon Mobil Corp.		12,266		1,071
Fastenal Co.		911		38
Federal Realty Investment Trust REIT		900		139
FedEx Corp.		954		167

	Shares		Value (000)
Fidelity National Information Services, Inc.		111	$	9
Fifth Third Bancorp		6,631		136
First American Financial Corp.		2,400		94
First Solar, Inc. (h)		275		11
FirstEnergy Corp.		1,736		57
Fiserv, Inc. (h)		776		77
Flowserve Corp.		460		22
Fluor Corp.		406		21
FMC Corp.		442		21
FMC Technologies, Inc. (h)		1,281		38
Ford Motor Co.		4,959		60
Fortive Corp.		198		10
Four Corners Property Trust, Inc. REIT		274		6
Franklin Resources, Inc.		2,828		101
Freeport-McMoRan, Inc.		1,460		16
Frontier Communications Corp.		4,687		19
GameStop Corp., Class A		416		11
Gannett Co., Inc.		116		1
Gap, Inc. (The)		836		19
General Dynamics Corp.		701		109
General Electric Co.		10,958		325
General Growth Properties, Inc. REIT		8,306		229
General Mills, Inc.		2,484		159
Genuine Parts Co.		111		11
Genworth Financial, Inc., Class A (h)		10,700		53
Gilead Sciences, Inc.		4,530		358
Goldman Sachs Group, Inc. (The)		3,472		560
Grifols SA		1,898		41
Grifols SA, (Preference) Class B		252		4
H&R Block, Inc.		1,797		42
Halliburton Co.		3,478		156
Halyard Health, Inc. (h)		335		12
Harman International Industries, Inc.		43		4
Harris Corp.		23		2
Hartford Financial Services Group, Inc. (The)		228		10
Hasbro, Inc.		176		14
HCP, Inc. REIT		7,026		267
Helmerich & Payne, Inc.		440		30
Henry Schein, Inc. (h)		360		59
Hershey Co. (The)		428		41
Hess Corp.		779		42
Hewlett Packard Enterprise Co.		5,676		129
Hologic, Inc. (h)		836		32
Home Depot, Inc.		691		89
Honeywell International, Inc.		2,440		284
Host Hotels & Resorts, Inc. REIT		14,251		222
HP, Inc.		5,676		88
Humana, Inc.		384		68
Huntington Bancshares, Inc.		2,730		27
Huntington Ingalls Industries, Inc.		59		9
IHS Markit Ltd. (h)		1,607		60
Illinois Tool Works, Inc.		1,184		142
Illumina, Inc. (h)		422		77

The accompanying notes are an integral part of the financial statements.
21

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Shares		Value (000)
United States (cont'd)
IMI PLC		1,678	$	23
Ingersoll-Rand PLC		587		40
Ingevity Corp. (h)		30		1
Intel Corp.		9,646		364
Intercontinental Exchange, Inc.		758		204
International Business Machines Corp.		3,971		631
International Flavors & Fragrances, Inc.		233		33
International Game Technology PLC		399		10
International Paper Co.		410		20
Interpublic Group of Cos., Inc. (The)		2,511		56
Interval Leisure Group, Inc.		199		3
Intuit, Inc.		1,602		176
Intuitive Surgical, Inc. (h)		415		301
Invesco Ltd.		3,291		103
Iron Mountain, Inc. REIT		4,678		176
ITT, Inc.		219		8
Jabil Circuit, Inc.		222		5
Jacobs Engineering Group, Inc. (h)		511		26
Janus Capital Group, Inc.		111		2
JB Hunt Transport Services, Inc.		228		18
JC Penney Co., Inc. (h)		222		2
JetBlue Airways Corp. (h)		8,116		140
JM Smucker Co. (The)		459		62
Johnson & Johnson		19,198		2,268
Johnson Controls International PLC		1,616		75
Jones Lang LaSalle, Inc.		700		80
Joy Global, Inc.		231		6
JPMorgan Chase & Co.		30,407		2,025
Juniper Networks, Inc.		2,911		70
KB Home		1,800		29
KBR, Inc.		562		8
Kellogg Co.		960		74
KeyCorp		8,435		103
Keysight Technologies, Inc. (h)		649		21
Kimberly-Clark Corp.		2,007		253
Kimco Realty Corp. REIT		6,739		195
KLA-Tencor Corp.		749		52
Knowles Corp. (h)		113		2
Kohl's Corp.		989		43
Koninklijke Ahold Delhaize N.V.		25,444		580
Kraft Heinz Co. (The)		1,535		137
Kroger Co. (The)		6,650		197
L Brands, Inc.		1,051		74
L-3 Communications Holdings, Inc.		111		17
Laboratory Corp. of America Holdings (h)		429		59
Lam Research Corp.		422		40
Las Vegas Sands Corp.		955		55
Legg Mason, Inc.		1,154		39
Lennar Corp., Class A		4,450		188
Leucadia National Corp.		2,132		41
Lexmark International, Inc., Class A		111		4
Li & Fung Ltd. (d)		40,000		21

	Shares		Value (000)
Liberty Global PLC, Class A (h)		1,161	$	40
Liberty Global PLC Series C (h)		2,889		95
Liberty Property Trust REIT		2,409		97
Linear Technology Corp.		939		56
Lockheed Martin Corp.		443		106
Loews Corp.		366		15
Louisiana-Pacific Corp. (h)		3,050		57
Lowe's Cos., Inc.		3,233		233
LyondellBasell Industries N.V., Class A		414		33
M&T Bank Corp.		1,042		121
M/I Homes, Inc. (h)		450		11
Macerich Co. (The) REIT		1,867		151
Macy's, Inc.		173		6
Mallinckrodt PLC (h)		724		51
Manpowergroup, Inc.		779		56
Marathon Oil Corp.		1,965		31
Marathon Petroleum Corp.		2,046		83
Marriott International, Inc., Class A		1,336		90
Marriott Vacations Worldwide Corp.		194		14
Marsh & McLennan Cos., Inc.		366		25
Martin Marietta Materials, Inc.		1,400		251
Marvell Technology Group Ltd.		1,529		20
Masco Corp.		7,200		247
Mastercard, Inc., Class A		4,920		501
Mattel, Inc.		805		24
Maxim Integrated Products, Inc.		910		36
McDonald's Corp.		2,682		309
McKesson Corp.		981		164
MDC Holdings, Inc.		1,050		27
Mead Johnson Nutrition Co.		873		69
Medtronic PLC		4,592		397
Merck & Co., Inc.		19,669		1,228
Meritage Homes Corp. (h)		850		29
MetLife, Inc.		430		19
MGIC Investment Corp. (h)		7,400		59
MGM Resorts International (h)		1,254		33
Microchip Technology, Inc.		483		30
Micron Technology, Inc. (h)		2,786		50
Microsoft Corp.		19,920		1,147
Mohawk Industries, Inc. (h)		1,600		321
Molson Coors Brewing Co., Class B		747		82
Mondelez International, Inc., Class A		4,218		185
Monsanto Co.		1,486		152
Moody's Corp.		1,165		126
Mosaic Co. (The)		848		21
Motorola Solutions, Inc.		749		57
Murphy Oil Corp.		474		14
Murphy USA, Inc. (h)		228		16
Mylan N.V. (h)		2,641		101
NASDAQ, Inc.		1,742		118
National Oilwell Varco, Inc.		2,139		79
Navient Corp.		3,730		54
NetApp, Inc.		1,776		64

The accompanying notes are an integral part of the financial statements.
22

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Shares		Value (000)
United States (cont'd)
Netflix, Inc. (h)		915	$	90
NetScout Systems, Inc. (h)		3,693		108
New York Community Bancorp, Inc.		2,201		31
Newfield Exploration Co. (h)		416		18
Newmont Mining Corp.		1,481		58
News Corp., Class A		2,051		29
News Corp., Class B		405		6
NextEra Energy, Inc.		1,567		192
NIKE, Inc., Class B		3,312		174
NiSource, Inc.		64		2
Noble Corp., PLC		431		3
Noble Energy, Inc.		1,490		53
Nordstrom, Inc.		210		11
Norfolk Southern Corp.		1,990		193
Northern Trust Corp.		633		43
Northrop Grumman Corp.		409		88
NOW, Inc. (h)		507		11
Nucor Corp.		426		21
NVIDIA Corp.		1,816		124
NVR, Inc. (h)		80		131
O'Reilly Automotive, Inc. (h)		593		166
Occidental Petroleum Corp.		3,737		272
Old Republic International Corp.		5,650		100
Omnicom Group, Inc.		1,081		92
ONE Gas, Inc.		422		26
ONEOK, Inc.		1,470		76
Oracle Corp.		12,281		482
Owens Corning		2,450		131
Owens-Illinois, Inc. (h)		242		4
PACCAR, Inc.		1,526		90
Paragon Offshore PLC (h)		303		—	@
Patterson Cos., Inc.		176		8
Paychex, Inc.		893		52
PayPal Holdings, Inc. (h)		3,967		163
Peabody Energy Corp. (h)		168		—	@
Pentair PLC		189		12
People's United Financial, Inc.		1,197		19
PepsiCo, Inc.		3,657		398
Perrigo Co., PLC		821		76
Pfizer, Inc.		41,259		1,397
PG&E Corp.		1,697		104
Philip Morris International, Inc.		4,250		413
Phillips 66		2,053		165
Pioneer Natural Resources Co.		582		108
Pitney Bowes, Inc.		1,481		27
PNC Financial Services Group, Inc. (The)		3,509		316
PPG Industries, Inc.		324		33
PPL Corp.		2,202		76
Praxair, Inc.		869		105
Procter & Gamble Co. (The)		10,438		937
Progressive Corp. (The)		239		8
ProLogis, Inc. REIT		8,949		479

	Shares		Value (000)
Prudential Financial, Inc.		200	$	16
Public Service Enterprise Group, Inc.		2,224		93
Public Storage REIT		3,466		773
Pulte Group, Inc.		7,450		149
QEP Resources, Inc.		723		14
QUALCOMM, Inc.		6,536		448
Quest Diagnostics, Inc.		530		45
Radian Group, Inc.		4,650		63
Ralph Lauren Corp.		47		5
Range Resources Corp.		747		29
Rayonier Advanced Materials, Inc.		175		2
Rayonier, Inc. REIT		405		11
Raytheon Co.		534		73
Realogy Holdings Corp.		2,000		52
Realty Income Corp. REIT		3,300		221
Regency Centers Corp. REIT		1,531		119
Regions Financial Corp.		11,109		110
Republic Services, Inc.		1,538		78
Reynolds American, Inc.		3,692		174
Robert Half International, Inc.		900		34
Rockwell Automation, Inc.		902		110
Rockwell Collins, Inc.		402		34
Roper Technologies, Inc.		236		43
Ross Stores, Inc.		1,490		96
Royal Caribbean Cruises Ltd.		918		69
RR Donnelley & Sons Co.		1,494		23
S&P Global, Inc.		2,395		303
Salesforce.com, Inc. (h)		2,226		159
Schlumberger Ltd.		6,209		488
Scotts Miracle-Gro Co. (The), Class A		1,250		104
Scripps Networks Interactive, Inc., Class A		461		29
Sealed Air Corp.		267		12
Sempra Energy		1,123		120
Sherwin-Williams Co. (The)		61		17
Simon Property Group, Inc. REIT		6,448		1,335
Skyline Corp. (h)		200		3
SL Green Realty Corp. REIT		1,300		141
SLM Corp. (h)		2,730		20
Southern Co. (The)		3,470		178
Southwest Airlines Co.		16,689		649
Southwestern Energy Co. (h)		1,722		24
Spectra Energy Corp.		2,242		96
Sprint Corp. (h)		11,934		79
St. Jude Medical, Inc.		1,606		128
Stanley Black & Decker, Inc.		238		29
Staples, Inc.		2,918		25
Starbucks Corp.		4,734		256
State Street Corp.		2,748		191
Stericycle, Inc. (h)		397		32
Stewart Information Services Corp.		450		20
Stryker Corp.		1,447		168
SunTrust Banks, Inc.		3,817		167
Symantec Corp.		3,312		83

The accompanying notes are an integral part of the financial statements.
23

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Shares		Value (000)
United States (cont'd)
Synchrony Financial		2,450	$	69
Sysco Corp.		3,552		174
T-Mobile US, Inc. (h)		116		5
T. Rowe Price Group, Inc.		2,411		160
Talen Energy Corp. (h)		344		5
Target Corp.		1,198		82
TE Connectivity Ltd.		1,500		97
TEGNA, Inc.		233		5
Tenaris SA		4,172		59
Tenet Healthcare Corp. (h)		131		3
Texas Instruments, Inc.		5,675		398
Textron, Inc.		962		38
Thermo Fisher Scientific, Inc.		1,504		239
Tiffany & Co.		241		18
Time Warner, Inc.		3,359		267
Time, Inc.		431		6
TJX Cos., Inc. (The)		2,180		163
Toll Brothers, Inc. (h)		3,600		107
Travelers Cos., Inc. (The)		408		47
TripAdvisor, Inc. (h)		232		15
Twenty-First Century Fox, Inc., Class A		7,695		186
Twenty-First Century Fox, Inc., Class B		1,682		42
Tyson Foods, Inc., Class A		1,268		95
Ultra Petroleum Corp. (h)		670		3
Union Pacific Corp.		2,210		216
United Continental Holdings, Inc. (h)		8,356		438
United Parcel Service, Inc., Class B		1,880		206
United States Steel Corp.		421		8
United Technologies Corp.		1,473		150
UnitedHealth Group, Inc.		2,522		353
Universal Forest Products, Inc.		400		39
Urban Edge Properties REIT		154		4
Urban Outfitters, Inc. (h)		186		6
US Bancorp		11,903		511
Valero Energy Corp.		1,931		102
Varian Medical Systems, Inc. (h)		497		49
Vectrus, Inc. (h)		12		—	@
Ventas, Inc. REIT		4,927		348
VEREIT, Inc. REIT		11,300		117
Verisk Analytics, Inc. (h)		928		75
Veritiv Corp. (h)		15		1
Verizon Communications, Inc.		23,100		1,201
Vertex Pharmaceuticals, Inc. (h)		422		37
VF Corp.		1,222		68
Viacom, Inc., Class B		2,023		77
Visa, Inc., Class A		6,358		526
Vornado Realty Trust REIT		2,309		234
Vulcan Materials Co.		2,850		324
Wal-Mart Stores, Inc.		10,851		783
Walgreens Boots Alliance, Inc.		5,368		433
Walt Disney Co. (The)		5,284		491
Washington Prime Group, Inc. REIT		1,274		16

	Shares		Value (000)
Waste Management, Inc.		1,989	$	127
Waters Corp. (h)		221		35
Watsco, Inc.		800		113
Weatherford International PLC (h)		2,296		13
WEC Energy Group, Inc.		1,550		93
Wells Fargo & Co.		33,617		1,489
Welltower, Inc. REIT		5,097		381
Western Digital Corp.		357		21
Western Union Co. (The)		2,949		61
WestRock Co.		180		9
Weyerhaeuser Co. REIT		12,119		387
Whole Foods Market, Inc.		2,186		62
Williams Cos., Inc. (The)		4,031		124
WPX Energy, Inc. (h)		1,965		26
WW Grainger, Inc.		368		83
Wyndham Worldwide Corp.		208		14
Wynn Resorts Ltd.		420		41
Xcel Energy, Inc.		2,156		89
Xerox Corp.		2,936		30
Xilinx, Inc.		948		52
Xylem, Inc.		978		51
Yahoo!, Inc. (h)		3,349		144
Zimmer Biomet Holdings, Inc.		977		127
Zions Bancorporation		822		25
Zoetis, Inc.		6,694		348
				83,126
Total Common Stocks (Cost $167,443)				201,156
Investment Companies (0.1%)
United States (0.1%)
iShares MSCI Emerging Markets Index Fund		8,000		299
Morgan Stanley Institutional Fund, Inc. — Emerging Markets Portfolio (See Note G)		4,949		113
Total Investment Companies (Cost $500)				412
	No. of Rights
Rights (0.0%)
United States (0.0%)
Safeway Casa Ley CVR (h)		577		1
Safeway PDC, LLC CVR (h)		577		—	@
Total Rights (Cost $1)				1
	No. of Warrants
Warrants (0.0%)
France (0.0%)
Peugeot SA, expires 4/29/17 (h)		1,221		4
United States (0.0%)
Seventy Seven Energy, Inc., expires 8/1/21 (h)(j)		13		—
Seventy Seven Energy, Inc., expires 8/1/23 (h)(j)		15		—
				—
Total Warrants (Cost $2)				4

The accompanying notes are an integral part of the financial statements.
24

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Strategist Portfolio

	Notional Amount (000)		Value (000)
Call Option Purchased (0.1%)
United States (0.1%)
United States Oil Fund LP December 2016 @ $11.50, Goldman Sachs & Co. (k) (Cost $217)	$	557	$	290
	Shares
Short-Term Investments (3.9%)
Investment Company (1.7%)
Morgan Stanley Institutional Liquidity Funds — Government Portfolio — Institutional Class (See Note G) (Cost $5,955)		5,955,495		5,955
	Face Amount (000)
Sovereign (0.5%)
Argentina (0.5%)
Letras del Banco Central de la Republica Argentina,
25.00%, 1/11/17 - 1/25/17	ARS	18,774		1,139
26.00%, 1/11/17		1,530		93
26.25%, 1/11/17 - 1/18/17		6,390		389
Total Sovereign (Cost $1,701)				1,621
U.S. Treasury Securities (1.7%)
U.S. Treasury Note,
0.63%, 12/31/16	$	2,000		2,002
U.S. Treasury Bill,
0.41%, 3/23/17 (l)(m)		3,950		3,942
Total U.S. Treasury Securities (Cost $5,944)				5,944
Total Short-Term Investments (Cost $13,600)				13,520
Total Investments (99.5%) (Cost $317,739) (n)(o)(p)				357,120
Other Assets in Excess of Liabilities (0.5%)				1,844
Net Assets (100.0%)			$	358,964

(a) Security is subject to delayed delivery.

(b) Variable/Floating Rate Security — Interest rate changes on these instruments are based on changes in a designated base rate. The rates shown are those in effect on September 30, 2016.

(c) 144A security — Certain conditions for public sale may exist. Unless otherwise noted, these securities are deemed to be liquid.

(d) Security trades on the Hong Kong exchange.

(f) When-issued security.

(g) Multi-step — Coupon rate changes in predetermined increments to maturity. Rate disclosed is as of September 30, 2016. Maturity date disclosed is the ultimate maturity date.

(h) Non-income producing security.

(i) Security has been deemed illiquid at September 30, 2016.

(j) At September 30, 2016, the Portfolio held fair valued securities valued at less than $500, representing less than 0.05% of net assets. These securities have been fair valued as determined in good faith under procedures established by and under the general supervision of the Fund's Trustees.

(k) Cleared option.

(l) Rate shown is the yield to maturity at September 30, 2016.

(m) All or a portion of the security was pledged to cover margin requirements for swap agreements.

(n) Securities are available for collateral in connection with securities purchased on a forward commitment basis, foreign currency forward exchange contracts, futures contracts and swap agreements.

(o) The approximate fair value and percentage of net assets, $94,547,000 and 26.3%, respectively, represent the securities that have been fair valued under the fair valuation policy for international investments as described in Note A-1 within the Notes to the Financial Statements.

(p) At September 30, 2016, the aggregate cost for federal income tax purposes is approximately $321,204,000. The aggregate gross unrealized appreciation is approximately $52,314,000 and the aggregate gross unrealized depreciation is approximately $16,398,000 resulting in net unrealized appreciation of approximately $35,916,000.

@ Value is less than $500.

ADR American Depositary Receipt.

CDI CHESS Depositary Interest.

CVA Certificaten Van Aandelen.

IO Interest Only.

MTN Medium Term Note.

OAT Obligations Assimilables du Trésor (French Treasury Obligation).

REIT Real Estate Investment Trust.

REMIC Real Estate Mortgage Investment Conduit.

SDR Swedish Depositary Receipt.

TBA To Be Announced.

Foreign Currency Forward Exchange Contracts:

The Portfolio had the following foreign currency forward exchange contracts open at September 30, 2016:

Counterparty	Contracts to Deliver (000)		In Exchange For (000)		Delivery Date	Unrealized Appreciation (Depreciation) (000)
Australia and New Zealand Banking Group	AUD	733	$	561	10/5/16	$	(—	@)
Australia and New Zealand Banking Group	CAD	2,361	$	1,819	10/5/16		19
Australia and New Zealand Banking Group	EUR	109	GBP	94	10/5/16		(—	@)
Australia and New Zealand Banking Group	EUR	481	GBP	415	10/5/16		(2	)
Australia and New Zealand Banking Group	EUR	1,232	NZD	1,900	10/5/16		(1	)
Australia and New Zealand Banking Group	KRW	1,658,797	$	1,504	10/5/16		(2	)

The accompanying notes are an integral part of the financial statements.
25

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Strategist Portfolio

Foreign Currency Forward Exchange Contracts: (cont'd)

Counterparty	Contracts to Deliver (000)		In Exchange For (000)		Delivery Date	Unrealized Appreciation (Depreciation) (000)
Australia and New Zealand Banking Group	MYR	1,600	$	388	10/5/16	$	1
Australia and New Zealand Banking Group	NZD	1,900	EUR	1,224	10/5/16		(8	)
Australia and New Zealand Banking Group	NZD	1,007	$	734	10/5/16		—	@
Australia and New Zealand Banking Group	PLN	4,392	$	1,154	10/5/16		6
Australia and New Zealand Banking Group	RUB	17,145	$	271	10/5/16		(2	)
Australia and New Zealand Banking Group	SGD	340	$	250	10/5/16		—	@
Australia and New Zealand Banking Group	THB	13,100	$	379	10/5/16		—	@
Australia and New Zealand Banking Group	TRY	613	$	204	10/5/16		(—	@)
Australia and New Zealand Banking Group	$	72	EUR	64	10/5/16		—	@
Australia and New Zealand Banking Group	$	616	EUR	549	10/5/16		—	@
Australia and New Zealand Banking Group	$	67	GBP	51	10/5/16		(1	)
Australia and New Zealand Banking Group	$	3,833	JPY	388,142	10/5/16		(5	)
Australia and New Zealand Banking Group	$	1,505	KRW	1,658,797	10/5/16		1
Australia and New Zealand Banking Group	$	386	MYR	1,600	10/5/16		1
Australia and New Zealand Banking Group	$	728	NZD	1,007	10/5/16		5
Australia and New Zealand Banking Group	$	378	THB	13,100	10/5/16		—	@
Australia and New Zealand Banking Group	$	206	TRY	613	10/5/16		(2	)
Australia and New Zealand Banking Group	ZAR	23,716	$	1,661	10/5/16		(67	)
Barclays Bank PLC	EUR	293	$	330	10/5/16		1
Barclays Bank PLC	$	40	JPY	4,099	10/5/16		—	@
Barclays Bank PLC	$	731	PLN	2,829	10/5/16		8
Citibank NA	EUR	3,581	$	4,023	10/5/16		1
Citibank NA	NOK	5,400	EUR	601	10/5/16		(—	@)
Citibank NA	NOK	6,572	$	823	10/5/16		1
Citibank NA	$	2,087	CAD	2,733	10/5/16		(4	)
HSBC Bank PLC	EUR	296	SEK	2,850	10/5/16		(—	@)
HSBC Bank PLC	EUR	11	$	13	10/5/16		(—	@)
HSBC Bank PLC	GBP	17	$	23	10/5/16		—	@
HSBC Bank PLC	GBP	34	$	44	10/5/16		—	@
HSBC Bank PLC	JPY	849	$	8	10/5/16		(—	@)
HSBC Bank PLC	SEK	8,237	$	961	10/5/16		1
HSBC Bank PLC	$	6	CAD	8	10/5/16		(—	@)
HSBC Bank PLC	$	912	ZAR	13,254	10/5/16		54
JPMorgan Chase Bank NA	EUR	581	NOK	5,400	10/5/16		23
JPMorgan Chase Bank NA	EUR	692	$	774	10/5/16		(4	)
JPMorgan Chase Bank NA	EUR	509	$	568	10/5/16		(3	)
JPMorgan Chase Bank NA	GBP	415	EUR	486	10/5/16		8
JPMorgan Chase Bank NA	MYR	1,600	$	386	10/5/16		(1	)
JPMorgan Chase Bank NA	PLN	2,600	EUR	605	10/5/16		(1	)
JPMorgan Chase Bank NA	SEK	2,850	EUR	300	10/5/16		4
JPMorgan Chase Bank NA	$	2,294	BRL	7,477	10/5/16		5
JPMorgan Chase Bank NA	$	1,529	MXN	29,369	10/5/16		(14	)
JPMorgan Chase Bank NA	$	397	MYR	1,600	10/5/16		(11	)
JPMorgan Chase Bank NA	$	1,169	NOK	9,672	10/5/16		41
JPMorgan Chase Bank NA	$	2,901	PLN	11,105	10/5/16		3
JPMorgan Chase Bank NA	$	262	RUB	17,145	10/5/16		11
JPMorgan Chase Bank NA	$	972	SEK	8,237	10/5/16		(12	)
JPMorgan Chase Bank NA	$	250	SGD	340	10/5/16		(1	)
JPMorgan Chase Bank NA	$	848	ZAR	12,180	10/5/16		40
JPMorgan Chase Bank NA	ZAR	1,718	$	125	10/5/16		(—	@)
Royal Bank of Canada	CAD	380	$	291	10/5/16		1
State Street Bank and Trust Co.	NOK	3,100	$	382	10/5/16		(6	)
UBS AG	BRL	7,477	$	2,293	10/5/16		(5	)
UBS AG	CAD	782	MXN	11,200	10/5/16		(19	)
UBS AG	CHF	720	EUR	662	10/5/16		2
UBS AG	CHF	214	$	220	10/5/16		—	@
UBS AG	DKK	2,500	$	376	10/5/16		(1	)
UBS AG	EUR	659	CHF	720	10/5/16		1
UBS AG	EUR	600	PLN	2,600	10/5/16		6
UBS AG	EUR	455	$	508	10/5/16		(4	)

The accompanying notes are an integral part of the financial statements.
26

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Strategist Portfolio

Foreign Currency Forward Exchange Contracts: (cont'd)

Counterparty	Contracts to Deliver (000)		In Exchange For (000)		Delivery Date	Unrealized Appreciation (Depreciation) (000)
UBS AG	GBP	93	EUR	109	10/5/16	$	2
UBS AG	JPY	61,826	MXN	11,800	10/5/16		(1	)
UBS AG	JPY	391,392	$	3,868	10/5/16		8
UBS AG	KRW	1,658,797	$	1,505	10/5/16		(1	)
UBS AG	MXN	11,200	CAD	759	10/5/16		1
UBS AG	MXN	11,800	JPY	64,357	10/5/16		26
UBS AG	MXN	19,293	$	1,037	10/5/16		42
UBS AG	MXN	10,076	$	521	10/5/16		2
UBS AG	PLN	5,603	$	1,451	10/5/16		(14	)
UBS AG	PLN	2,450	$	631	10/5/16		(10	)
UBS AG	PLN	1,489	$	387	10/5/16		(3	)
UBS AG	$	558	AUD	733	10/5/16		3
UBS AG	$	220	CHF	214	10/5/16		(—	@)
UBS AG	$	378	DKK	2,500	10/5/16		(—	@)
UBS AG	$	5,543	EUR	4,928	10/5/16		(6	)
UBS AG	$	1,486	KRW	1,658,797	10/5/16		20
Bank of America NA	CHF	1,913	$	1,956	10/20/16		(15	)
Bank of America NA	EUR	1,807	$	2,023	10/20/16		(8	)
Bank of America NA	JPY	34,534	$	340	10/20/16		(1	)
Bank of America NA	PLN	4,301	$	1,119	10/20/16		(6	)
Bank of America NA	$	1,117	PLN	4,274	10/20/16		—	@
Bank of America NA	$	3,049	SEK	26,014	10/20/16		(14	)
Bank of Montreal	AUD	125	$	95	10/20/16		(1	)
Bank of Montreal	$	47	ILS	179	10/20/16		—	@
Bank of New York Mellon	CHF	284	$	290	10/20/16		(2	)
Bank of New York Mellon	$	2	GBP	1	10/20/16		(—	@)
Bank of New York Mellon	$	18	SEK	157	10/20/16		(—	@)
Barclays Bank PLC	AUD	3,319	$	2,507	10/20/16		(32	)
Barclays Bank PLC	EUR	7,198	$	8,060	10/20/16		(32	)
Barclays Bank PLC	RUB	15,362	$	244	10/20/16		(—	@)
Barclays Bank PLC	$	3,606	GBP	2,759	10/20/16		(29	)
Barclays Bank PLC	$	1,249	RUB	82,170	10/20/16		54
Barclays Bank PLC	$	2,540	RUB	161,147	10/20/16		16
BNP Paribas SA	JPY	81,559	$	805	10/20/16		1
BNP Paribas SA	$	1,510	CAD	1,991	10/20/16		8
BNP Paribas SA	$	2,556	CAD	3,344	10/20/16		(7	)
BNP Paribas SA	$	46	ILS	175	10/20/16		—	@
Citibank NA	CHF	313	$	320	10/20/16		(2	)
Citibank NA	EUR	3,269	$	3,661	10/20/16		(14	)
Citibank NA	HKD	4,475	$	577	10/20/16		(—	@)
Citibank NA	JPY	508	$	5	10/20/16		(—	@)
Citibank NA	SEK	23,136	$	2,686	10/20/16		(14	)
Citibank NA	$	2,703	EUR	2,410	10/20/16		7
Citibank NA	$	418	EUR	372	10/20/16		(—	@)
Citibank NA	$	1,067	GBP	816	10/20/16		(9	)
Citibank NA	$	103	SEK	877	10/20/16		(—	@)
Citibank NA	$	327	THB	11,364	10/20/16		1
Commonwealth Bank of Australia	AUD	2,294	$	1,733	10/20/16		(22	)
Commonwealth Bank of Australia	JPY	15,911	$	157	10/20/16		(—	@)
Credit Suisse International	CHF	306	$	313	10/20/16		(2	)
Credit Suisse International	EUR	4,655	$	5,213	10/20/16		(21	)
Credit Suisse International	MXN	4,244	$	216	10/20/16		(3	)
Credit Suisse International	$	6	GBP	4	10/20/16		(—	@)
Credit Suisse International	$	482	ILS	1,818	10/20/16		3
Credit Suisse International	$	55	NZD	76	10/20/16		(—	@)
Credit Suisse International	$	381	SGD	519	10/20/16		(1	)
Credit Suisse International	ZAR	648	$	46	10/20/16		(1	)
Goldman Sachs International	BRL	3,740	$	1,123	10/20/16		(22	)
Goldman Sachs International	BRL	1,900	$	586	10/20/16		4
Goldman Sachs International	BRL	1,297	$	399	10/20/16		1

The accompanying notes are an integral part of the financial statements.
27

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Strategist Portfolio

Foreign Currency Forward Exchange Contracts: (cont'd)

Counterparty	Contracts to Deliver (000)		In Exchange For (000)		Delivery Date	Unrealized Appreciation (Depreciation) (000)
Goldman Sachs International	CHF	304	$	311	10/20/16	$	(2	)
Goldman Sachs International	EUR	4,116	$	4,609	10/20/16		(18	)
Goldman Sachs International	HUF	4,523	$	16	10/20/16		(—	@)
Goldman Sachs International	RUB	69,554	$	1,059	10/20/16		(44	)
Goldman Sachs International	TRY	8,064	$	2,692	10/20/16		14
Goldman Sachs International	$	327	EUR	290	10/20/16		(1	)
Goldman Sachs International	$	7	NZD	9	10/20/16		(—	@)
Goldman Sachs International	$	1,985	RUB	130,468	10/20/16		85
JPMorgan Chase Bank NA	AUD	629	$	475	10/20/16		(6	)
JPMorgan Chase Bank NA	CHF	968	$	990	10/20/16		(8	)
JPMorgan Chase Bank NA	EUR	2,552	$	2,858	10/20/16		(11	)
JPMorgan Chase Bank NA	NOK	16,960	$	2,050	10/20/16		(71	)
JPMorgan Chase Bank NA	TRY	175	$	58	10/20/16		—	@
JPMorgan Chase Bank NA	$	1,019	EUR	911	10/20/16		5
JPMorgan Chase Bank NA	$	3,109	MXN	61,498	10/20/16		57
JPMorgan Chase Bank NA	$	1,582	MXN	30,749	10/20/16		1
JPMorgan Chase Bank NA	$	102	NOK	845	10/20/16		4
JPMorgan Chase Bank NA	$	2,537	NOK	20,428	10/20/16		18
JPMorgan Chase Bank NA	$	140	NZD	191	10/20/16		(1	)
JPMorgan Chase Bank NA	$	707	SEK	6,033	10/20/16		(3	)
Northern Trust Company	$	295	SGD	401	10/20/16		(1	)
State Street Bank and Trust Co.	DKK	435	$	65	10/20/16		(—	@)
State Street Bank and Trust Co.	$	394	MYR	1,626	10/20/16		(1	)
UBS AG	CHF	990	$	1,012	10/20/16		(8	)
UBS AG	DKK	6,987	$	1,050	10/20/16		(5	)
UBS AG	EUR	5,291	$	5,925	10/20/16		(23	)
UBS AG	KRW	237,248	$	211	10/20/16		(5	)
UBS AG	MXN	9,448	$	480	10/20/16		(6	)
UBS AG	$	548	GBP	420	10/20/16		(4	)
UBS AG	$	465	GBP	359	10/20/16		(—	@)
UBS AG	$	2,458	NOK	20,348	10/20/16		87
UBS AG	$	1,278	RUB	83,873	10/20/16		53
UBS AG	$	602	SGD	819	10/20/16		(1	)
UBS AG	ZAR	183	$	13	10/20/16		(—	@)
Australia and New Zealand Banking Group	$	269	RUB	17,145	11/3/16		2
Australia and New Zealand Banking Group	GBP	94	EUR	109	11/4/16		—	@
Australia and New Zealand Banking Group	GBP	415	EUR	480	11/4/16		2
Australia and New Zealand Banking Group	NZD	1,900	EUR	1,229	11/4/16		1
Australia and New Zealand Banking Group	$	560	AUD	733	11/4/16		—	@
Australia and New Zealand Banking Group	$	1,504	KRW	1,658,797	11/4/16		2
Australia and New Zealand Banking Group	$	388	MYR	1,600	11/4/16		(1	)
Australia and New Zealand Banking Group	$	733	NZD	1,007	11/4/16		(—	@)
Australia and New Zealand Banking Group	$	250	SGD	340	11/4/16		(—	@)
Australia and New Zealand Banking Group	$	379	THB	13,100	11/4/16		(1	)
Australia and New Zealand Banking Group	$	203	TRY	613	11/4/16		—	@
Citibank NA	CAD	2,733	$	2,087	11/4/16		4
Citibank NA	EUR	600	NOK	5,400	11/4/16		—	@
Citibank NA	$	4,029	EUR	3,581	11/4/16		(1	)
Citibank NA	$	823	NOK	6,572	11/4/16		(1	)
HSBC Bank PLC	SEK	2,850	EUR	296	11/4/16		—	@
HSBC Bank PLC	$	44	GBP	34	11/4/16		(—	@)
HSBC Bank PLC	$	963	SEK	8,237	11/4/16		(1	)
JPMorgan Chase Bank NA	BRL	7,477	$	2,274	11/4/16		(5	)
JPMorgan Chase Bank NA	EUR	603	PLN	2,600	11/4/16		1
JPMorgan Chase Bank NA	PLN	11,105	$	2,899	11/4/16		(3	)
JPMorgan Chase Bank NA	$	869	BRL	2,861	11/4/16		3
JPMorgan Chase Bank NA	$	124	ZAR	1,718	11/4/16		—	@
UBS AG	CAD	757	MXN	11,200	11/4/16		(1	)
UBS AG	EUR	662	CHF	720	11/4/16		(2	)
UBS AG	MXN	11,800	JPY	61,522	11/4/16		1

The accompanying notes are an integral part of the financial statements.
28

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Strategist Portfolio

Foreign Currency Forward Exchange Contracts: (cont'd)

Counterparty	Contracts to Deliver (000)		In Exchange For (000)		Delivery Date	Unrealized Appreciation (Depreciation) (000)
UBS AG	$	221	CHF	214	11/4/16	$	(—	@)
UBS AG	$	377	DKK	2,500	11/4/16		1
UBS AG	$	3,873	JPY	391,392	11/4/16		(8	)
UBS AG	$	519	MXN	10,076	11/4/16		(2	)
Citibank NA	CNH	35,621	$	5,403	3/16/17		111
Citibank NA	$	5,342	CNH	35,621	3/16/17		(50	)
Citibank NA	CNH	23,577	$	3,473	5/11/17		(20	)
Citibank NA	CNH	23,648	$	3,482	5/11/17		(22	)
Citibank NA	CNH	9,493	$	1,398	5/11/17		(9	)
Citibank NA	CNH	76,741	$	11,444	5/11/17		74
Citibank NA	$	397	CNH	2,674	5/11/17		(1	)
Citibank NA	$	7,010	CNH	47,472	5/11/17		24
Citibank NA	$	5,405	CNH	36,773	5/11/17		43
JPMorgan Chase Bank NA	CNH	23,577	$	3,491	5/11/17		(2	)
JPMorgan Chase Bank NA	CNH	36,228	$	5,328	5/11/17		(40	)
JPMorgan Chase Bank NA	CNH	4,921	$	732	5/11/17		3
JPMorgan Chase Bank NA	CNH	8,728	$	1,284	5/11/17		(9	)
JPMorgan Chase Bank NA	CNH	36,228	$	5,343	5/11/17		(24	)
JPMorgan Chase Bank NA	$	467	CNH	3,150	5/11/17		(—	@)
JPMorgan Chase Bank NA	$	3,775	CNH	25,562	5/11/17		12
						$	160

Futures Contracts:

The Portfolio had the following futures contracts open at September 30, 2016:

	Number of Contracts		Value (000)			Expiration Date	Unrealized Appreciation (Depreciation) (000)
Long:
Amsterdam Index (Netherlands)		3	$	305		Oct-16	$	7
CAC 40 Index (France)		7		349		Oct-16		5
German Euro BOBL (Germany)		19		2,819		Dec-16		14
MSCI Emerging Market E Mini (United States)		20		913		Dec-16		(17	)
MSCI Singapore Free Index (Singapore)		42		971		Oct-16		10
NIKKEI 225 Index (Japan)		13		1,061		Dec-16		(17	)
OMXS 30 Index (Sweden)		19		319		Oct-16		9
S&P 500 E Mini Index (United States)		436		47,097		Dec-16		735
U.S. Treasury 2 yr. Note (United States)		58		12,671		Dec-16		22
U.S. Treasury 5 yr. Note (United States)		76		9,235		Dec-16		9
U.S. Treasury 10 yr. Ultra Long Bond (United States)		1		144		Dec-16		(—	@)
UK Long Gilt Bond (United Kingdom)		5		844		Dec-16		(7	)
Short:
Euro Stoxx 50 Index (Germany)		374		(12,579	)	Dec-16		(203	)
German Euro Bund (Germany)		29		(5,398	)	Dec-16		(36	)
Hang Seng Index (Hong Kong)		5		(751	)	Oct-16		4
Japanese 10 yr. Bond (Japan)		2		(3,005	)	Dec-16		(14	)
S&P TSX 60 Index (Canada)		13		(1,695	)	Dec-16		(2	)
SPI 200 Index (Australia)		16		(1,658	)	Dec-16		(28	)
U.S. Treasury 10 yr. Note (United States)		246		(32,257	)	Dec-16		(45	)
U.S. Treasury 10 yr. Ultra Long Bond (United States)		34		(4,901	)	Dec-16		4
U.S. Treasury Long Bond (United States)		24		(4,036	)	Dec-16		57
U.S. Treasury Ultra Bond (United States)		6		(1,103	)	Dec-16		21
UK Long Gilt Bond (United Kingdom)		5		(844	)	Dec-16		6
							$	534

The accompanying notes are an integral part of the financial statements.
29

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Strategist Portfolio

Credit Default Swap Agreement:

The Portfolio had the following credit default swap agreement open at September 30, 2016:

Swap Counterparty and Reference Obligation				Buy/Sell Protection				Notional Amount (000)				Pay/Receive Fixed Rate				Termination Date				Upfront Payment (Received) (000)				Unrealized Appreciation (000)				Value (000)				Credit Rating of Reference Obligation† (Unaudited)
Barclays Bank PLC Russian Federation				Sell				$	2,912				1.00	%		6/20/21				$	(244	)		$	108			$	(136	)		BB+

Interest Rate Swap Agreements:

The Portfolio had the following interest rate swap agreements open at September 30, 2016:

Swap Counterparty	Floating Rate Index	Pay/Receive Floating Rate	Fixed Rate			Termination Date	Notional Amount (000)		Unrealized Appreciation (Depreciation) (000)
Bank of America NA	6 Month BBSW	Pay		2.50	%	5/6/26	AUD	3,016	$	78
Citibank NA	6 Month BBSW	Pay		2.51		5/6/26		3,009		80
JPMorgan Chase Bank NA	6 Month BBSW	Pay		2.55		5/5/26	AUD	3,009		87
JPMorgan Chase Bank NA	6 Month BBSW	Pay		2.44		5/20/26		5,281		116
Morgan Stanley & Co., LLC*	3 Month LIBOR	Receive		1.71		3/19/20	$	7,400		(157	)
Morgan Stanley & Co., LLC*	3 Month LIBOR	Receive		1.29		3/7/21		6,160		(36	)
Morgan Stanley & Co., LLC*	3 Month LIBOR	Receive		1.20		7/28/21		330		(1	)
Morgan Stanley & Co., LLC*	3 Month LIBOR	Receive		2.45		7/17/25		3,400		(304	)
Morgan Stanley & Co., LLC*	3 Month LIBOR	Receive		1.80		3/14/26		8,220		(253	)
Morgan Stanley & Co., LLC*	3 Month LIBOR	Receive		1.66		4/6/26		6,450		(156	)
Morgan Stanley & Co., LLC*	3 Month LIBOR	Pay		1.61		4/13/26		16,730		460
Morgan Stanley & Co., LLC*	3 Month LIBOR	Receive		1.76		4/26/26		760		(25	)
Morgan Stanley & Co., LLC*	3 Month LIBOR	Receive		1.62		5/13/26		8,200		(156	)
Morgan Stanley & Co., LLC*	6 Month EURIBOR	Receive		0.58		5/23/26	EUR	3,341		(138	)
Morgan Stanley & Co., LLC*	6 Month EURIBOR	Receive		0.46		6/14/26		15,077		(226	)
Morgan Stanley & Co., LLC*	3 Month LIBOR	Receive		1.50		6/16/26	$	980		(6	)
Morgan Stanley & Co., LLC*	3 Month LIBOR	Receive		1.51		7/28/26		870		(3	)
									$	(640	)

Total Return Swap Agreements:

The Portfolio had the following total return swap agreements open at September 30, 2016:

Swap Counterparty

Index

Notional
Amount
(000)

Floating
Rate

Pay/Receive
Total Return
of Referenced
Index

Maturity
Date

Upfront
Payment
(Received)
(000)

Unrealized
Appreciation
(Depreciation)
(000)

Bank of America NA

U.S. Apartment REITs††

6,162

3 Month USD LIBOR
minus 0.24%

Pay

4/20/17

—

237

Bank of America NA

U.S. Apartment REITs††

358

3 Month USD LIBOR
minus 0.24%

Pay

4/20/17

—

Bank of America NA

U.S. Apartment REITs††

369

3 Month USD LIBOR
minus 0.24%

Pay

4/20/17

—

)

Bank of America NA

U.S. Apartment REITs††

1,090

3 Month USD LIBOR
minus 0.24%

Pay

4/20/17

—

Barclays Bank PLC

MSCI Emerging
Market Index

24,105

3 Month USD LIBOR
minus 0.08%

Receive

3/3/17

—

298

Barclays Bank PLC

Barclays Short
Elevators Index††

1,058

3 Month USD LIBOR
plus 0.12%

Pay

9/8/17

—

)

Citibank NA

U.S. Media Index††

7,770

3 Month USD LIBOR
minus 0.15%

Pay

2/8/17

—

Goldman Sachs
International

USD Liquid High
Yield Index

5,270

3 Month USD LIBOR
plus 0.64%

Receive

12/23/16

)

350

The accompanying notes are an integral part of the financial statements.
30

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Strategist Portfolio

Total Return Swap Agreements: (cont'd)

Swap Counterparty	Index	Notional Amount (000)		Floating Rate	Pay/Receive Total Return of Referenced Index	Maturity Date	Upfront Payment (Received) (000)		Unrealized Appreciation (Depreciation) (000)
Goldman Sachs International	U.S. Consumer Staples Index††	$	3,987	3 Month USD LIBOR minus 0.14%	Pay	3/2/17	$	—	$	65
Goldman Sachs International	U.S. Consumer Staples Index††		2,319	3 Month USD LIBOR minus 0.15%	Pay	3/2/17		—		38
Goldman Sachs International	Global Aerospace Index††		3,962	3 Month USD LIBOR minus 0.25%	Pay	4/6/17		—		(146	)
Goldman Sachs International	Global Aerospace Index††		5,811	3 Month USD LIBOR minus 0.25%	Pay	4/6/17		—		(214	)
Goldman Sachs International	Global Aerospace Index††		1,978	3 Month USD LIBOR minus 0.25%	Pay	4/6/17		—		(73	)
JPMorgan Chase Bank NA	Short European Staples Index††		3,549	3 Month USD LIBOR plus 0.03%	Pay	8/11/17		—		(49	)
JPMorgan Chase Bank NA	JPM Short Luxury Index††		5,518	3 Month USD LIBOR minus 0.05%	Pay	9/6/17		—		(58	)
									$	513

†† See tables below for details of the equity basket holdings underlying the swap.

The following table represents the equity basket holdings underlying the total return swap with U.S. Apartment REITs as of September 30, 2016.

Security Description	Index Weight
U.S. Apartment REITs
Apartment Investment & Management Co.		7.26	%
AvalonBay Communities, Inc.		24.44
Camden Property Trust		7.29
Equity Residential		23.53
Essex Property Trust, Inc.		14.71
Independence Realty Trust, Inc.		0.36
Mid-America Apartment Communities, Inc.		7.12
Monogram Residential Trust, Inc.		1.38
Post Properties, Inc.		4.23
UDR, Inc.		9.68
		100.00	%

The following table represents the equity basket holdings underlying the total return swap with Barclays Short Elevators Index as of September 30, 2016.

Security Description	Index Weight
Barclays Short Elevators Index
Fujitec Co., Ltd		1.32	%
Kone OYJ		56.81
Schindler Holding AG		41.37
Yungtay Engineering Co., Ltd		0.50
		100.00	%

The following table represents the equity basket holdings underlying the total return swap with U.S. Media Index as of September 30, 2016.

Security Description	Index Weight
U.S. Media Index
CBS Corp.		3.81	%
Charter Communications, Inc.		9.18
Comcast Corp.		25.69
Discovery Communications, Inc.		1.78
DISH Network Corp.		1.92
Interpublic Group of Cos, Inc. (The)		1.44
Liberty Global PLC		4.59
Liberty Global PLC LiLAC		0.48
Liberty Media Corporation-Liberty Braves		0.08
Liberty Media Corporation-Liberty Media		0.32
Liberty Media Corporation-Liberty SiriusXM		1.56
News Corp.		0.84
Omnicom Group, Inc.		3.25
Scripps Networks Interactive, Inc.		0.75
Sirius XM Holdings, Inc.		1.59
TEGNA, Inc.		0.74
Time Warner, Inc.		10.21
Twenty-First Century Fox, Inc.		6.36
Viacom, Inc.		2.08
Walt Disney Co. (The)		23.33
		100.00	%

The accompanying notes are an integral part of the financial statements.
31

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Strategist Portfolio

The following table represents the equity basket holdings underlying the total return swap with U.S. Consumer Staples Index as of September 30, 2016.

Security Description	Index Weight
U.S. Consumer Staples Index
Altria Group, Inc.		6.57	%
Archer-Daniels-Midland Co.		1.33
Brown-Forman Corp.		0.51
Campbell Soup Co.		0.52
Church & Dwight Co., Inc.		0.67
Clorox Co. (The)		0.86
Coca-Cola Co. (The)		8.78
Coca-Cola European Partners PLC		0.44
Colgate-Palmolive Co.		3.52
ConAgra Foods, Inc.		1.08
Constellation Brands, Inc.		1.53
Costco Wholesale Corp.		3.54
CVS Health Corp.		5.22
Dr. Pepper Snapple Group, Inc.		0.91
Estee Lauder Cos, Inc. (The)		1.04
General Mills, Inc.		2.02
Hershey Co. (The)		0.73
Hormel Foods Corp.		0.54
JM Smucker Co. (The)		0.86
Kellogg Co.		1.05
Kimberly-Clark Corp.		2.43
Kraft Heinz Co. (The)		2.82
Kroger Co. (The)		1.53
McCormick & Co., Inc.		0.62
Mead Johnson Nutrition Co.		0.78
Molson Coors Brewing Co.		1.06
Mondelez International, Inc.		3.70
Monster Beverage Corp.		1.17
PepsiCo, Inc.		8.40
Philip Morris International, Inc.		7.99
Procter & Gamble Co. (The)		12.95
Reynolds American, Inc.		2.07
Sysco Corp.		1.36
Tyson Foods, Inc.		1.17
Walgreens Boots Alliance, Inc.		3.72
Wal-Mart Stores, Inc.		6.00
Whole Foods Market, Inc.		0.51
		100.00	%

The following table represents the equity basket holdings underlying the total return swap with Global Aerospace Index as of September 30, 2016.

Security Description	Index Weight
Global Aerospace Index
Airbus Group SE		19.71	%
B/E Aerospace, Inc.		2.23
Boeing Co. (The)		36.77
KLX, Inc.		0.80
Rolls-Royce Holdings PLC		7.05
Safran SA		12.52
Spirit AeroSystems Holdings, Inc.		4.64
Thales SA		3.97
TransDigm Group, Inc.		6.52
Zodiac Aerospace		5.79
		100.00	%

The following table represents the equity basket holdings underlying the total return swap with Short European Staples Index as of September 30, 2016.

Security Description	Index Weight
Short European Staples Index
Anheuser-Busch InBev N.V.		8.81	%
Aryzta AG		0.32
Associated British Foods PLC		1.01
Barry Callebaut AG		0.24
Beiersdorf AG		0.80
British American Tobacco PLC		9.98
Carlsberg A/S		0.85
Carrefour SA		1.20
Casino Guichard Perrachon SA		0.23
Chocoladefabriken Lindt & Spruengli AG		1.06
Coca-Cola European Partners PLC		0.72
Coca-Cola HBC AG		0.35
Colruyt SA		0.31
Danone SA		3.66
Diageo PLC		6.04
Distribuidora Internacional de Alimentac		0.32
Heineken Holding N.V.		0.68
Heineken N.V.		1.70
Henkel AG & Co. KGaA		3.04
ICA Gruppen AB		0.22
Imperial Brands PLC		4.14
J Sainsbury PLC		0.36
Jeronimo Martins SGPS SA		0.37
Kerry Group PLC		1.10
Koninklijke Ahold Delhaize N.V.		2.44
L'Oreal SA		4.00
Marine Harvest ASA		0.57
METRO AG		0.44
Nestle SA		21.02
Orkla ASA		0.71
Pernod Ricard SA		2.10
Reckitt Benckiser Group PLC		5.02
Remy Cointreau SA		0.16
Svenska Cellulosa AB SCA		1.51
Swedish Match AB		0.61
Tate & Lyle PLC		0.38
Tesco PLC		1.62
Unilever N.V.		6.29
Unilever PLC		5.09
WM Morrison Supermarkets PLC		0.53
		100.00	%

The following table represents the equity basket holdings underlying the total return swap with JPM Short Luxury Index as of September 30, 2016.

Security Description	Index Weight
JPM Short Luxury Index
Brunello Cucinelli SpA		0.13	%
Burberry Group PLC		5.87
Christian Dior SE		2.43
Cie Financiere Richemont SA		20.39
Coach, Inc.		5.83
Hermes International		3.51
Hugo Boss AG		2.88
Kering		9.07
LVMH Moet Hennessy Louis Vuitton SE		28.91
Moncler SpA		2.29
Salvatore Ferragamo SpA		2.97
Swatch Group AG (The)		15.28
Tod's SpA		0.44
		100.00	%

The accompanying notes are an integral part of the financial statements.
32

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Global Strategist Portfolio

@ Value is less than $500.

† Credit rating as issued by Standard & Poor's.

* Cleared swap agreement, the broker is Morgan Stanley & Co., LLC.

BBSW Australia's Bank Bill Swap

EURIBOR Euro Interbank Offered Rate.

LIBOR London Interbank Offered Rate.

STIBOR Stockholm Interbank Offered Rate.

ARS — Argentine Peso

AUD — Australian Dollar

BRL — Brazilian Real

CAD — Canadian Dollar

CHF — Swiss Franc

CNH — Chinese Yuan Renminbi

DKK — Danish Krone

EUR — Euro

GBP — British Pound

HKD — Hong Kong Dollar

HUF — Hungarian Forint

ILS — Israeli Shekel

JPY — Japanese Yen

KRW — South Korean Won

MXN — Mexican Peso

MYR — Malaysian Ringgit

NOK — Norwegian Krone

NZD — New Zealand Dollar

PLN — Polish Zloty

RUB — Russian Ruble

SEK — Swedish Krona

SGD — Singapore Dollar

THB — Thai Baht

TRY — Turkish Lira

USD — United States Dollar

ZAR — South African Rand

Portfolio Composition

Classification	Percentage of Total Investments
Common Stocks		56.3	%
Fixed Income Securities		39.7
Other*		4.0
Total Investments		100.0	%**

* Industries and/or investment types representing less than 5% of total investments.

** Does not include open long/short futures contracts with an underlying face amount of approximately $144,955,000 with net unrealized appreciation of approximately $534,000. Does not include open foreign currency forward exchange contracts with net unrealized appreciation of approximately $160,000 and does not include open swap agreements with net unrealized depreciation of approximately $19,000.

The accompanying notes are an integral part of the financial statements.
33

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Global Strategist Portfolio

Statement of Assets and Liabilities	September 30, 2016 (000)
Assets:
Investments in Securities of Unaffiliated Issuers, at Value (Cost $311,651)	$	351,052
Investment in Securities of Affiliated Issuer, at Value (Cost $6,088)		6,068
Total Investments in Securities, at Value (Cost $317,739)		357,120
Foreign Currency, at Value (Cost $524)		530
Cash		12
Receivable for Variation Margin on Futures Contracts		4,595
Receivable for Investments Sold		1,962
Unrealized Appreciation on Swap Agreements		1,525
Unrealized Appreciation on Foreign Currency Forward Exchange Contracts		1,051
Interest Receivable		945
Dividends Receivable		329
Tax Reclaim Receivable		254
Receivable for Variation Margin on Swap Agreements		57
Receivable for Portfolio Shares Sold		26
Receivable from Affiliate		2
Other Assets		61
Total Assets		368,469
Liabilities:
Payable for Investments Purchased		5,268
Due to Broker		1,062
Unrealized Depreciation on Foreign Currency Forward Exchange Contracts		891
Payable for Advisory Fees		546
Unrealized Depreciation on Swap Agreements		543
Payable for Portfolio Shares Redeemed		388
Premium Received on Open Swap Agreements		252
Payable for Custodian Fees		86
Payable for Trustees' Fees and Expenses		80
Payable for Shareholder Services Fees — Class A		54
Payable for Distribution and Shareholder Services Fees — Class L		14
Payable for Distribution and Shareholder Services Fees — Class C		1
Payable for Sub Transfer Agency Fees — Class I		3
Payable for Sub Transfer Agency Fees — Class A		52
Payable for Sub Transfer Agency Fees — Class L		7
Payable for Sub Transfer Agency Fees — Class C		—	@
Payable for Organizational Costs (Note K)		58
Payable for Administration Fees		24
Payable for Professional Fees		21
Payable for Transfer Agency Fees — Class I		3
Payable for Transfer Agency Fees — Class A		12
Payable for Transfer Agency Fees — Class L		2
Payable for Transfer Agency Fees — Class C		1
Payable for Transfer Agency Fees — Class IS		—	@
Other Liabilities		137
Total Liabilities		9,505
Net Assets	$	358,964
Net Assets Consist Of:
Paid-in-Capital	$	329,084
Accumulated Undistributed Net Investment Income		1,214
Accumulated Net Realized Loss		(11,382	)
Unrealized Appreciation (Depreciation) on:
Investments		39,401
Investments in Affiliates		(20	)
Futures Contracts		534
Swap Agreements		(19	)
Foreign Currency Forward Exchange Contracts		160
Foreign Currency Translations		(8	)
Net Assets	$	358,964

The accompanying notes are an integral part of the financial statements.
34

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Global Strategist Portfolio

Statement of Assets and Liabilities (cont'd)	September 30, 2016 (000)
CLASS I:
Net Assets	$	74,158
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		4,697,891
Net Asset Value, Offering and Redemption Price Per Share	$	15.79
CLASS A:
Net Assets	$	259,999
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		16,619,583
Net Asset Value, Redemption Price Per Share	$	15.64
Maximum Sales Load		5.25	%
Maximum Sales Charge	$	0.87
Maximum Offering Price Per Share	$	16.51
CLASS L:
Net Assets	$	23,051
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		1,490,042
Net Asset Value, Offering and Redemption Price Per Share	$	15.47
CLASS C:
Net Assets	$	1,613
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		104,613
Net Asset Value, Offering and Redemption Price Per Share	$	15.42
CLASS IS:
Net Assets	$	143
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		9,054
Net Asset Value, Offering and Redemption Price Per Share	$	15.79

@ Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
35

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Global Strategist Portfolio

Statement of Operations	Year Ended September 30, 2016 (000)
Investment Income:
Dividends from Securities of Unaffiliated Issuers (Net of $359 of Foreign Taxes Withheld)	$	5,681
Interest from Securities of Unaffiliated Issuers		3,761
Dividends from Securities of Affiliated Issuer (Note G)		56
Total Investment Income		9,498
Expenses:
Advisory Fees (Note B)		1,683
Shareholder Services Fees — Class A (Note D)		681
Distribution and Shareholder Services Fees — Class L (Note D)		182
Distribution and Shareholder Services Fees — Class C (Note D)		17
Custodian Fees (Note F)		354
Sub Transfer Agency Fees — Class I		30
Sub Transfer Agency Fees — Class A		254
Sub Transfer Agency Fees — Class L		30
Sub Transfer Agency Fees — Class C		—	@
Administration Fees (Note C)		299
Pricing Fees		130
Professional Fees		100
Registration Fees		86
Shareholder Reporting Fees		66
Transfer Agency Fees — Class I (Note E)		12
Transfer Agency Fees — Class A (Note E)		41
Transfer Agency Fees — Class L (Note E)		4
Transfer Agency Fees — Class C (Note E)		3
Transfer Agency Fees — Class IS (Note E)		2
Organizational Costs (Note K)		58
Trustees' Fees and Expenses		9
Other Expenses		37
Total Expenses		4,078
Rebate from Morgan Stanley Affiliate (Note G)		(25	)
Reimbursement of Class Specific Expenses — Class IS (Note B)		(2	)
Reimbursement of Custodian Fees (Note F)		(452	)
Net Expenses		3,599
Net Investment Income		5,899
Realized Gain (Loss):
Investments Sold		5,978
Foreign Currency Forward Exchange Contracts		(1,490	)
Foreign Currency Transactions		441
Futures Contracts		3,649
Options Written		174
Swap Agreements		(3,283	)
Net Realized Gain		5,469
Change in Unrealized Appreciation (Depreciation):
Investments		15,689
Investments in Affiliates		14
Foreign Currency Forward Exchange Contracts		124
Foreign Currency Translations		36
Futures Contracts		1,194
Swap Agreements		234
Net Change in Unrealized Appreciation (Depreciation)		17,291
Net Realized Gain and Change in Unrealized Appreciation (Depreciation)		22,760
Net Increase in Net Assets Resulting from Operations	$	28,659

@ Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
36

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Global Strategist Portfolio

Statements of Changes in Net Assets	Year Ended September 30, 2016 (000)			Year Ended September 30, 2015 (000)
Increase (Decrease) in Net Assets:
Operations:
Net Investment Income	$	5,899		$	6,483
Net Realized Gain (Loss)		5,469			(18,236	)
Net Change in Unrealized Appreciation (Depreciation)		17,291			(28,597	)
Net Increase (Decrease) in Net Assets Resulting from Operations		28,659			(40,350	)
Distributions from and/or in Excess of:
Class I:
Net Investment Income		—			(1,528	)
Net Realized Gain		(87	)		(2,679	)
Class A:
Net Investment Income		—			(6,120	)
Net Realized Gain		(309	)		(13,028	)
Class L:
Net Investment Income		—			(334	)
Net Realized Gain		(27	)		(1,018	)
Class C:
Net Realized Gain		(2	)		—
Class IS:
Net Realized Gain		(—	@)		—
Total Distributions		(425	)		(24,707	)
Capital Share Transactions:⁽¹⁾
Class I:
Subscribed		9,802			54,340
Distributions Reinvested		86			4,190
Redeemed		(25,460	)		(35,485	)
Class A:
Subscribed		3,171			16,757
Distributions Reinvested		304			18,802
Redeemed		(51,527	)		(64,828	)
Class L:
Exchanged		2,564			—
Subscribed		—			4,778
Distributions Reinvested		27			1,327
Redeemed		(5,770	)		(5,643	)
Class C:
Subscribed		800			1,467	*
Distributions Reinvested		2			—
Redeemed		(681	)		(—	@)*
Class IS:
Subscribed		128			10	**
Net Decrease in Net Assets Resulting from Capital Share Transactions		(66,554	)		(4,285	)
Total Decrease in Net Assets		(38,320	)		(69,342	)
Net Assets:
Beginning of Period		397,284			466,626
End of Period (Including Accumulated Undistributed Net Investment Income and Distributions in Excess of Net Investment Income of $1,214 and $(921), respectively)	$	358,964		$	397,284
(1) Capital Share Transactions:
Class I:
Shares Subscribed		648			3,417
Shares Issued on Distributions Reinvested		6			269
Shares Redeemed		(1,711	)		(2,225	)
Net Increase (Decrease) in Class I Shares Outstanding		(1,057	)		1,461
Class A:
Shares Subscribed		211			1,040
Shares Issued on Distributions Reinvested		21			1,211
Shares Redeemed		(3,439	)		(4,081	)
Net Decrease in Class A Shares Outstanding		(3,207	)		(1,830	)

The accompanying notes are an integral part of the financial statements.
37

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Global Strategist Portfolio

Statements of Changes in Net Assets (cont'd)	Year Ended September 30, 2016 (000)			Year Ended September 30, 2015 (000)
Class L:
Shares Exchanged	$	174		$	—
Shares Subscribed		—			305
Shares Issued on Distributions Reinvested		2			86
Shares Redeemed		(389	)		(358	)
Net Increase (Decrease) in Class L Shares Outstanding		(213	)		33
Class C:
Shares Subscribed		55			95	*
Shares Issued on Distributions Reinvested		—	@@		—
Shares Redeemed		(45	)		(—	@@)*
Net Increase in Class C Shares Outstanding		10			95
Class IS:
Shares Subscribed		8			1	**

* For the period April 30, 2015 through September 30, 2015.

** For the period May 29, 2015 through September 30, 2015.

@ Amount is less than $500.

@@ Amount is less than 500 shares.

The accompanying notes are an integral part of the financial statements.
38

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Global Strategist Portfolio

	Class I
	Year Ended September 30,
Selected Per Share Data and Ratios	2016††			2015			2014			2013			2012
Net Asset Value, Beginning of Period	$	14.58		$	16.99		$	16.96		$	15.22		$	12.50
Income (Loss) from Investment Operations:
Net Investment Income†		0.28			0.28			0.34			0.35			0.14
Net Realized and Unrealized Gain (Loss)		0.95			(1.73	)		1.15			1.44			2.79
Total from Investment Operations		1.23			(1.45	)		1.49			1.79			2.93
Distributions from and/or in Excess of:
Net Investment Income		—			(0.35	)		(0.23	)		(0.05	)		(0.21	)
Net Realized Gain		(0.02	)		(0.61	)		(1.23	)		—			—
Total Distributions		(0.02	)		(0.96	)		(1.46	)		(0.05	)		(0.21	)
Net Asset Value, End of Period	$	15.79		$	14.58		$	16.99		$	16.96		$	15.22
Total Return++		8.42	%*		(8.87	)%		9.37	%		11.79	%		23.66	%
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	74,158		$	83,930		$	72,952		$	52,170		$	23,756
Ratio of Expenses to Average Net Assets ⁽¹⁾		0.68	%+		0.73	%+		0.72	%+		0.69	%+		1.37	%+
Ratio of Expenses to Average Net Assets Excluding Non Operating Expenses		N/A			N/A			N/A			0.76	%+		N/A
Ratio of Net Investment Income to Average Net Assets ⁽¹⁾		1.84	%+		1.78	%+		1.99	%+		2.18	%+		1.01	%+
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.01	%		0.01	%		0.02	%		0.01	%		0.02	%
Portfolio Turnover Rate		103	%		98	%		62	%		107	%		168	%
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		0.81	%		0.83	%		0.83	%		0.82	%		N/A
Net Investment Income to Average Net Assets		1.71	%		1.68	%		1.88	%		2.05	%		N/A

†† Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class I shares. The Ratio of Expenses to Average Net Assets would have been 0.05% higher and the Ratio of Net Investment Income to Average Net Assets would have been 0.05% lower had the custodian not reimbursed the Portfolio.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value as of the last business day of the period.

* Performance was positively impacted by approximately 0.21% due to the receipt of proceeds from the settlement of class action suits involving the Portfolio's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class I shares would have been approximately 8.21%.

The accompanying notes are an integral part of the financial statements.
39

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Global Strategist Portfolio

	Class A
	Year Ended September 30,
Selected Per Share Data and Ratios	2016††			2015			2014			2013			2012
Net Asset Value, Beginning of Period	$	14.50		$	16.88		$	16.88		$	15.18		$	12.47
Income (Loss) from Investment Operations:
Net Investment Income†		0.23			0.23			0.27			0.42			0.10
Net Realized and Unrealized Gain (Loss)		0.93			(1.71	)		1.15			1.32			2.79
Total from Investment Operations		1.16			(1.48	)		1.42			1.74			2.89
Distributions from and/or in Excess of:
Net Investment Income		—			(0.29	)		(0.19	)		(0.04	)		(0.18	)
Net Realized Gain		(0.02	)		(0.61	)		(1.23	)		—			—
Total Distributions		(0.02	)		(0.90	)		(1.42	)		(0.04	)		(0.18	)
Net Asset Value, End of Period	$	15.64		$	14.50		$	16.88		$	16.88		$	15.18
Total Return++		7.98	%*		(9.16	)%		9.02	%		11.49	%		23.33	%
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	259,999		$	287,438		$	365,642		$	373,559		$	20,487
Ratio of Expenses to Average Net Assets ⁽¹⁾		0.99	%+		1.05	%+		1.07	%+		0.47	%+^		1.64	%+
Ratio of Expenses to Average Net Assets Excluding Non Operating Expenses		N/A			N/A			N/A			1.03	%+^		N/A
Ratio of Net Investment Income to Average Net Assets ⁽¹⁾		1.56	%+		1.44	%+		1.64	%+		2.60	%+^		0.69	%+
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.01	%		0.01	%		0.02	%		0.01	%		0.02	%
Portfolio Turnover Rate		103	%		98	%		62	%		107	%		168	%
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		1.11	%		1.11	%		1.14	%		1.11	%		N/A
Net Investment Income to Average Net Assets		1.44	%		1.38	%		1.57	%		1.96	%		N/A

†† Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class A shares. The Ratio of Expenses to Average Net Assets would have been 0.07% higher and the Ratio of Net Investment Income to Average Net Assets would have been 0.07% lower had the custodian not reimbursed the Portfolio.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

^ Effective September 16, 2013, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 1.09% for Class A shares. Prior to September 16, 2013, the maximum ratio was 0.99% for Class A shares.

* Performance was positively impacted by approximately 0.27% due to the receipt of proceeds from the settlement of class action suits involving the Portfolio's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class A shares would have been approximately 7.71%.

The accompanying notes are an integral part of the financial statements.
40

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Global Strategist Portfolio

	Class L
	Year Ended September 30,												Period from April 27, 2012^ to
Selected Per Share Data and Ratios	2016††			2015			2014			2013			September 30, 2012
Net Asset Value, Beginning of Period	$	14.41		$	16.79		$	16.78		$	15.15		$	14.42
Income (Loss) from Investment Operations:
Net Investment Income (Loss)†		0.15			0.15			0.19			0.23			(0.02	)
Net Realized and Unrealized Gain (Loss)		0.93			(1.72	)		1.15			1.42			0.78
Total from Investment Operations		1.08			(1.57	)		1.34			1.65			0.76
Distributions from and/or in Excess of:
Net Investment Income		—			(0.20	)		(0.10	)		(0.02	)		(0.03	)
Net Realized Gain		(0.02	)		(0.61	)		(1.23	)		—			—
Total Distributions		(0.02	)		(0.81	)		(1.33	)		(0.02	)		(0.03	)
Net Asset Value, End of Period	$	15.47		$	14.41		$	16.79		$	16.78		$	15.15
Total Return++		7.47	%**		(9.66	)%		8.49	%		10.91	%		5.30	%#
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	23,051		$	24,544		$	28,032		$	29,025		$	11
Ratio of Expenses to Average Net Assets ⁽¹⁾		1.52	%+		1.58	%+		1.57	%+		1.42	%+^^		2.39	%+*
Ratio of Expenses to Average Net Assets Excluding Non Operating Expenses		N/A			N/A			N/A			1.49	%+^^		N/A
Ratio of Net Investment Income (Loss) to Average Net Assets ⁽¹⁾		1.03	%+		0.93	%+		1.14	%+		1.44	%+^^		(0.29	)%+*
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.01	%		0.01	%		0.02	%		0.01	%		0.03	%*
Portfolio Turnover Rate		103	%		98	%		62	%		107	%		168	%#
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		1.64	%		1.69	%*		1.70	%		1.54	%		N/A
Net Investment Income to Average Net Assets		0.91	%		0.82	%*		1.01	%		1.32	%		N/A

†† Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class L shares. The Ratio of Expenses to Average Net Assets would have been 0.06% higher and the Ratio of Net Investment Income (Loss) to Average Net Assets would have been 0.06% lower had the custodian not reimbursed the Portfolio.

^ Commencement of Offering.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value as of the last business day of the period.

+ The Ratios of Expenses and Net Investment Income (Loss) reflect the rebate of certain Portfolio expenses in connection with the investments in Morgan Stanley affiliates during the period. The effect of the rebate on the ratios is disclosed in the above table as "Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets."

^^ Effective September 16, 2013, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 1.59% for Class L shares. Prior to September 16, 2013, the maximum ratio was 1.49% for Class L shares.

# Not Annualized.

* Annualized.

** Performance was positively impacted by approximately 0.20% due to the receipt of proceeds from the settlement of class action suits involving the Portfolio's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class L shares would have been approximately 7.27%.

The accompanying notes are an integral part of the financial statements.
41

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Global Strategist Portfolio

	Class C
Selected Per Share Data and Ratios	Year Ended September 30, 2016††			Period from April 30, 2015^ to September 30, 2015
Net Asset Value, Beginning of Period	$	14.41		$	16.03
Income (Loss) from Investment Operations:
Net Investment Income†		0.10			0.03
Net Realized and Unrealized Gain (Loss)		0.93			(1.65	)
Total from Investment Operations		1.03			(1.62	)
Distributions from and/or in Excess of:
Net Realized Gain		(0.02	)		—
Net Asset Value, End of Period	$	15.42		$	14.41
Total Return++		7.13	%**		(10.11	)%#
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	1,613		$	1,363
Ratio of Expenses to Average Net Assets ⁽¹⁾		1.81	%+		1.83	%+*
Ratio of Net Investment Income to Average Net Assets ⁽¹⁾		0.71	%+		0.54	%+*
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.01	%		0.01	%*
Portfolio Turnover Rate		103	%		98	%#
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		1.94	%		2.28	%*
Net Investment Income to Average Net Assets		0.58	%		0.09	%*

†† Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class C shares. The Ratio of Expenses to Average Net Assets would have been 0.02% higher and the Ratio of Net Investment Income to Average Net Assets would have been 0.02% lower had the custodian not reimbursed the Portfolio.

^ Commencement of Offering.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

# Not Annualized.

* Annualized.

** Performance was positively impacted by approximately 0.21% due to the receipt of proceeds from the settlement of class action suits involving the Portfolio's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class C shares would have been approximately 6.92%.

The accompanying notes are an integral part of the financial statements.
42

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Global Strategist Portfolio

	Class IS
Selected Per Share Data and Ratios	Year Ended September 30, 2016††			Period from May 29, 2015^ to September 30, 2015
Net Asset Value, Beginning of Period	$	14.59		$	15.97
Income (Loss) from Investment Operations:
Net Investment Income†		0.26			0.09
Net Realized and Unrealized Gain (Loss)		0.96			(1.47	)
Total from Investment Operations		1.22			(1.38	)
Distributions from and/or in Excess of:
Net Realized Gain		(0.02	)		—
Net Asset Value, End of Period	$	15.79		$	14.59
Total Return++		8.42	%**		(8.70	)%#
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	143		$	9
Ratio of Expenses to Average Net Assets ⁽¹⁾		0.70	%+		0.71	%+*
Ratio of Net Investment Income to Average Net Assets ⁽¹⁾		1.68	%+		1.66	%+*
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.01	%		0.00	%§*
Portfolio Turnover Rate		103	%		98	%#
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		5.44	%		16.27	%*
Net Investment Loss to Average Net Assets		(3.06	)%		(13.90	)%*

†† Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class IS shares. The Ratio of Expenses to Average Net Assets and the Ratio of Net Investment Income to Average Net Assets would be unchanged as the change to current period custodian fees was offset against current period expense waivers/reimbursements with no impact to net expenses or net investment income.

^ Commencement of Offering.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value as of the last business day of the period.

§ Amount is less than 0.005%.

# Not Annualized.

* Annualized.

** Performance was positively impacted by approximately 0.35% due to the receipt of proceeds from the settlement of class action suits involving the Portfolio's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class IS shares would have been approximately 8.07%.

The accompanying notes are an integral part of the financial statements.
43

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements

The accompanying financial statements relate to the Global Strategist Portfolio. The Portfolio seeks above-average total return over a market cycle of three to five years. The Portfolio offers five classes of shares — Class I, Class A, Class L, Class C and Class IS.

On April 30, 2015, the Portfolio suspended offering Class L shares to all investors. Existing Class L shareholders may invest through reinvestment of dividends and distributions.

last reported bid and asked prices if such bid and asked prices are available on the relevant exchanges; (3) all other equity portfolio securities for which over-the-counter ("OTC") market quotations are readily available are valued at the latest reported sales price (or at the market official closing price if such market reports an official closing price), and if there was no trading in the security on a given day and if there is no official closing price from relevant markets for that day, the security is valued at the mean between the last reported bid and asked prices if such bid and asked prices are available on the relevant markets. Listed equity securities not traded on the valuation date with no reported bid and asked prices available on the exchange are valued at the mean between the current bid and asked prices obtained from one or more reputable brokers or dealers. An unlisted equity security that does not trade on the valuation date and for which bid and asked prices from the relevant markets are unavailable is valued at the mean between the current bid and asked prices obtained from one or more reputable brokers or dealers. In cases where a security is traded on more than one exchange, the security is valued on the exchange designated as the primary market; (4) futures are valued at the latest price published by the commodities exchange on which they trade; (5) swaps are marked-to-market daily based upon quotations from market makers; (6) listed options are valued at the last reported sales price on the exchange on which they are listed (or at the exchange official closing price if such exchange reports an official closing price). If an official closing price or last reported sales price is unavailable, the listed option should be fair valued at the mean between their latest bid and asked price. Unlisted options and swaps are valued by an outside pricing service approved by the Trustees or quotes from a broker or dealer; (7) when market quotations are not readily available, including circumstances under which Morgan Stanley Investment Management Inc. (the "Adviser") determines that the closing price, last sale price or the mean between the last reported bid and asked prices are not reflective of a security's market value, portfolio securities are valued at their fair value as determined in good faith under procedures established by and under the general supervision of the Trustees. Occasionally, developments affecting the closing prices of securities and other assets may occur between the times at which valuations of such securities are determined (that is, close of the foreign market on which the securities trade) and the close of business of the

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

New York Stock Exchange ("NYSE"). If developments occur during such periods that are expected to materially affect the value of such securities, such valuations may be adjusted to reflect the estimated fair value of such securities as of the close of the NYSE, as determined in good faith by the Trustees or by the Adviser using a pricing service and/or procedures approved by the Trustees; (8) quotations of foreign portfolio securities, other assets and liabilities and forward contracts stated in foreign currency are translated into U.S. dollar equivalents at the prevailing market rates prior to the close of the NYSE; and (9) investments in mutual funds, including the Morgan Stanley Institutional Liquidity Funds, are valued at the net asset value ("NAV") as of the close of each business day.

duration of any restrictions on the disposition of the investments. Due to the inherent uncertainty of valuations of such investments, the fair values may differ significantly from the values that would have been used had an active market existed. The Valuation Committee employs various methods for calibrating these valuation approaches including a regular review of valuation methodologies, key inputs and assumptions, transactional back-testing or disposition analysis, and reviews of any related market activity.

• Level 1 – unadjusted quoted prices in active markets for identical investments

• Level 2 – other significant observable inputs (including quoted prices for similar investments, interest rates, prepayment speeds, credit risk, etc.)

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

issuer's financial statements or other available documents and, if necessary, available information concerning other securities in similar circumstances

The following is a summary of the inputs used to value the Portfolio's investments as of September 30, 2016.

Investment Type	Level 1 Unadjusted quoted prices (000)		Level 2 Other significant observable inputs (000)		Level 3 Significant unobservable inputs (000)			Total (000)
Assets:
Fixed Income Securities
Agency Adjustable Rate Mortgage	$	—	$	319	$	—		$	319
Agency Fixed Rate Mortgages		—		11,516		—			11,516
Asset-Backed Security		—		387		—			387
Collateralized Mortgage Obligations — Agency Collateral Series		—		1,877		—			1,877
Commercial Mortgage- Backed Securities		—		2,814		—			2,814
Corporate Bonds		—		31,662		—			31,662
Mortgages — Other		—		2,546		—			2,546
Sovereign		—		66,786		—			66,786
U.S. Treasury Securities		—		23,830		—			23,830
Total Fixed Income Securities		—		141,737		—			141,737
Common Stocks
Aerospace & Defense		877		417		—			1,294
Air Freight & Logistics		464		349		—			813
Airlines		2,522		3,305		—			5,827
Auto Components		298		1,141		—			1,439
Automobiles		671		5,274		—			5,945
Banks		12,480		10,279		—	†		22,759	†
Beverages		1,246		2,573		—			3,819
Biotechnology		1,835		930		—			2,765
Building Products		433		2,250		—			2,683
Capital Markets		4,049		2,229		—			6,278
Chemicals		1,223		3,684		—			4,907
Commercial Services & Supplies		444		659		—			1,103
Communications Equipment		943		388		—			1,331
Construction & Engineering		667		2,253		—			2,920
Construction Materials		1,197		246		—			1,443
Consumer Finance		838		35		—			873
Containers & Packaging		175		155		—			330
Distributors		11		—		—			11
Diversified Consumer Services		45		—		—			45

Investment Type	Level 1 Unadjusted quoted prices (000)		Level 2 Other significant observable inputs (000)		Level 3 Significant unobservable inputs (000)			Total (000)
Common Stocks (cont'd)
Diversified Financial Services	$	1,013	$	674	$	—		$	1,687
Diversified Telecommunication Services		2,780		2,446		—			5,226
Electric Utilities		1,431		1,555		—			2,986
Electrical Equipment		340		1,541		—			1,881
Electronic Equipment, Instruments & Components		198		930		—			1,128
Energy Equipment & Services		1,010		153		—	†		1,163	†
Equity Real Estate Investment Trusts (REITs)		9,593		1,080		—			10,673
Food & Staples Retailing		2,350		1,865		—			4,215
Food Products		1,077		3,826		—			4,903
Gas Utilities		72		467		—			539
Health Care Equipment & Supplies		2,073		674		—			2,747
Health Care Providers & Services		1,764		470		—			2,234
Health Care Technology		70		—		—			70
Hotels, Restaurants & Leisure		2,030		795		—			2,825
Household Durables		1,556		588		—			2,144
Household Products		1,618		1,177		—			2,795
Independent Power Producers & Energy Traders		21		34		—			55
Independent Power and Renewable Electricity Producers		20		—		—			20
Industrial Conglomerates		877		1,752		—			2,629
Information Technology Services		4,163		290		—			4,453
Insurance		2,908		2,902		—			5,810
Internet & Direct Marketing Retail		1,244		99		—			1,343
Internet Software & Services		1,795		57		—			1,852
Leisure Products		38		—		—			38
Life Sciences Tools & Services		403		169		—			572
Machinery		994		2,263		—			3,257
Marine		—		284		—			284
Media		3,154		1,647		—			4,801
Metals & Mining		821		2,340		—			3,161
Multi-Utilities		1,090		763		—			1,853
Multi-line Retail		191		127		—			318
Oil, Gas & Consumable Fuels		5,364		3,847		—			9,211
Paper & Forest Products		74		322		—			396
Personal Products		157		1,918		—			2,075
Pharmaceuticals		9,008		6,375		—			15,383
Professional Services		1,042		1,394		—			2,436
Real Estate Management & Development		470		1,805		—			2,275
Road & Rail		1,335		1,767		—			3,102

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

Investment Type	Level 1 Unadjusted quoted prices (000)			Level 2 Other significant observable inputs (000)			Level 3 Significant unobservable inputs (000)			Total (000)
Common Stocks (cont'd)
Semiconductors & Semiconductor Equipment	$	2,103		$	598		$	—	@	$	2,701
Software		2,442			1,145			—			3,587
Specialty Retail		1,620			565			—			2,185
Tech Hardware, Storage & Peripherals		3,468			464			—			3,932
Textiles, Apparel & Luxury Goods		582			1,406			—			1,988
Thrifts & Mortgage Finance		153			22			—			175
Tobacco		901			1,558			—			2,459
Trading Companies & Distributors		297			1,157			—			1,454
Transportation Infrastructure		189			1,310			—			1,499
Water Utilities		47			55			—			102
Wireless Telecommunication Services		245			1,704			—			1,949
Total Common Stocks		106,609			94,547			—	@†		201,156	†
Investment Companies		412			—			—			412
Rights		—			1			—			1
Warrants		4			—			—	†		4	†
Call Option Purchased		290			—			—			290
Short-Term Investments
Investment Company		5,955			—			—			5,955
Sovereign		—			1,621			—			1,621
U.S. Treasury Securities		—			5,944			—			5,944
Total Short-Term Investments		5,955			7,565			—			13,520
Foreign Currency Forward Exchange Contracts		—			1,051			—			1,051
Futures Contracts		903			—			—			903
Credit Default Swap Agreement		—			108			—			108
Interest Rate Swap Agreements		—			821			—			821
Total Return Swap Agreements		—			1,056			—			1,056
Total Assets		114,173			246,886			—	@†		361,059	†
Liabilities:
Foreign Currency Forward Exchange Contracts		—			(891	)		—			(891	)
Futures Contracts		(369	)		—			—			(369	)
Interest Rate Swap Agreements		—			(1,461	)		—			(1,461	)
Total Return Swap Agreements		—			(543	)		—			(543	)
Total Liabilities		(369	)		(2,895	)		—			(3,264	)
Total	$	113,804		$	243,991		$	—	@†	$	357,795	†

† Includes one or more securities which are valued at zero.

@ Value is less than $500.

Transfers between investment levels may occur as the markets fluctuate and/or the availability of data used in an investment's valuation changes. The Portfolio recognizes transfers between the levels as of the end of the period. As of September 30, 2016, securities with a total value of approximately $13,507,000 transferred from Level 2 to Level 1. Securities that were valued using other significant observable inputs at September 30, 2015 were valued using unadjusted quoted prices at September 30, 2016. At September 30, 2016, the fair value of certain securities were adjusted due to developments which occurred between the time of the close of the foreign markets on which they trade and the close of business on the NYSE which resulted in their Level 2 classification.

Following is a reconciliation of investments in which significant unobservable inputs (Level 3) were used in determining fair value.

	Common Stocks (000)			Warrants
Beginning Balance	$	6		$	—	†
Purchases		5			—	@
Sales		—			—
Amortization of discount		—			—
Transfers in		—			—
Transfers out		—			—
Corporate actions		—			(—	@)
Change in unrealized appreciation (depreciation)		(11	)		(—	@)
Realized gains (losses)		—			—
Ending Balance	$	—	@	$	—	†
Net change in unrealized appreciation (depreciation) from investments still held as of September 30, 2016	$	(11	)	$	(—	@)

† Includes one or more securities which are valued at zero.

@ Value is less than $500.

– investments, other assets and liabilities at the prevailing rate of exchange on the valuation date;

– investment transactions and investment income at the prevailing rates of exchange on the dates of such transactions.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

in the foreign exchange rates from the fluctuations arising from changes in the market prices of securities held at period end. Similarly, the Portfolio does not isolate the effect of changes in foreign exchange rates from the fluctuations arising from changes in the market prices of securities sold during the period. Accordingly, realized and unrealized foreign currency gains (losses) on investments in securities are included in the reported net realized and unrealized gains (losses) on investment transactions and balances. However, pursuant to U.S. federal income tax regulations, gains and losses from certain foreign currency transactions and the foreign currency portion of gains and losses realized on sales and maturities of foreign denominated debt securities are treated as ordinary income for U.S. federal income tax purposes.

individual companies to prevent, among other concerns, violations of foreign investment limitations. As a result, an additional class of shares (identified as "Foreign" in the Portfolio of Investments) may be created and offered for investment. The "local" and "foreign shares" market values may differ. In the absence of trading of the foreign shares in such markets, the Portfolio values the foreign shares at the closing exchange price of the local shares.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

seeks to use derivatives to further the Portfolio's investment objectives, there is no assurance that the use of derivatives will achieve this result.

Following is a description of the derivative instruments and techniques that the Portfolio used during the period and their associated risks:

be equal only to the net amount to be paid or received under the agreement, based on the relative values of the positions held by each party. Cleared swap transactions may help reduce counterparty credit risk. In a cleared swap, the Portfolio's ultimate counterparty is a clearinghouse rather than a swap dealer, bank or other financial institution. OTC swap agreements are not entered into or traded on exchanges and often there is no central clearing or guaranty function for OTC swaps. These OTC swaps are often subject to credit risk or the risk of default or non-performance by the counterparty. Both OTC and cleared swaps could result in losses if interest rates, foreign currency exchange rates or other factors are not correctly anticipated by the Portfolio or if the reference index, security or investments do not perform as expected. During the period swap agreements are open, payments are received from or made to the clearinghouse or counterparty based upon changes in the value of the contract (variation margin). The Dodd-Frank Wall Street Reform and Consumer Protection Act and related regulatory developments require the clearing and exchange-trading of certain standardized swap transactions. Mandatory exchange-trading and clearing is occurring on a phased-in basis.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

If the Portfolio is a seller of protection and a credit event occurs, as defined under the terms of that particular swap agreement, the Portfolio will either (i) pay to the buyer of protection an amount equal to the notional amount of the swap agreement and take delivery of the referenced obligation, other deliverable obligations or underlying securities comprising the referenced index or (ii) pay a net settlement amount in the form of cash or securities equal to the notional amount of the swap agreement less the recovery value of the referenced obligation or underlying securities comprising the referenced index. If the Portfolio is a buyer of protection and a credit event occurs, as defined under the terms of that particular swap agreement, the Portfolio will either (i) receive from the seller of protection an amount equal to the notional amount of the swap agreement and deliver the referenced obligation, other deliverable obligations or underlying securities comprising the referenced index or (ii) receive a net settlement amount in the form of cash or securities equal to the notional amount of the swap agreement less the recovery value of the referenced obligation or underlying securities comprising the referenced index. Recovery values are estimated by market makers considering either industry standard recovery rates or entity specific factors and considerations until a credit event occurs. If a credit event has occurred, the recovery value is determined by a facilitated auction whereby a minimum number of allowable broker bids, together with a specified valuation method, are used to calculate the settlement value. The Portfolio's maximum risk of loss from counterparty risk, either as the protection seller or as the protection buyer, is the fair value of the swap agreement.

When the Portfolio has an unrealized loss on a swap agreement, the Portfolio has instructed the custodian to

pledge cash or liquid securities as collateral with a value approximately equal to the amount of the unrealized loss. Collateral pledges are monitored and subsequently adjusted if and when the swap valuations fluctuate. If applicable, cash collateral is included with "Due from (to) Broker" in the Statement of Assets and Liabilities.

Upfront payments paid or received by the Portfolio will be reflected as an asset or liability, respectively, in the Statement of Assets and Liabilities.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

contracts involves the risk of loss from the insolvency or bankruptcy of the counterparty to the contract or the failure of the counterparty to make payments or otherwise comply with the terms of the contract. A currency contract is marked-to-market daily and the change in market value is recorded by the Portfolio as unrealized gain or loss. The Portfolio records realized gains (losses) when the currency contract is closed equal to the difference between the value of the currency contract at the time it was opened and the value at the time it was closed.

Options: With respect to options, the Portfolio is subject to equity risk, interest rate risk and foreign currency exchange risk in the normal course of pursuing its investment objectives. If the Portfolio buys an option, it buys a legal contract giving it the right to buy or sell a specific amount of the underlying instrument or foreign currency, or futures contract on the underlying instrument or foreign currency, at an agreed-upon price typically in exchange for a premium paid by the Portfolio. The Portfolio may purchase and/or sell put and call options. Purchasing call options tends to increase the Portfolio's exposure to the underlying (or similar) instrument. Purchasing put options tends to decrease the Portfolio's exposure to the underlying (or similar) instrument. When entering into purchased option contracts, the Portfolio bears the risk of interest or exchange rates or securities prices moving unexpectedly, in which case, the Portfolio may not achieve the anticipated benefits of the purchased option contracts; however the risk of loss is limited to the premium paid. Purchased options are reported as part of "Total Investments in Securities" in the Statement of Assets and Liabilities. Premium paid for purchasing options which expired are treated as realized losses. If the Portfolio sells an option, it sells to another party the right to buy from or sell to the Portfolio a specific amount of the underlying instrument or foreign currency, or futures contract on the underlying instrument or foreign currency, at an agreed- upon price typically in exchange for a premium received by the Portfolio. The Portfolio may write call and put options on stock indexes, futures, securities or currencies it owns or in which it may invest. Writing put options tend to increase the Portfolio's exposure to the underlying instrument. Writing call options tend to decrease the Portfolio's exposure to the underlying instruments. When the Portfolio writes a call or put option,

an amount equal to the premium received is recorded as a liability. Any liability recorded is subsequently adjusted to reflect the current value of the options written. Premiums received from writing options which expire are treated as realized gains. Premiums received from writing options which are exercised or are closed are added to or offset against the proceeds or amount paid on the transaction to determine the net realized gain or loss. The Portfolio as a writer of an option has no control over whether the underlying future, security or currency may be sold (call) or purchased (put) and as a result bears the market risk of an unfavorable change in the price of the future, security or currency underlying the written option. When options are purchased OTC, the Portfolio bears the risk that the counterparty that wrote the option will be unable or unwilling to perform its obligations under the option contract. Options may also be illiquid and the Portfolio may have difficulty closing out its position. A decision as to whether, when and how to use options involves the exercise of skill and judgment and even a well-conceived option transaction may be unsuccessful because of market behavior or unexpected events. The prices of options can be highly volatile and the use of options can lower total returns.

Transactions in written options for the year ended September 30, 2016 were as follows:

Written Options	Notional Amount (000)			Premiums Received (000)
Options outstanding at September 30, 2015		—		$	—
Options written		27,590			194
Options closed		(27,590	)		(194	)
Options exercised		—			—
Options expired		—			—
Options outstanding at September 30, 2016		—		$	—

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

The following tables set forth the fair value of the Portfolio's derivative contracts by primary risk exposure as of September 30, 2016.

Asset Derivatives
Statement of Assets and
Liabilities Location

Primary Risk
Exposure

Value
(000)

Option Purchased

Investments, at Value
(Option Purchased)

Equity Risk

290

(a)

Foreign Currency
Forward Exchange
Contracts

Unrealized Appreciation on
Foreign Currency Forward
Exchange Contracts

Currency Risk

1,051

Futures Contracts

Variation Margin on
Futures Contracts

Equity Risk

770

(b)

Futures Contracts

Variation Margin on
Futures Contracts

Interest Rate Risk

133

(b)

Swap Agreement

Unrealized Appreciation on
Swap Agreement

Credit Risk

108

Swap Agreements

Unrealized Appreciation on
Swap Agreements

Equity Risk

1,056

Swap Agreements

Unrealized Appreciation on
Swap Agreements

Interest Rate Risk

361

Swap Agreement

Variation Margin on
Swap Agreement

Interest Rate Risk

460

(b)

Total

4,229

Liability Derivatives
Statement of Assets and
Liabilities Location

Primary Risk
Exposure

Value
(000)

Foreign Currency
Forward Exchange
Contracts

Unrealized Depreciation on
Foreign Currency Forward
Exchange Contracts

Currency Risk

(891

)

Futures Contracts

Variation Margin on
Futures Contracts

Equity Risk

(267

)(b)

Futures Contracts

Variation Margin on
Futures Contracts

Interest Rate Risk

(102

)(b)

Swap Agreements

Unrealized Depreciation on
Swap Agreements

Equity Risk

(543

)

Swap Agreements

Variation Margin on
Swap Agreements

Interest Rate Risk

(1,461

)(b)

Total

(3,264

)

(a) Amounts are included in Investments in Securities in the Statement of Assets and Liabilities.

Realized Gain (Loss)
Primary Risk Exposure	Derivative Type	Value (000)
Currency Risk	Options Purchased	$	(252	)(c)
Currency Risk	Options Written		174
Currency Risk	Foreign Currency Forward Exchange Contracts		(1,490)
Commodity Risk	Futures Contracts		(595	)
Currency Risk	Futures Contracts		(95	)
Equity Risk	Futures Contracts		6,792
Interest Rate Risk	Futures Contracts		(2,453	)
Credit Risk	Swap Agreements		80
Equity Risk	Swap Agreements		(982	)
Interest Rate Risk	Swap Agreements		(2,381	)
Total		$	(1,202	)
Change in Unrealized Appreciation (Depreciation)
Primary Risk Exposure	Derivative Type	Value (000)
Equity Risk	Options Purchased	$	73	(c)
Currency Risk	Foreign Currency Forward Exchange Contracts		124
Commodity Risk	Futures Contracts		155
Currency Risk	Futures Contracts		(63	)
Equity Risk	Futures Contracts		542
Interest Rate Risk	Futures Contracts		560
Credit Risk	Swap Agreements		48
Equity Risk	Swap Agreements		490
Interest Rate Risk	Swap Agreements		(304	)
Total		$	1,625

At September 30, 2016, the Portfolio's derivative assets and liabilities are as follows:

Gross Amounts of Assets and Liabilities Presented in the Statement of Assets and Liabilities
Derivatives(d)	Assets(e) (000)		Liabilities(e) (000)
Foreign Currency Forward Exchange Contracts	$	1,051	$	(891	)
Swap Agreements		1,525		(543	)
Total	$	2,576	$	(1,434	)

(d) Excludes exchange traded derivatives.

(e) Absent an event of default or early termination, OTC derivative assets and liabilities are presented gross and not offset in the Statement of Assets and Liabilities.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

default, termination and/or potential deterioration in the credit quality of the counterparty. Various Master Agreements govern the terms of certain transactions with counterparties, including transactions such as swap, forward, repurchase and reverse repurchase agreements. These Master Agreements typically attempt to reduce the counterparty risk associated with such transactions by specifying credit protection mechanisms and providing standardization that improves legal certainty. Cross-termination provisions under Master Agreements typically provide that a default in connection with one transaction between the Portfolio and a counterparty gives the non-defaulting party the right to terminate any other transactions in place with the defaulting party to create one single net payment due to/due from the defaulting party and may be a feature in certain Master Agreements. In the event the Portfolio exercises its right to terminate a Master Agreement after a counterparty experiences a termination event as defined in the Master Agreement, the return of collateral with market value in excess of the Portfolio's net liability may be delayed or denied.

The following tables present derivative financial instruments that are subject to enforceable netting arrangements as of September 30, 2016.

Gross Amounts Not Offset in the Statement of Assets and Liabilities
Counterparty	Gross Asset Derivatives Presented in Statement of Assets and Liabilities (000)			Financial Instrument (000)			Collateral Received(f) (000)			Net Amount (not less than $0) (000)
Australia and New Zealand Banking Group	$	40		$	(40	)	$	—		$	0
Bank of America NA		370			(1	)		(248	)		121
Bank of Montreal		—	@		(—	@)		—			0
Barclays Bank PLC		485			(81	)		(404	)		0
BNP Paribas SA		9			(7	)		—			2
Citibank NA		359			(147	)		(212	)		0
Credit Suisse International		3			(3	)		—			0
Goldman Sachs International		557			(520	)		—			37
HSBC Bank PLC		55			(1	)		—			54
JPMorgan Chase Bank NA		442			(337	)		—			105
Royal Bank of Canada		1			—			—			1
UBS AG		255			(129	)		—			126
Total	$	2,576		$	(1,266	)	$	(864	)	$	446

(f) In some instances, the actual collateral received may be more than the amount shown here due to overcollateralization.

Gross Amounts Not Offset in the Statement of Assets and Liabilities
Counterparty	Gross Liability Derivatives Presented in Statement of Assets and Liabilities (000)		Financial Instrument (000)			Collateral Pledged (000)		Net Amount (not less than $0) (000)
Australia and New Zealand Banking Group	$	92	$	(40	)	$	—	$	52
Bank of America NA		45		(1	)		—		44
Bank of Montreal		1		(—	@)		—		1
Bank of New York Mellon		2		—			—		2
Barclays Bank PLC		95		(81	)		—		14
BNP Paribas SA		7		(7	)		—		0
Citibank NA		147		(147	)		—		0
Commonwealth Bank of Australia		22		—			—		22
Credit Suisse International		28		(3	)		—		25
Goldman Sachs International		520		(520	)		—		0
HSBC Bank PLC		1		(1	)		—		0
JPMorgan Chase Bank NA		337		(337	)		—		0
Northern Trust Company		1		—			—		1
State Street Bank and Trust Co.		7		—			—		7
UBS AG		129		(129	)		—		0
Total	$	1,434	$	(1,266	)	$	—	$	168

For the year ended September 30, 2016, the approximate average monthly amount outstanding for each derivative type is as follows:

Foreign Currency Forward Exchange Contracts:
Average monthly principal amount	$	227,342,000
Futures Contracts:
Average monthly original value	$	267,933,000
Swap Agreements:
Average monthly notional amount	$	140,075,000
Options Purchased:
Average monthly notional amount		15,371,000
Options Written:
Average monthly notional amount		15,324,000

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

lower than the agreed upon purchase price, in which case there could be an unrealized loss at the time of delivery. Purchasing investments on a when-issued or delayed delivery basis may be considered a form of leverage which may increase the impact that gains (losses) may have on the Portfolio.

7. Dividends and Distributions to Shareholders: Dividend income and distributions to shareholders are recorded on the ex-dividend date. Dividends from net investment income, if any, are declared and paid annually. Net realized capital gains, if any, are distributed at least annually.

C. Administration Fees: The Adviser also serves as Administrator to the Fund and provides administrative services pursuant to an Administration Agreement for an annual fee, accrued daily and paid monthly, of 0.08% of the Portfolio's average daily net assets. Under a Sub-Administration Agreement between the Administrator and State Street Bank and Trust Company ("State Street"), State Street provides certain administrative services to the Fund. For such services, the Administrator pays State Street a portion of the fee the Administrator receives from the Portfolio.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

and paid monthly, at an annual rate of 0.25% of the Portfolio's average daily net assets attributable to Class A shares.

The Fund has adopted a Distribution and Shareholder Services Plan with respect to Class L shares pursuant to Rule 12b-1 under the Act. Under the Distribution and Shareholder Services Plan, the Portfolio pays the Distributor a distribution fee, accrued daily and paid monthly, at an annual rate of 0.50% and a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Portfolio's average daily net assets attributable to Class L shares.

which was recognized as a change in accounting estimate and was reflected as "Reimbursement of Custodian Fees" in the Statement of Operations. Pursuant to the expense limitations described in Note B, the Portfolio has experienced expenses reimbursed by the Adviser during the current period. Accordingly, the reimbursement of out-of-pocket expenses in the current period resulted in the reduction in the current period expenses reimbursed by the Adviser.

G. Security Transactions and Transactions with Affiliates: For the year ended September 30, 2016, purchases and sales of investment securities for the Portfolio, other than long-term U.S. Government securities and short-term investments, were approximately $145,854,000 and $202,230,000, respectively. For the year ended September 30, 2016, purchases and sales of long-term U.S. Government securities were approximately $213,287,000 and $190,444,000, respectively.

The Portfolio invests in the Institutional Class of the Morgan Stanley Institutional Liquidity Funds (the "Liquidity Funds"), an open-end management investment company managed by the Adviser. Advisory fees paid by the Portfolio are reduced by an amount equal to its pro-rata share of the advisory and administration fees paid by the Portfolio due to its investment in the Liquidity Funds. For the year ended September 30, 2016, advisory fees paid were reduced by approximately $24,000 relating to the Portfolio's investment in the Liquidity Funds.

A summary of the Portfolio's transactions in shares of the Liquidity Funds during the year ended September 30, 2016 is as follows:

Value September 30, 2015 (000)				Purchases at Cost (000)				Sales (000)				Dividend Income (000)				Value September 30, 2016 (000)
$	30,788			$	198,791			$	223,624			$	55			$	5,955

The Portfolio invests in Morgan Stanley Institutional Fund, Inc. — Emerging Markets Portfolio ("Emerging Markets Portfolio"), an open-end management investment company advised by an affiliate of the Adviser. Advisory fees paid by the Portfolio are reduced by an amount equal to its pro-rata share of the advisory and administration fees paid by the Emerging Markets Portfolio. For the year ended September 30, 2016, advisory fees paid were reduced by approximately $1,000 relating to the Portfolio's investment in the Emerging Markets Portfolio. The Emerging Markets Portfolio has a cost basis of approximately $133,000 at September 30, 2016.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

A summary of the Portfolio's transactions in shares of the Emerging Markets Portfolio during the year ended September 30, 2016 is as follows:

Value September 30, 2015 (000)				Purchases at Cost (000)				Sales (000)				Dividend Income (000)				Value September 30, 2016 (000)
$	98			$	1			$	—			$	1			$	113

certain tax positions that would require recognition in the financial statements. If applicable, the Portfolio recognizes interest accrued related to unrecognized tax benefits in "Interest Expense" and penalties in "Other Expenses" in the Statement of Operations. The Portfolio files tax returns with the U.S. Internal Revenue Service, New York and various states. Each of the tax years in the four-year period ended September 30, 2016, remains subject to examination by taxing authorities.

2016 Distributions Paid From:				2015 Distributions Paid From:
Ordinary Income (000)		Long-Term Capital Gain (000)		Ordinary Income (000)		Long-Term Capital Gain (000)
$	—	$	425	$	17,981	$	6,726

Permanent differences, primarily due to differing treatments of gains (losses) related to foreign currency transactions, basis adjustments for swap transactions, paydown adjustments, distribution redesignations and tax adjustments on passive foreign investment companies sold by the Portfolio, resulted in the following reclassifications among the components of net assets at September 30, 2016:

Accumulated Undistributed Net Investment Income (000)				Accumulated Net Realized Loss (000)				Paid-in-Capital (000)
$	(3,764	)		$	3,764			$	—

At September 30, 2016, the components of distributable earnings for the Portfolio on a tax basis were as follows:

Undistributed Ordinary Income (000)				Undistributed Long-Term Capital Gain (000)
$	2,855			$	—

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

At September 30, 2016, the Portfolio had available for federal income tax purposes unused short term capital losses of approximately $8,160,000 that do not have an expiration date.

K. Subsequent Event: Effective October 3, 2016, the Portfolio may, consistent with its principal investment strategies, invest up to 25% of its total assets in a wholly-owned subsidiary of the Portfolio organized as a company under the laws of the Cayman Islands (the "Subsidiary"). The Subsidiary may invest, directly or indirectly through the use of derivatives, in securities, commodities, commodity-related instruments and other investments, primarily futures, swaps and notes. The initial startup cost, including legal and other costs associated with the creation of the Subsidiary, was approximately $58,000 and is reflected as "Organizational Costs" in the Statement of Operations. The Subsidiary is advised by the Adviser.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Report of Independent Registered Public Accounting Firm

To the Shareholders and Board of Trustees of
Morgan Stanley Institutional Fund Trust —
Global Strategist Portfolio

We have audited the accompanying statement of assets and liabilities, including the portfolio of investments, of Global Strategist Portfolio (one of the portfolios constituting Morgan Stanley Institutional Fund Trust) (the "Portfolio") as of September 30, 2016, and the related statement of operations for the year then ended, the statements of changes in net assets for each of the two years in the period then ended and the financial highlights for each of the years or periods indicated therein. These financial statements and financial highlights are the responsibility of the Portfolio's management. Our responsibility is to express an opinion on these financial statements and financial highlights based on our audits.

In our opinion, the financial statements and financial highlights referred to above present fairly, in all material respects, the financial position of Global Strategist Portfolio (one of the portfolios constituting Morgan Stanley Institutional Fund Trust) at September 30, 2016, the results of its operations for the year then ended, the changes in its net assets for the two years in the period then ended and the financial highlights for each of the years or periods indicated therein, in conformity with U.S. generally accepted accounting principles.

Boston, Massachusetts
November 22, 2016

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Advisory Agreement Approval (unaudited)

Nature, Extent and Quality of Services

Performance, Fees and Expenses of the Portfolio

The Board reviewed the performance, fees and expenses of the Portfolio compared to its peers, as determined by Broadridge, and to appropriate benchmarks where applicable. The Board discussed with the Adviser the performance goals and the actual results achieved in managing the Portfolio. When considering a fund's performance, the Board and the Adviser place emphasis on trends and longer-term returns (focusing on one-year, three-year and five-year performance, as of December 31, 2015, or since inception, as applicable). When a fund underperforms its benchmark and/or its peer group average, the Board and the Adviser discuss the causes of such underperformance and, where necessary, they discuss specific changes to investment strategy or investment personnel. The Board noted that the Portfolio's performance was better than its peer group average for the three- and five-year periods but below its peer group average for the one-year period. The Board discussed with the Adviser the level of the advisory and administration fees (together, the "management fee") for this Portfolio relative to comparable funds and/or other accounts advised by the Adviser and/or compared to its peers as determined by Broadridge. In addition to the management fee, the Board also reviewed the Portfolio's total expense ratio. The Board noted that the Portfolio's management fee and total expense ratio were lower than its peer group averages. After discussion, the Board concluded that the Portfolio's performance (i) was competitive with its peer group average; and (ii) management fee and total expense ratio were competitive with its peer group averages.

Economies of Scale

The Board considered the size and growth prospects of the Portfolio and how that relates to the Portfolio's total expense ratio and particularly the Portfolio's management fee rate, which does not include breakpoints. In conjunction with its review of the Adviser's profitability, the Board discussed with the Adviser how a change in assets can affect the efficiency or effectiveness of managing the Portfolio and whether the management fee level is appropriate relative to current and projected asset levels and/or whether the management fee structure reflects economies of scale as asset levels change. The Board has determined that its review of the actual and/or potential economies of scale of the Portfolio supports its decision to approve the Management Agreement.

Profitability of the Adviser and Affiliates

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Advisory Agreement Approval (unaudited) (cont'd)

Other Benefits of the Relationship

Resources of the Adviser and Historical Relationship Between the Portfolio and the Adviser

Other Factors and Current Trends

General Conclusion

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Federal Tax Notice (unaudited)

For federal income tax purposes, the following information is furnished with respect to the distributions paid by the Portfolio during its taxable year ended September 30, 2016.

The Portfolio designated and paid approximately $425,000 as a long-term capital gain distribution.

The Fund intends to pass through foreign tax credits of approximately $360,000 and has derived net income from sources within foreign countries amounting to approximately $4,124,000.

In January, the Portfolio provides tax information to shareholders for the preceding calendar year.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Privacy Notice (unaudited)

MORGAN STANLEY INVESTMENT MANAGEMENT INC.
AN IMPORTANT NOTICE CONCERNING OUR U.S. PRIVACY POLICY

WE RESPECT YOUR PRIVACY

1. WHAT PERSONAL INFORMATION DO WE COLLECT ABOUT YOU?

For example:

• We may obtain information about your creditworthiness and credit history from consumer reporting agencies.

• We may collect background information from and through third-party vendors to verify representations you have made and to comply with various regulatory requirements.

2. WHEN DO WE DISCLOSE PERSONAL INFORMATION WE COLLECT ABOUT YOU?

We may disclose personal information we collect about you to other Morgan Stanley companies and to non-affiliated third parties.

a. Information We Disclose to Other Morgan Stanley Companies.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Privacy Notice (unaudited) (cont'd)

b. Information We Disclose to Non-affiliated Third Parties.

3. HOW DO WE PROTECT THE SECURITY AND CONFIDENTIALITY OF PERSONAL INFORMATION WE COLLECT ABOUT YOU?

4. HOW CAN YOU LIMIT THE SHARING OF CERTAIN TYPES OF PERSONAL INFORMATION WITH OTHER MORGAN STANLEY COMPANIES?

5. HOW CAN YOU LIMIT THE USE OF CERTAIN TYPES OF PERSONAL INFORMATION BY OTHER MORGAN STANLEY COMPANIES FOR MARKETING?

6. HOW CAN YOU SEND US AN OPT-OUT INSTRUCTION?

• Calling us at (800) 548-7786
Monday–Friday between 8a.m. and 6p.m.(EST)

• Writing to us at the following address:

Boston Financial Data Services, Inc.
c/o Privacy Coordinator
P.O. Box 219804
Kansas City, Missouri 64121

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Privacy Notice (unaudited) (cont'd)

7. WHAT IF AN AFFILIATED COMPANY BECOMES A NON-AFFILIATED THIRD PARTY?

SPECIAL NOTICE TO RESIDENTS OF VERMONT

If you wish to receive offers for investment products and services offered by or through other Morgan Stanley companies, please notify us in writing at the following address:

Boston Financial Data Services, Inc.
c/o Privacy Coordinator
P.O. Box 219804
Kansas City, Missouri 64121

SPECIAL NOTICE TO RESIDENTS OF CALIFORNIA

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited)

Independent Trustees:

Name, Age and Address of
Independent Trustee

Position(s)
Held with
Registrant

Length of Time
Served*

Principal Occupation(s) During Past 5 Years
and Other Relevant Professional Experience

Number of
Portfolios in
Fund Complex
Overseen by
Independent
Trustee**

Other Directorships
Held by Independent
Trustee***

Frank L. Bowman (71)
c/o Perkins Coie LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
August
2006

Kathleen A. Dennis (63)
c/o Perkins Coie LLP
Counsel to the Independent Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
August
2006

Director of various non-profit organizations.

Nancy C. Everett (61)
c/o Perkins Coie LLP
Counsel to the Independent Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
January
2015

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Age and Address of
Independent Trustee

Position(s)
Held with
Registrant

Length of Time
Served*

Principal Occupation(s) During Past 5 Years
and Other Relevant Professional Experience

Number of
Portfolios in
Fund Complex
Overseen by
Independent
Trustee**

Other Directorships
Held by Independent
Trustee***

Jakki L. Haussler (59)
c/o Perkins Coie LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
January
2015

Dr. Manuel H. Johnson (67)
c/o Johnson Smick
International, Inc.
220 I Street, N.E. —
Suite 200
Washington, D.C. 20002

Trustee

Since
July
1991

100

Director of NVR, Inc. (home construction).

Joseph J. Kearns (74)
c/o Kearns & Associates LLC
23823 Malibu Road
S-50-440
Malibu, CA 90265

Trustee

Since
August
1994

101

Director of Electro Rent Corporation (equipment leasing). Prior to December 31, 2013, Director of The Ford Family Foundation.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Age and Address of
Independent Trustee

Position(s)
Held with
Registrant

Length of Time
Served*

Principal Occupation(s) During Past 5 Years
and Other Relevant Professional Experience

Number of
Portfolios in
Fund Complex
Overseen by
Independent
Trustee**

Other Directorships
Held by Independent
Trustee***

Michael F. Klein (57)
c/o Perkins Coie LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
August
2006

Director of certain investment funds managed or sponsored by Aetos Capital, LLC; Director of Sanitized AG and Sanitized Marketing AG (specialty chemicals).

Michael E. Nugent (80)
522 Fifth Avenue
New York, NY 10036

Chair of the
Board and
Trustee

Chair of the Boards since
July 2006 and Trustee since
July 1991

100

None.

W. Allen Reed (69)
c/o Perkins Coie LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
August
2006

Director of Legg Mason, Inc.; formerly, Director of the Auburn University Foundation (2010-2015).

Fergus Reid (84)
c/o Joe Pietryka, Inc.
85 Charles Colman Blvd.
Pawling, NY 12564

Trustee

Since
June
1992

Chairman, Joe Pietryka, Inc.; Chairperson of the Governance Committee and Director or Trustee of various Morgan Stanley Funds (since June 1992).

100

Formerly, Trustee and Director of certain investment companies in the JP Morgan Fund Complex managed by JP Morgan Investment Management Inc. (1987-2012).

* This is the earliest date the Trustee began serving the Morgan Stanley Funds. Each Trustee serves an indefinite term, until his or her successor is elected.

*** This includes any directorships at public companies and registered investment companies held by the Trustee at any time during the past five years.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited) (cont'd)

Executive Officers:

Name, Age and Address of Executive Officer

Position(s) Held
with
Registrant

Length of
Time Served*

Principal Occupation(s) During Past 5 Years

John H. Gernon (53)
522 Fifth Avenue
New York, NY 10036

President and
Principal
Executive
Officer

Since
September
2013

Stefanie V. Chang Yu (49)
522 Fifth Avenue
New York, NY 10036

Chief
Compliance
Officer

Since
December
1997

Joseph C. Benedetti (51)
522 Fifth Avenue
New York, NY 10036

Vice President

Since
January
2014

Francis J. Smith (51)
522 Fifth Avenue
New York, NY 10036

Treasurer and
Principal
Financial
Officer

Treasurer
since July
2003 and
Principal
Financial
Officer since
September
2002

Executive Director of the Adviser and various entities affiliated with the Adviser; Treasurer (since July 2003) and Principal Financial Officer of various Morgan Stanley Funds (since September 2002).

Mary E. Mullin (49)
522 Fifth Avenue
New York, NY 10036

Secretary

Since
June
1999

Executive Director of the Adviser; Secretary of various Morgan Stanley Funds (since June 1999).

* This is the earliest date the officer began serving the Morgan Stanley Funds. Each officer serves a one-year term, until his or her successor is elected and has qualified.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Adviser and Administrator

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

Distributor

Morgan Stanley Distribution, Inc.
522 Fifth Avenue
New York, New York 10036

Dividend Disbursing and Transfer Agent

Boston Financial Data Services, Inc.
2000 Crown Colony Drive
Quincy, Massachusetts 02169

Custodian

State Street Bank and Trust Company
One Lincoln Street
Boston, Massachusetts 02111

Legal Counsel

Dechert LLP
1095 Avenue of the Americas
New York, New York 10036

Counsel to the Independent Trustees

Perkins Coie LLP
30 Rockefeller Plaza
New York, New York 10112

Independent Registered Public Accounting Firm

Ernst & Young LLP
200 Clarendon Street
Boston, Massachusetts 02116

Reporting to Shareholders

Proxy Voting Policies and Procedures and Proxy Voting Record

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable Portfolio of Morgan Stanley Institutional Funds Trust, which describes in detail the Portfolio's investment policies, risks, fees and expenses. Please read the prospectus carefully before you invest or send money. For additional information, including information regarding the investments comprising the Portfolio, please visit our website at www.morganstanley.com/im or call toll free 1 (800) 548-7786.

Printed in U.S.A.
This Report has been prepared for shareholders and may be distributed to others only if preceded or accompanied by a current prospectus.

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

IFTGSANN
1627512 EXP. 11.30.17

INVESTMENT MANAGEMENT

Morgan Stanley Institutional Fund Trust

High Yield Portfolio

Annual Report

September 30, 2016

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Table of Contents

Shareholders' Letter					2
Expense Example					3
Investment Overview					4
Portfolio of Investments					7
Statement of Assets and Liabilities					14
Statement of Operations					16
Statements of Changes in Net Assets					17
Financial Highlights					19
Notes to Financial Statements					24
Report of Independent Registered Public Accounting Firm					32
Investment Advisory Agreement Approval					33
Privacy Notice					35
Trustee and Officer Information					38

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Shareholders' Letter (unaudited)

Dear Shareholders,

We are pleased to provide this Annual report, in which you will learn how your investment in High Yield Portfolio (the "Portfolio") performed during the latest twelve-month period.

As always, we thank you for selecting Morgan Stanley Investment Management, and look forward to working with you in the months and years ahead.

Sincerely,

John H. Gernon
President and Principal Executive Officer

October 2016

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Expense Example (unaudited)

High Yield Portfolio

This example is based on an investment of $1,000 invested at the beginning of the six-month period ended September 30, 2016 and held for the entire six-month period (unless otherwise noted).

Actual Expenses

Hypothetical Example for Comparison Purposes

	Beginning Account Value 4/1/16		Actual Ending Account Value 9/30/16		Hypothetical Ending Account Value		Actual Expenses Paid During Period*		Hypothetical Expenses Paid During Period*		Net Expense Ratio During Period**
High Yield Portfolio Class I	$	1,000.00	$	1,103.60	$	1,021.75	$	3.42	$	3.29		0.65	%***
High Yield Portfolio Class A		1,000.00		1,100.70		1,020.00		5.25		5.05		1.00	***
High Yield Portfolio Class L		1,000.00		1,099.30		1,018.75		6.56		6.31		1.25	***
High Yield Portfolio Class C		1,000.00		1,096.90		1,016.25		9.17		8.82		1.75	***
High Yield Portfolio Class IS		1,000.00		1,103.80		1,021.90		3.26		3.13		0.62	***

** Annualized.

*** Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Overview (unaudited)

High Yield Portfolio

The Portfolio seeks total return.

Performance

For the fiscal year ended September 30, 2016, the Portfolio's Class I shares had a total return based on net asset value and reinvestment of distributions per share of 8.72%, net of fees. The Portfolio's Class I shares underperformed against the Portfolio's benchmark, the Bloomberg Barclays U.S. Corporate High Yield Index (the "Index"), which returned 12.73%.

Factors Affecting Performance

• Concerns about global growth, monetary policy, the U.K. referendum, and commodities kept markets volatile during the period. The fourth quarter of 2015 closed a difficult year in the credit markets. A combination of weak commodity prices driven by soft global economic growth, market disappointment with the actions taken by the European Central Bank at its December meeting and a first rate hike by the Federal Reserve (Fed) late in the month constrained investors' risk appetite. The global high yield credit market saw spreads move wider and as a result both the U.S. and European benchmarks reported negative excess returns for the quarter.

• Asset prices continued to suffer in the first quarter of 2016, as risk premia rose on commodity concerns. January through mid-February was a period of extreme investor risk aversion, largely due to falling oil prices and uncertainty about China's slowing economic growth and possible currency devaluation. The early part of the quarter saw declines in many asset prices, a widening of yield spreads between U.S. Treasuries and non-Treasury fixed income sectors, and a rally in developed market government bonds.

• June marked the occurrence of a risk event that captured market attention, as the unexpected outcome of the U.K. referendum vote resulted in high volatility in the days following its conclusion. However, this volatility cleared quickly as the month went on. In July, spreads rallied alongside other risk assets globally as accommodative policy led to a search for yield across the asset class.

• Over the 12-month reporting period, yields on U.S. Treasuries fell across the medium and long part of the curve. With lower growth globally, as well as diminished expectations for economic growth and inflation, intermediate and long bonds rallied over the period (as bond prices and yields move in opposite directions). Specifically, the 5-, 10- and 30-year Treasury yields ended 24, 44 and 54 basis points lower, respectively.⁽¹⁾ U.S. 2-year Treasury yields ended the period higher, up 13 basis points.

• In the beginning of the first quarter, the high yield sector saw a continuation of the weakness that began in the second half of 2015 as markets faced ongoing worry about falling oil prices, global recession risk, China's economic concerns and European bank solvency issues. High yield assets moved in lockstep with oil prices, which bottomed at $26.21 on February 11, 2016.⁽²⁾ This led to one of the high yield market's worst-ever starts to a quarter. The asset class lost over 5% through the first six weeks of the first quarter, as represented by the Index. Fortunately, this quarter was a tale of two separate and distinct halves. From February 11 through the end of the first quarter, the high yield sector, as measured by the Index, bounced back from February's oversold conditions and returned almost 9%. This coincided with oil's strongest five-week rally since 2011.

• The second quarter of the year brought about a continued rally in high yield as rising commodity prices and accommodative policy led to a search for yield across the asset class. Geopolitical risks across the globe diminished as China and emerging market concerns lessened. Oil prices continued to rise, almost doubling from the lows experienced during early February. This led to a significant rally in commodity-related sectors, especially within energy as the sector returned over 18% during the quarter.

⁽¹⁾ Source for U.S. Treasury yields: Bloomberg L.P.

⁽²⁾ Source: Bloomberg. Data as of March 31, 2016.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Overview (unaudited) (cont'd)

High Yield Portfolio

• The strong performance in high yield this year extended into the third quarter. Total return for the high yield Index was positive for an eighth consecutive month, generating +0.67% in September and extending year-to-date (YTD) total return to +15.1%. At this time last year, the Index's YTD total return was –2.5%. Higher-beta credit continued to outperform, while lower-beta and defensive segments of the market continued to lag. Yields on the asset class are now at their lowest level since June 2015 after declining over 350 basis points from the mid-February high of 10.1%.⁽³⁾

• From February 11, when oil reached $26 dollars a barrel, to the end of September, we have seen an 84% increase in the price of oil.⁽⁴⁾ As the price of oil has recovered significantly, higher-beta parts of the market, such as commodity-related and lower rated credits, have led a massive rally. The largest detractor during this period has been an underweight to these lower-quality energy names, as well as an underweight to communications, another high-beta sector. Our exposure to energy remains biased towards higher-quality issues, rather than the most distressed energy credits that rallied the most. We still believe many of these very low dollar-price distressed bonds will ultimately need to restructure and believe we are positioned favorably longer term.

• Our overweight positioning to building materials & diversified manufacturing helped to somewhat offset this underperformance. Our positioning in food & beverage names also contributed positively to performance.

• The Fund's performance is in line with how we expect high yield middle market credits (which we define as companies with $150 million to $1 billion of total debt outstanding) to perform: in periods where the broad market rallies rapidly, this market segment tends to underperform. The converse is true during broad sell-offs; the portfolio will typically outperform. The rally this year has been particularly strong, which dampened the Fund's relative performance in the reporting period overall. Since the lows of mid-February 2016, the Index is up over 20% through the end of September.⁽³⁾ This type of performance is rarely seen over the course of an entire year, let alone eight months.

Management Strategies

• The Portfolio is focused on middle-market high yield credits. We believe that this segment of the high yield market offers attractive opportunities, as market participants (including asset managers and sell-side research analysts) do not cover it as closely as they do the largest high yield credits. We seek middle market issuers that we believe offer a yield advantage over the broader high yield market, high coupons, shorter maturities and lower volatility than larger issuers.

• Within energy, prefer companies with low balance sheet leverage, excellent liquidity, and that have acreage in low-cost producing areas. Within metals/mining, prefer select companies that are generating cash and own real assets.

• We remain focused on middle market-sized credits and maintain the Portfolio's overweight in B-rated and CCC-rated bonds.

• We continue to be overweight transports and building materials, and remain underweight communications in the Portfolio.

* Minimum Investment

** Commenced operations on February 7, 2012.

In accordance with SEC regulations, the Portfolio's performance shown assumes that all recurring fees (including management fees) were deducted and all dividends and distributions were reinvested. The performance of Class A, Class L, Class C and Class IS shares will vary from the performance of Class I shares based upon their different inception dates and will be negatively impacted by additional fees assessed to those classes (where applicable).

⁽³⁾ Barclays. Data as of September 30, 2016.

⁽⁴⁾ Source: Bloomberg L.P. Data as of September 30, 2016

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Overview (unaudited) (cont'd)

High Yield Portfolio

Performance Compared to the Bloomberg Barclays U.S. Corporate High Yield Index⁽¹⁾ and the Lipper High Current Yield Bond Funds Index⁽²⁾

	Period Ended September 30, 2016 Total Returns⁽³⁾
				Average Annual
	One Year			Five Years		Ten Years		Since Inception⁽⁷⁾
Portfolio — Class I Shares w/o sales charges⁽⁴⁾		8.72	%		—		—		8.60	%
Portfolio — Class A Shares w/o sales charges⁽⁴⁾		8.24			—		—		8.24
Portfolio — Class A Shares with maximum 4.25% sales charges⁽⁴⁾		3.68			—		—		7.25
Portfolio — Class L Shares w/o sales charges⁽⁴⁾		7.95			—		—		7.97
Portfolio — Class C Shares w/o sales charges⁽⁶⁾		7.47			—		—		2.41
Portfolio — Class C Shares with maximum 1.00% deferred sales charges⁽⁶⁾		6.47			—		—		2.41
Portfolio — Class IS Shares w/o sales charges⁽⁵⁾		8.75			—		—		2.86
Bloomberg Barclays U.S. Corporate High Yield Index		12.73			—		—		6.68
Lipper High Current Yield Bond Funds Index		9.45			—		—		5.87

⁽¹⁾ The Bloomberg Barclays U.S. Corporate High Yield Index measures the market of USD-denominated, non-investment grade, fixed-rate, taxable corporate bonds. Securities are classified as high yield if the middle rating of Moody's, Fitch, and S&P is Ba1/BB+/BB+ or below. The index excludes emerging market debt. The Index is unmanaged and its returns do not include any sales charges or fees. Such costs would lower performance. It is not possible to invest directly in an index.

⁽²⁾ The Lipper High Current Yield Bond Funds Index is an equally weighted performance index of the largest qualifying funds (based on net assets) in the Lipper High Current Yield Bond Funds classification. The Index, which is adjusted for capital gains distributions and income dividends, is unmanaged and should not be considered an investment. There are currently 30 funds represented in this Index. As of the date of this report, the Portfolio was in the Lipper High Current Yield Bond Funds classification.

⁽³⁾ Total returns for the Portfolio reflect expenses waived and/or reimbursed, if applicable, by the Adviser. Without such waivers and/or reimbursements, total returns would have been lower.

⁽⁴⁾ Commenced operations on February 7, 2012.

⁽⁵⁾ Commenced operations on March 28, 2014.

⁽⁶⁾ Commenced operations on April 30, 2015.

⁽⁷⁾ For comparative purposes, average annual since inception returns listed for the Indexes refer to the inception date of Class I of the Portfolio, not the inception of the Indexes.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments

High Yield Portfolio

	Face Amount (000)		Value (000)
Fixed Income Securities (99.8%)
Corporate Bonds (94.5%)
Basic Materials (5.3%)
American Gilsonite Co.
11.50%, 9/1/17 (a)	$	500	$	352
Chemtura Corp.
5.75%, 7/15/21		525		552
Eco Services Operations LLC/Eco Finance Corp.
8.50%, 11/1/22 (a)		750		784
Hexion, Inc.,
8.88%, 2/1/18		550		527
10.00%, 4/15/20		250		247
HudBay Minerals, Inc.
9.50%, 10/1/20		750		756
International Wire Group, Inc.
10.75%, 8/1/21 (a)		750		716
Lundin Mining Corp.
7.50%, 11/1/20 (a)		500		534
MSCI, Inc.
4.75%, 8/1/26 (a)		400		406
Prince Mineral Holding Corp.
11.50%, 12/15/19 (a)		800		754
Signode Industrial Group Lux SA/Signode Industrial Group US, Inc.
6.38%, 5/1/22 (a)		750		763
Versum Materials, Inc.
5.50%, 9/30/24 (a)		225		232
				6,623
Communications (9.6%)
Bankrate, Inc.
6.13%, 8/15/18 (a)		565		573
Cable One, Inc.
5.75%, 6/15/22 (a)		630		660
CCO Holdings LLC/CCO Holdings Capital Corp.
5.75%, 1/15/24		600		639
Columbus Cable Barbados Ltd.
7.38%, 3/30/21 (a)		750		798
CommScope Technologies Finance LLC
6.00%, 6/15/25 (a)		400		428
CommScope, Inc.
5.50%, 6/15/24 (a)		400		422
CSC Holdings LLC,
5.25%, 6/1/24		500		476
5.50%, 4/15/27 (a)		450		461
DISH DBS Corp.
7.75%, 7/1/26 (a)		400		426
GCI, Inc.,
6.75%, 6/1/21		250		258
6.88%, 4/15/25		250		258
Gray Television, Inc.
5.88%, 7/15/26 (a)		500		505
Intelsat Jackson Holdings SA
8.00%, 2/15/24 (a)		500		504

	Face Amount (000)		Value (000)
inVentiv Health, Inc.
9.00%, 1/15/18 (a)	$	500	$	514
Lamar Media Corp.,
5.38%, 1/15/24		250		264
5.75%, 2/1/26		300		324
MDC Partners, Inc.
6.50%, 5/1/24 (a)		500		465
Midcontinent Communications & Midcontinent Finance Corp.,
6.25%, 8/1/21 (a)		450		474
6.88%, 8/15/23 (a)		350		375
Netflix, Inc.
5.88%, 2/15/25		500		542
Outfront Media Capital LLC/Outfront Media Capital Corp.
5.63%, 2/15/24		500		522
SFR Group SA
6.00%, 5/15/22 (a)		500		512
Sinclair Television Group, Inc.
5.88%, 3/15/26 (a)		450		469
Syniverse Holdings, Inc.
9.13%, 1/15/19		250		190
T-Mobile USA, Inc.
6.84%, 4/28/23		500		541
Virgin Media Secured Finance PLC
5.50%, 8/15/26 (a)		500		511
				12,111
Consumer, Cyclical (21.9%)
Accuride Corp.
9.50%, 8/1/18		750		754
Air Canada
7.75%, 4/15/21 (a)		750		814
Algeco Scotsman Global Finance PLC
8.50%, 10/15/18 (a)		200		182
Allied Specialty Vehicles, Inc.
8.50%, 11/1/19 (a)		750		778
American Airlines Group, Inc.
5.50%, 10/1/19 (a)		500		523
American Builders & Contractors Supply Co., Inc.
5.63%, 4/15/21 (a)		500		520
Aramark Services, Inc.,
4.75%, 6/1/26 (a)		400		403
5.13%, 1/15/24		250		261
AV Homes, Inc.
8.50%, 7/1/19		750		782
Beacon Roofing Supply, Inc.
6.38%, 10/1/23		500		542
Beazer Homes USA, Inc.
8.75%, 3/15/22 (a)		750		793
Carrols Restaurant Group, Inc.
8.00%, 5/1/22		500		543
CCM Merger, Inc.
9.13%, 5/1/19 (a)		100		105

The accompanying notes are an integral part of the financial statements.
7

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

High Yield Portfolio

	Face Amount (000)		Value (000)
Consumer, Cyclical (cont'd)
Century Communities, Inc.
6.88%, 5/15/22	$	750	$	761
Chester Downs & Marina LLC/Chester Downs Finance Corp.
9.25%, 2/1/20 (a)		700		649
Churchill Downs, Inc.
5.38%, 12/15/21 (a)		300		314
Commercial Vehicle Group, Inc.
7.88%, 4/15/19		750		752
Downstream Development Authority of the Quapaw Tribe of Oklahoma
10.50%, 7/1/19 (a)		417		423
Eldorado Resorts, Inc.
7.00%, 8/1/23		400		427
EMI Music Publishing Group North America Holdings, Inc.
7.63%, 6/15/24 (a)		550		597
Empire Today LLC/Empire Today Finance Corp.
11.38%, 2/1/17 (a)		805		810
Exide Technologies
8.63%, 2/1/18 (b)(c)(d)		100		—
FelCor Lodging LP
6.00%, 6/1/25		450		470
Gibson Brands, Inc.
8.88%, 8/1/18 (a)		500		375
Global Partners LP/GLP Finance Corp.
6.25%, 7/15/22		750		699
Golden Nugget Escrow, Inc.
8.50%, 12/1/21 (a)		250		264
Greektown Holdings LLC/Greektown Mothership Corp.
8.88%, 3/15/19 (a)		710		754
Guitar Center, Inc.
6.50%, 4/15/19 (a)		700		619
Hanesbrands, Inc.
4.88%, 5/15/26 (a)		500		514
JC Penney Corp., Inc.,
5.88%, 7/1/23 (a)		400		418
8.13%, 10/1/19		500		547
KFC Holding Co/Pizza Hut Holdings LLC/Taco Bell of America LLC
5.00%, 6/1/24 (a)		500		524
Landry's, Inc.
6.75%, 10/15/24 (a)(e)		700		714
Logan's Roadhouse, Inc.
10.75%, 10/15/17 (b)(c)		550		41
Meritor, Inc.
6.25%, 2/15/24		750		722
National CineMedia LLC
5.75%, 8/15/26 (a)		550		572
Neiman Marcus Group Ltd., LLC
8.75%, 10/15/21 (a)(f)		350		277

	Face Amount (000)		Value (000)
Oshkosh Corp.
5.38%, 3/1/22	$	750	$	793
Party City Holdings, Inc.
6.13%, 8/15/23 (a)		500		536
Performance Food Group, Inc.
5.50%, 6/1/24 (a)		250		259
Playa Resorts Holding BV
8.00%, 8/15/20 (a)		500		513
Rite Aid Corp.,
6.13%, 4/1/23 (a)		250		271
6.75%, 6/15/21		500		528
Rivers Pittsburgh Borrower LP/Rivers Pittsburgh Finance Corp.
6.13%, 8/15/21 (a)		750		776
RSI Home Products, Inc.
6.50%, 3/15/23 (a)		450		477
Sally Holdings LLC/Sally Capital, Inc.
5.63%, 12/1/25		500		541
Sonic Automotive, Inc.
5.00%, 5/15/23		500		495
Speedway Motorsports, Inc.
5.13%, 2/1/23		335		344
Sugarhouse HSP Gaming Prop Mezz LP/ Sugarhouse HSP Gaming Finance Corp.
6.38%, 6/1/21 (a)		694		697
Tempur Sealy International, Inc.
5.50%, 6/15/26 (a)		500		516
Tops Holding LLC/Tops Markets II Corp.
8.00%, 6/15/22 (a)		750		679
United Continental Holdings, Inc.
6.38%, 6/1/18		400		422
VistaJet Malta Finance PLC/VistaJet Co., Finance LLC
7.75%, 6/1/20 (a)		300		134
Wolverine World Wide, Inc.
5.00%, 9/1/26 (a)		500		506
				27,730
Consumer, Non-Cyclical (12.8%)
Acadia Healthcare Co., Inc.,
5.13%, 7/1/22		250		249
5.63%, 2/15/23		500		510
Ahern Rentals, Inc.
7.38%, 5/15/23 (a)		400		261
Alere, Inc.
6.38%, 7/1/23 (a)		200		205
Amsurg Corp.
5.63%, 7/15/22		400		411
APX Group, Inc.
6.38%, 12/1/19		500		512
Beverages & More, Inc.
10.00%, 11/15/18 (a)		739		705
Brand Energy & Infrastructure Services, Inc.
8.50%, 12/1/21 (a)		750		754

The accompanying notes are an integral part of the financial statements.
8

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

High Yield Portfolio

	Face Amount (000)		Value (000)
Consumer, Non-Cyclical (cont'd)
Bumble Bee Holdco SCA
9.63%, 3/15/18 (a)(f)	$	465	$	463
Bumble Bee Holdings, Inc.
9.00%, 12/15/17 (a)		500		504
Central Garden & Pet Co.
6.13%, 11/15/23		500		537
Cenveo Corp.
6.00%, 8/1/19 (a)		750		669
Concordia International Corp.
7.00%, 4/15/23 (a)		250		162
DPx Holdings BV
7.50%, 2/1/22 (a)		100		106
DS Services of America, Inc.
10.00%, 9/1/21 (a)		304		340
Endo Ltd./Endo Finance LLC/Endo Finco, Inc.
6.00%, 7/15/23 (a)		750		686
FAGE International SA/FAGE USA Dairy Industry, Inc.
5.63%, 8/15/26 (a)		500		516
Great Lakes Dredge & Dock Corp.
7.38%, 2/1/19		750		739
Harland Clarke Holdings Corp.
9.75%, 8/1/18 (a)		750		772
HCA, Inc.
5.25%, 6/15/26		450		479
Jaguar Holding Co. II/Pharmaceutical Product Development LLC
6.38%, 8/1/23 (a)		500		521
Mallinckrodt International Finance SA/ Mallinckrodt CB LLC
5.50%, 4/15/25 (a)		500		478
MPH Acquisition Holdings LLC
7.13%, 6/1/24 (a)		150		162
Pinnacle Foods Finance LLC/Pinnacle Foods Finance Corp.
5.88%, 1/15/24 (a)		450		483
Pinnacle Operating Corp.
9.00%, 11/15/20 (a)		400		280
Quintiles Transnational Corp.
4.88%, 5/15/23 (a)		300		310
Service Corp. International
5.38%, 1/15/22		250		261
Spectrum Brands, Inc.
5.75%, 7/15/25		500		542
Teleflex, Inc.
4.88%, 6/1/26		200		208
Tenet Healthcare Corp.
4.35%, 6/15/20 (g)		525		530
TMS International Corp.
7.63%, 10/15/21 (a)		975		838
TreeHouse Foods, Inc.
6.00%, 2/15/24 (a)		500		541

	Face Amount (000)		Value (000)
United Rentals North America, Inc.
5.75%, 11/15/24	$	500	$	521
Valeant Pharmaceuticals International, Inc.,
5.88%, 5/15/23 (a)		250		217
6.13%, 4/15/25 (a)		250		216
Wells Enterprises, Inc.
6.75%, 2/1/20 (a)		500		518
				16,206
Diversified (0.6%)
Horizon Pharma, Inc.
6.63%, 5/1/23		250		237
PetSmart, Inc.
7.13%, 3/15/23 (a)		500		525
				762
Energy (13.7%)
Antero Midstream Partners LP/Antero Midstream Finance Corp.
5.38%, 9/15/24 (a)		500		507
Blue Racer Midstream LLC/Blue Racer Finance Corp.
6.13%, 11/15/22 (a)		500		491
Callon Petroleum Co.
6.13%, 10/1/24 (a)(e)		400		415
Carrizo Oil & Gas, Inc.
6.25%, 4/15/23		800		796
Concho Resources, Inc.
5.50%, 4/1/23		750		777
Continental Resources, Inc.
5.00%, 9/15/22		750		750
Crestwood Midstream Partners LP/Crestwood Midstream Finance Corp.
6.25%, 4/1/23		250		254
CrownRock LP/CrownRock Finance, Inc.
7.75%, 2/15/23 (a)		200		216
DCP Midstream LLC
5.35%, 3/15/20 (a)		400		412
Denbury Resources, Inc.
5.50%, 5/1/22		650		470
Endeavor Energy Resources LP/EER Finance, Inc.,
7.00%, 8/15/21 (a)		250		258
8.13%, 9/15/23 (a)		500		535
Ensco PLC
4.50%, 10/1/24		700		506
Hilcorp Energy I LP/Hilcorp Finance Co.,
5.00%, 12/1/24 (a)		500		481
5.75%, 10/1/25 (a)		250		250
Holly Energy Partners LP/Holly Energy Finance Corp.
6.00%, 8/1/24 (a)		200		208
Laredo Petroleum, Inc.,
5.63%, 1/15/22		250		244
6.25%, 3/15/23		450		443
Lonestar Resources America, Inc.
8.75%, 4/15/19 (a)		600		381

The accompanying notes are an integral part of the financial statements.
9

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

High Yield Portfolio

	Face Amount (000)		Value (000)
Energy (cont'd)
Matador Resources Co.
6.88%, 4/15/23	$	225	$	234
Murphy Oil Corp.
6.88%, 8/15/24		400		414
Newfield Exploration Co.
5.38%, 1/1/26		500		504
Northern Oil and Gas, Inc.
8.00%, 6/1/20		750		581
Northern Tier Energy LLC/Northern Tier Finance Corp.
7.13%, 11/15/20		550		565
ONEOK, Inc.
4.25%, 2/1/22		500		492
Pacific Drilling V Ltd.
7.25%, 12/1/17 (a)		450		184
Parsley Energy LLC/Parsley Finance Corp.
7.50%, 2/15/22 (a)		750		801
PDC Energy, Inc.
6.13%, 9/15/24 (a)		500		519
Rice Energy, Inc.
6.25%, 5/1/22		750		778
Rose Rock Midstream LP/Rose Rock Finance Corp.
5.63%, 11/15/23		450		412
RSP Permian, Inc.
6.63%, 10/1/22		500		526
Seven Generations Energy Ltd.
8.25%, 5/15/20 (a)		350		374
SM Energy Co.,
5.00%, 1/15/24		750		709
6.75%, 9/15/26		325		329
Tallgrass Energy Partners LP/Tallgrass Energy Finance Corp.
5.50%, 9/15/24 (a)		210		212
Tesoro Logistics LP/Tesoro Logistics Finance Corp.
6.38%, 5/1/24		500		539
Whiting Petroleum Corp.
5.75%, 3/15/21		750		705
				17,272
Finance (9.7%)
Baytex Energy Corp.
5.63%, 6/1/24 (a)		350		287
CNO Financial Group, Inc.
4.50%, 5/30/20		500		514
Compiler Finance Sub, Inc.
7.00%, 5/1/21 (a)		500		235
CTR Partnership LP/CareTrust Capital Corp.
5.88%, 6/1/21		500		520
DuPont Fabros Technology LP
5.63%, 6/15/23		500		527
HUB International Ltd.
7.88%, 10/1/21 (a)		700		716

	Face Amount (000)		Value (000)
Icahn Enterprises LP/Icahn Enterprises Finance Corp.
6.00%, 8/1/20	$	750	$	757
Infinity Acquisition LLC/Infinity Acquisition Finance Corp.
7.25%, 8/1/22 (a)		250		219
Interface Security Systems Holdings, Inc./Interface Security Systems LLC
9.25%, 1/15/18		500		508
Iron Mountain, Inc.
6.00%, 10/1/20 (a)		500		529
iStar, Inc.
6.50%, 7/1/21		500		509
Jefferies Finance LLC/JFIN Co-Issuer Corp.
6.88%, 4/15/22 (a)		450		421
KCG Holdings, Inc.
6.88%, 3/15/20 (a)		750		750
Kennedy-Wilson, Inc.
5.88%, 4/1/24		500		506
MGIC Investment Corp.
5.75%, 8/15/23		400		417
MPT Operating Partnership LP/MPT Finance Corp.
6.38%, 3/1/24		250		273
NewStar Financial, Inc.
7.25%, 5/1/20		400		396
Oxford Finance LLC/Oxford Finance Co-Issuer, Inc.
7.25%, 1/15/18 (a)		800		804
Post Holdings, Inc.
5.00%, 8/15/26 (a)		450		449
Provident Funding Associates LP/PFG Finance Corp.
6.75%, 6/15/21 (a)		500		507
Radian Group, Inc.
7.00%, 3/15/21		525		591
Sabra Health Care LP/Sabra Capital Corp.
5.50%, 2/1/21		500		524
SPX FLOW, Inc.
5.63%, 8/15/24 (a)		600		610
Valvoline, Inc.
5.50%, 7/15/24 (a)		200		210
VEREIT Operating Partnership LP
4.88%, 6/1/26		450		477
				12,256
Industrials (17.9%)
ADS Tactical, Inc.
11.00%, 4/1/18 (a)		800		824
Apex Tool Group LLC
7.00%, 2/1/21 (a)		500		481
ARD Finance SA
7.13%, 9/15/23 (a)(f)		800		798
Artesyn Embedded Technologies, Inc.
9.75%, 10/15/20 (a)		753		687
Associated Asphalt Partners LLC/Road Holdings III LLC/Associated Asphalt Finance
8.50%, 2/15/18 (a)		517		525

The accompanying notes are an integral part of the financial statements.
10

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

High Yield Portfolio

	Face Amount (000)		Value (000)
Industrials (cont'd)
Associated Materials LLC/AMH New Finance, Inc.
9.13%, 11/1/17	$	200	$	190
Belden, Inc.
5.25%, 7/15/24 (a)		500		510
BlueLine Rental Finance Corp.
7.00%, 2/1/19 (a)		750		658
CEVA Group PLC
4.00%, 5/1/18 (a)		750		667
Cleaver-Brooks, Inc.
8.75%, 12/15/19 (a)		750		789
Consolidated Container Co., LLC/Consolidated Container Capital, Inc.
10.13%, 7/15/20 (a)		600		613
Coveris Holdings SA
7.88%, 11/1/19 (a)		200		206
CPG Merger Sub LLC
8.00%, 10/1/21 (a)		750		769
CTP Transportation Products LLC/CTP Finance, Inc.
8.25%, 12/15/19 (a)		750		591
DH Services Luxembourg Sarl
7.75%, 12/15/20 (a)		50		52
Dollar Tree, Inc.
5.75%, 3/1/23		500		541
Eagle Materials, Inc.
4.50%, 8/1/26		400		406
Emeco Pty Ltd.
9.88%, 3/15/19 (a)		200		139
EnPro Industries, Inc.
5.88%, 9/15/22		452		468
Flexi-Van Leasing, Inc.
7.88%, 8/15/18 (a)		550		499
GCP Applied Technologies, Inc.
9.50%, 2/1/23 (a)		750		859
Gibraltar Industries, Inc.
6.25%, 2/1/21		586		608
Iracore International Holdings, Inc.
9.50%, 6/1/18 (a)		400		210
Jac Holding Corp.
11.50%, 10/1/19 (a)		737		782
JB Poindexter & Co., Inc.
9.00%, 4/1/22 (a)		650		691
Kemet Corp.
10.50%, 5/1/18		450		452
LMI Aerospace, Inc.
7.38%, 7/15/19		500		505
Martin Midstream Partners LP/Martin Midstream Finance Corp.
7.25%, 2/15/21		750		709
MasTec, Inc.
4.88%, 3/15/23		600		595
Michael Baker Holdings LLC/Michael Baker Finance Corp.
8.88%, 4/15/19 (a)(f)		384		358

	Face Amount (000)		Value (000)
Michael Baker International LLC/CDL Acquisition Co., Inc.
8.25%, 10/15/18 (a)	$	450	$	453
Novelis Corp.
5.88%, 9/30/26 (a)		225		231
OPE KAG Finance Sub, Inc.
7.88%, 7/31/23 (a)		500		476
Plastipak Holdings, Inc.
6.50%, 10/1/21 (a)		500		521
SAExploration Holdings, Inc.
10.00%, 4/14/19 (a)(f)		416		295
SBA Communications Corp.
4.88%, 9/1/24 (a)		300		303
Standard Industries, Inc.
5.50%, 2/15/23 (a)		550		577
Summit Materials LLC/Summit Materials Finance Corp.
6.13%, 7/15/23		500		512
Syncreon Group BV/Syncreon Global Finance US, Inc.
8.63%, 11/1/21 (a)		450		335
Techniplas LLC
10.00%, 5/1/20 (a)		500		418
US Concrete, Inc.
6.38%, 6/1/24		400		416
Vander Intermediate Holding II Corp.
9.75%, 2/1/19 (a)(f)		105		56
Wise Metals Intermediate Holdings LLC/Wise Holdings Finance Corp.
9.75%, 6/15/19 (a)(f)		658		635
XPO Logistics, Inc.
6.13%, 9/1/23 (a)		500		514
Zachry Holdings, Inc.
7.50%, 2/1/20 (a)		750		750
				22,674
Technology (2.2%)
BCP Singapore VI Cayman Financing Co., Ltd.
8.00%, 4/15/21 (a)		450		445
Boxer Parent Co., Inc.
9.00%, 10/15/19 (a)(f)		450		410
DynCorp International, Inc.
11.88%, 11/30/20 (f)		498		371
First Data Corp.
7.00%, 12/1/23 (a)		500		530
JDA Escrow LLC/JDA Bond Finance, Inc.
7.38%, 10/15/24 (a)(e)		475		489
Western Digital Corp.
7.38%, 4/1/23 (a)		500		551
				2,796
Utilities (0.8%)
DPL, Inc.
6.75%, 10/1/19		600		625

The accompanying notes are an integral part of the financial statements.
11

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

High Yield Portfolio

	Face Amount (000)		Value (000)
Utilities (cont'd)
LBC Tank Terminals Holding Netherlands BV
6.88%, 5/15/23 (a)	$	400	$	400
				1,025
				119,455
Sovereign (0.9%)
Government (0.9%)
Select Medical Corp.
6.38%, 6/1/21		350		346
Shape Technologies Group, Inc.
7.63%, 2/1/20 (a)		770		791
				1,137
Variable Rate Senior Loan Interests (4.4%)
Basic Materials (0.4%)
FMG Resources August 2006 Pty Ltd., Term B
3.75%, 6/30/19		549		550
Consumer, Cyclical (0.9%)
Graton Economic Development Authority, Term B
4.75%, 7/28/22		269		271
Navistar International Corp., Term B
6.50%, 8/17/17		397		399
Neiman Marcus Group Ltd., Inc., Term Loan
1.00%, 10/25/20 (h)		500		461
				1,131
Consumer, Non-Cyclical (0.4%)
Concordia International Corp., Term Loan
1.00%, 10/21/21 (h)		500		448
Finance (0.2%)
Istar Financial, Inc., Term B
5.50%, 7/1/20		250		253
Industrials (2.5%)
American Bath Group LLC, 1st Lien Term
1.00%, 9/27/23 (h)		600		600
Atkore International, Inc., 2nd Lien Term
7.75%, 10/9/21		300		302
Commercial Barge Line Co., 1st Lien Term
9.75%, 11/6/20		488		476
Coveris Holdings SA, Term B
4.50%, 5/8/19		299		299
Gates Global, Inc., Term B
4.25%, 7/5/21		390		385

	Face Amount (000)		Value (000)
Gruden Acquisition, Inc., 1st Lien Term
5.75%, 8/18/22	$	496	$	448
SAExploration Holdings, Inc., Term Loan
10.00%, 6/28/23 (i)		375		375
TTM Technologies, Inc., 1st Lien Term
5.25%, 4/21/22		326		329
				3,214
				5,596
Total Fixed Income Securities (Cost $125,514)				126,188
	Shares
Common Stocks (0.4%)
Auto Components (0.0%)
Exide Technologies (j)(k)(l)		592		1
Energy Equipment & Services (0.3%)
SAExploration Holdings, Inc. (j)(k)		55,100		453
Semiconductors & Semiconductor Equipment (0.1%)
UC Holdings, Inc. (j)		2,826		77
Total Common Stocks (Cost $71)				531
Participation Note (0.0%)
Semiconductors & Semiconductor Equipment (0.0%)
UC Holdings, Inc., Equity Linked Notes, expires 9/23/20 (d)(j) (Cost $—)		2,802		—
Short-Term Investment (0.3%)
Investment Company (0.3%)
Morgan Stanley Institutional Liquidity Funds — Government Portfolio — Institutional Class (See Note G) (Cost $399)		399,377		399
Total Investments (100.5%) (Cost $125,984) (m)				127,118
Liabilities in Excess of Other Assets (–0.5%)				(664	)
Net Assets (100.0%)			$	126,454

(a) 144A security — Certain conditions for public sale may exist. Unless otherwise noted, these securities are deemed to be liquid.

(b) Non-income producing security; bond in default.

(d) At September 30, 2016, the Portfolio held fair valued securities valued at $0, representing 0.0% of net assets. These securities have been fair valued as determined in good faith under procedures established by and under the general supervision of the Fund's Trustees.

(e) When-issued security.

(f) Payment-in-kind security.

(g) Variable/Floating Rate Security — Interest rate changes on these instruments are based on changes in a designated base rate. The rates shown are those in effect on September 30, 2016.

(h) Unsettled Position. The contract rate does not take effect until settlement date.

The accompanying notes are an integral part of the financial statements.
12

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

High Yield Portfolio

(i) In addition to the term loan, the Portfolio has an unfunded loan commitment of approximately $375,000, which could be extended at the option of the borrower. As of September 30, 2016, SAExploration Holdings, Inc. did not draw down any of the commitment.

(j) Non-income producing security.

(k) Security has been deemed illiquid at September 30, 2016.

(l) Security cannot be offered for public resale without first being registered under the Securities Act of 1933 and related rules ("restricted security"). Acquisition date represents the day on which an enforceable right to acquire such security is obtained and is presented along with related cost in the security description. The Portfolio has registration rights for certain restricted securities. Any costs related to such registration are borne by the issuer. The aggregate value of restricted securities (excluding 144A holdings) at September 30, 2016, amounts to approximately $1,000 and represents less than 0.05% of net assets.

(m) At September 30, 2016, the aggregate cost for federal income tax purposes is approximately $126,152,000. The aggregate gross unrealized appreciation is approximately $4,785,000 and the aggregate gross unrealized depreciation is approximately $3,819,000 resulting in net unrealized appreciation of approximately $966,000.

Portfolio Composition

Classification	Percentage of Total Investments
Consumer, Cyclical		21.8	%
Industrials		17.9
Energy		14.0
Consumer, Non-Cyclical		12.8
Finance		9.6
Communications		9.5
Other*		9.2
Basic Materials		5.2
Total Investments		100.0	%

* Industries and/or investment types representing less than 5% of total investments.

The accompanying notes are an integral part of the financial statements.
13

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

High Yield Portfolio

Statement of Assets and Liabilities	September 30, 2016 (000)
Assets:
Investments in Securities of Unaffiliated Issuers, at Value (Cost $125,585)	$	126,719
Investment in Security of Affiliated Issuer, at Value (Cost $399)		399
Total Investments in Securities, at Value (Cost $125,984)		127,118
Interest Receivable		2,402
Receivable for Investments Sold		2,025
Receivable for Portfolio Shares Sold		24
Receivable from Affiliate		—	@
Other Assets		32
Total Assets		131,601
Liabilities:
Payable for Investments Purchased		4,955
Payable for Advisory Fees		98
Payable for Professional Fees		20
Payable for Shareholder Services Fees — Class A		12
Payable for Distribution and Shareholder Services Fees — Class L		—	@
Payable for Distribution and Shareholder Services Fees — Class C		2
Payable for Portfolio Shares Redeemed		12
Payable for Sub Transfer Agency Fees — Class I		5
Payable for Sub Transfer Agency Fees — Class A		6
Payable for Sub Transfer Agency Fees — Class L		—	@
Payable for Sub Transfer Agency Fees — Class C		—	@
Payable for Administration Fees		8
Payable for Transfer Agency Fees — Class I		2
Payable for Transfer Agency Fees — Class A		1
Payable for Transfer Agency Fees — Class L		—	@
Payable for Transfer Agency Fees — Class C		1
Payable for Transfer Agency Fees — Class IS		1
Payable for Custodian Fees		2
Payable to the Adviser (Note F)		4
Other Liabilities		18
Total Liabilities		5,147
Net Assets	$	126,454
Net Assets Consist Of:
Paid-in-Capital	$	126,989
Accumulated Undistributed Net Investment Income		918
Accumulated Net Realized Loss		(2,587	)
Unrealized Appreciation (Depreciation) on:
Investments		1,134
Net Assets	$	126,454

The accompanying notes are an integral part of the financial statements.
14

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

High Yield Portfolio

Statement of Assets and Liabilities (cont'd)	September 30, 2016 (000)
CLASS I:
Net Assets	$	49,990
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		5,040,149
Net Asset Value, Offering and Redemption Price Per Share	$	9.92
CLASS A:
Net Assets	$	59,139
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		5,971,225
Net Asset Value, Redemption Price Per Share	$	9.90
Maximum Sales Load		4.25	%
Maximum Sales Charge	$	0.44
Maximum Offering Price Per Share	$	10.34
CLASS L:
Net Assets	$	628
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		63,381
Net Asset Value, Offering and Redemption Price Per Share	$	9.91
CLASS C:
Net Assets	$	2,908
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		293,905
Net Asset Value, Offering and Redemption Price Per Share	$	9.89
CLASS IS:
Net Assets	$	13,789
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		1,390,016
Net Asset Value, Offering and Redemption Price Per Share	$	9.92

@ Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
15

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

High Yield Portfolio

Statement of Operations	Year Ended September 30, 2016 (000)
Investment Income:
Interest from Securities of Unaffiliated Issuers	$	7,777
Dividends from Security of Affiliated Issuer (Note G)		4
Total Investment Income		7,781
Expenses:
Advisory Fees (Note B)		601
Shareholder Services Fees — Class A (Note D)		139
Distribution and Shareholder Services Fees — Class L (Note D)		3
Distribution and Shareholder Services Fees — Class C (Note D)		21
Sub Transfer Agency Fees — Class I		32
Sub Transfer Agency Fees — Class A		79
Sub Transfer Agency Fees — Class L		1
Sub Transfer Agency Fees — Class C		2
Professional Fees		91
Administration Fees (Note C)		80
Registration Fees		75
Pricing Fees		31
Shareholder Reporting Fees		16
Transfer Agency Fees — Class I (Note E)		6
Transfer Agency Fees — Class A (Note E)		3
Transfer Agency Fees — Class L (Note E)		2
Transfer Agency Fees — Class C (Note E)		2
Transfer Agency Fees — Class IS (Note E)		2
Custodian Fees (Note F)		10
Trustees' Fees and Expenses		4
Other Expenses		16
Total Expenses		1,216
Waiver of Advisory Fees (Note B)		(255	)
Reimbursement of Class Specific Expenses — Class I (Note B)		(28	)
Reimbursement of Class Specific Expenses — Class A (Note B)		(10	)
Reimbursement of Class Specific Expenses — Class L (Note B)		(2	)
Reimbursement of Class Specific Expenses — Class C (Note B)		(1	)
Reimbursement of Class Specific Expenses — Class IS (Note B)		(2	)
Rebate from Morgan Stanley Affiliate (Note G)		(1	)
Reimbursement of Custodian Fees (Note F)		(29	)
Net Expenses		888
Net Investment Income		6,893
Realized Gain (Loss):
Investments Sold		(1,186	)
Swap Agreements		43
Net Realized Loss		(1,143	)
Change in Unrealized Appreciation (Depreciation):
Investments		5,881
Net Realized Loss and Change in Unrealized Appreciation (Depreciation)		4,738
Net Increase in Net Assets Resulting from Operations	$	11,631

The accompanying notes are an integral part of the financial statements.
16

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

High Yield Portfolio

Statements of Changes in Net Assets	Year Ended September 30, 2016 (000)			Year Ended September 30, 2015 (000)
Increase (Decrease) in Net Assets:
Operations:
Net Investment Income	$	6,893		$	3,972
Net Realized Loss		(1,143	)		(1,431	)
Net Change in Unrealized Appreciation (Depreciation)		5,881			(4,386	)
Net Increase (Decrease) in Net Assets Resulting from Operations		11,631			(1,845	)
Distributions from and/or in Excess of:
Class I:
Net Investment Income		(2,238	)		(714	)
Net Realized Gain		—			(65	)
Class A:
Net Investment Income		(3,747	)		(2,818	)
Net Realized Gain		—			(216	)
Class L:
Net Investment Income		(47	)		(71	)
Net Realized Gain		—			(6	)
Class C:
Net Investment Income		(123	)		(24	)
Class IS:
Net Investment Income		(464	)		(16	)
Net Realized Gain		—			(—	@)
Total Distributions		(6,619	)		(3,930	)
Capital Share Transactions:⁽¹⁾
Class I:
Subscribed		41,355			13,941
Distributions Reinvested		2,236			339
Redeemed		(9,900	)		(13,226	)
Class A:
Subscribed		20,138			33,441
Distributions Reinvested		3,727			3,021
Redeemed		(21,559	)		(16,149	)
Class L:
Exchanged		99			—
Subscribed		—			527
Distributions Reinvested		47			71
Redeemed		(624	)		(884	)
Class C:
Subscribed		2,155			2,023	*
Distributions Reinvested		121			23	*
Redeemed		(752	)		(651	)*
Class IS:
Subscribed		13,688			1,828
Redeemed		(1,580	)		(1,224	)
Net Increase in Net Assets Resulting from Capital Share Transactions		49,151			23,080
Total Increase in Net Assets		54,163			17,305
Net Assets:
Beginning of Period		72,291			54,986
End of Period (Including Accumulated Undistributed Net Investment Income of $918 and $643)	$	126,454		$	72,291
(1) Capital Share Transactions:
Class I:
Shares Subscribed		4,503			1,367
Shares Issued on Distributions Reinvested		237			33
Shares Redeemed		(1,053	)		(1,286	)
Net Increase in Class I Shares Outstanding		3,687			114
Class A:
Shares Subscribed		2,115			3,271
Shares Issued on Distributions Reinvested		395			297
Shares Redeemed		(2,267	)		(1,586	)
Net Increase in Class A Shares Outstanding		243			1,982

The accompanying notes are an integral part of the financial statements.
17

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

High Yield Portfolio

Statements of Changes in Net Assets (cont'd)	Year Ended September 30, 2016 (000)			Year Ended September 30, 2015 (000)
Class L:
Shares Exchanged		10			—
Shares Subscribed		—			52
Shares Issued on Distributions Reinvested		5			7
Shares Redeemed		(65	)		(87	)
Net Decrease in Class L Shares Outstanding		(50	)		(28	)
Class C:
Shares Subscribed		228			197	*
Shares Issued on Distributions Reinvested		13			2	*
Shares Redeemed		(81	)		(65	)*
Net Increase in Class C Shares Outstanding		160			134
Class IS:
Shares Subscribed		1,500			180
Shares Redeemed		(169	)		(122	)
Net Increase in Class IS Shares Outstanding		1,331			58

* For the period April 30, 2015 through September 30, 2015.

@ Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
18

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

High Yield Portfolio

	Class I
	Year Ended September 30,												Period from February 7, 2012^ to
Selected Per Share Data and Ratios	2016††			2015			2014			2013			September 30, 2012
Net Asset Value, Beginning of Period	$	9.80		$	10.73		$	11.00		$	10.71		$	10.00
Income (Loss) from Investment Operations:
Net Investment Income†		0.67			0.71			0.75			0.81			0.50
Net Realized and Unrealized Gain (Loss)		0.13			(0.92	)		0.25			0.55			0.59
Total from Investment Operations		0.80			(0.21	)		1.00			1.36			1.09
Distributions from and/or in Excess of:
Net Investment Income		(0.68	)		(0.66	)		(0.77	)		(0.81	)		(0.38	)
Net Realized Gain		—			(0.06	)		(0.50	)		(0.26	)		—
Total Distributions		(0.68	)		(0.72	)		(1.27	)		(1.07	)		(0.38	)
Net Asset Value, End of Period	$	9.92		$	9.80		$	10.73		$	11.00		$	10.71
Total Return++		8.72	%		(2.10	)%		9.48	%		13.38	%		11.07	%#
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	49,990		$	13,255		$	13,300		$	12,678		$	10,975
Ratio of Expenses to Average Net Assets ⁽¹⁾		0.66	%+^^		0.74	%+		0.75	%+		0.75	%+		0.74	%+*
Ratio of Net Investment Income to Average Net Assets ⁽¹⁾		7.09	%+^^		6.88	%+		6.89	%+		7.42	%+		7.53	%+*
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.00	%§		0.00	%§		0.00	%§		0.00	%§		0.01	%*
Portfolio Turnover Rate		74	%		62	%		96	%		227	%		192	%#
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		1.02	%		1.17	%		1.85	%		3.16	%		3.17	%*
Net Investment Income to Average Net Assets		6.73	%		6.45	%		5.79	%		5.01	%		5.10	%*

^ Commencement of Operations.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value as of the last business day of the period.

^^ Effective January 4, 2016, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 0.65% for Class I shares. Prior to January 4, 2016, the maximum ratio was 0.75% for Class I shares.

§ Amount is less than 0.005%.

# Not Annualized.

* Annualized.

The accompanying notes are an integral part of the financial statements.
19

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

High Yield Portfolio

	Class A
	Year Ended September 30,												Period from February 7, 2012^ to
Selected Per Share Data and Ratios	2016††			2015			2014			2013			September 30, 2012
Net Asset Value, Beginning of Period	$	9.78		$	10.72		$	10.99		$	10.71		$	10.00
Income (Loss) from Investment Operations:
Net Investment Income†		0.64			0.66			0.65			0.77			0.48
Net Realized and Unrealized Gain (Loss)		0.12			(0.92	)		0.31			0.55			0.59
Total from Investment Operations		0.76			(0.26	)		0.96			1.32			1.07
Distributions from and/or in Excess of:
Net Investment Income		(0.64	)		(0.62	)		(0.73	)		(0.78	)		(0.36	)
Net Realized Gain		—			(0.06	)		(0.50	)		(0.26	)		—
Total Distributions		(0.64	)		(0.68	)		(1.23	)		(1.04	)		(0.36	)
Net Asset Value, End of Period	$	9.90		$	9.78		$	10.72		$	10.99		$	10.71
Total Return++		8.24	%		(2.43	)%		9.15	%		13.01	%		10.92	%#
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	59,139		$	56,042		$	40,157		$	1,092		$	107
Ratio of Expenses to Average Net Assets ⁽¹⁾		1.02	%+^^^		1.10	%+		1.02	%+		1.01	%+^^		0.99	%+*
Ratio of Net Investment Income to Average Net Assets ⁽¹⁾		6.76	%+^^^		6.49	%+		5.99	%+		7.04	%+^^		7.28	%+*
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.00	%§		0.00	%§		0.01	%		0.00	%§		0.01	%*
Portfolio Turnover Rate		74	%		62	%		96	%		227	%		192	%#
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		1.33	%		1.53	%		2.06	%		4.22	%		3.42	%*
Net Investment Income to Average Net Assets		6.45	%		6.06	%		4.95	%		3.83	%		4.85	%*

†† Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class A shares. The Ratio of Expenses to Average Net Assets and the Ratio of Net Investment Income to Average Net Assets would be unchanged as the change to current period custodian fees was offset against current period expense waivers/reimbursements with no impact to net expenses or net investment income.

^ Commencement of Operations.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

^^ Effective September 16, 2013, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 1.10% for Class A shares. Prior to September 16, 2013, the maximum ratio was 1.00% for Class A shares.

^^^ Effective January 4, 2016, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 1.00% for Class A shares. Prior to January 4, 2016, the maximum ratio was 1.10% for Class A shares.

§ Amount is less than 0.005%.

# Not Annualized.

* Annualized.

The accompanying notes are an integral part of the financial statements.
20

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

High Yield Portfolio

	Class L
	Year Ended September 30,												Period from February 7, 2012^ to
Selected Per Share Data and Ratios	2016††			2015			2014			2013			September 30, 2012
Net Asset Value, Beginning of Period	$	9.78		$	10.72		$	10.99		$	10.70		$	10.00
Income (Loss) from Investment Operations:
Net Investment Income†		0.62			0.64			0.67			0.75			0.46
Net Realized and Unrealized Gain (Loss)		0.13			(0.93	)		0.27			0.56			0.59
Total from Investment Operations		0.75			(0.29	)		0.94			1.31			1.05
Distributions from and/or in Excess of:
Net Investment Income		(0.62	)		(0.59	)		(0.71	)		(0.76	)		(0.35	)
Net Realized Gain		—			(0.06	)		(0.50	)		(0.26	)		—
Total Distributions		(0.62	)		(0.65	)		(1.21	)		(1.02	)		(0.35	)
Net Asset Value, End of Period	$	9.91		$	9.78		$	10.72		$	10.99		$	10.70
Total Return++		7.95	%		(2.70	)%		8.88	%		12.82	%		10.66	%#
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	628		$	1,111		$	1,519		$	326		$	107
Ratio of Expenses to Average Net Assets ⁽¹⁾		1.28	%+^^^		1.35	%+		1.35	%+		1.26	%+^^		1.24	%+*
Ratio of Net Investment Income to Average Net Assets ⁽¹⁾		6.51	%+^^^		6.25	%+		6.14	%+		6.90	%+^^		7.03	%+*
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.00	%§		0.00	%§		0.00	%§		0.00	%§		0.01	%*
Portfolio Turnover Rate		74	%		62	%		96	%		227	%		192	%#
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		1.83	%		1.84	%		2.52	%		4.11	%		3.67	%*
Net Investment Income to Average Net Assets		5.96	%		5.76	%		4.97	%		4.05	%		4.60	%*

†† Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class L shares. The Ratio of Expenses to Average Net Assets and the Ratio of Net Investment Income to Average Net Assets would be unchanged as the change to current period custodian fees was offset against current period expense waivers/reimbursements with no impact to net expenses or net investment income.

^ Commencement of Operations.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value as of the last business day of the period.

^^ Effective September 16, 2013, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 1.35% for Class L shares. Prior to September 16, 2013, the maximum ratio was 1.25% for Class L shares.

^^^ Effective January 4, 2016, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 1.25% for Class L shares. Prior to January 4, 2016, the maximum ratio was 1.35% for Class L shares.

§ Amount is less than 0.005%.

# Not Annualized.

* Annualized.

The accompanying notes are an integral part of the financial statements.
21

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

High Yield Portfolio

	Class C
Selected Per Share Data and Ratios	Year Ended September 30, 2016††			Period from April 30, 2015^ to September 30, 2015
Net Asset Value, Beginning of Period	$	9.78		$	10.39
Income (Loss) from Investment Operations:
Net Investment Income†		0.57			0.24
Net Realized and Unrealized Gain (Loss)		0.12			(0.62	)
Total from Investment Operations		0.69			(0.38	)
Distributions from and/or in Excess of:
Net Investment Income		(0.58	)		(0.23	)
Net Asset Value, End of Period	$	9.89		$	9.78
Total Return++		7.47	%		(3.75	)%#
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	2,908		$	1,309
Ratio of Expenses to Average Net Assets ⁽¹⁾		1.77	%+^^		1.84	%+*
Ratio of Net Investment Income to Average Net Assets ⁽¹⁾		6.00	%+^^		5.60	%+*
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.00	%§		0.00	%§*
Portfolio Turnover Rate		74	%		62	%#
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		2.12	%		2.15	%*
Net Investment Income to Average Net Assets		5.65	%		5.29	%*

†† Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class C shares. The Ratio of Expenses to Average Net Assets and the Ratio of Net Investment Income to Average Net Assets would be unchanged as the change to current period custodian fees was offset against current period expense waivers/reimbursements with no impact to net expenses or net investment income.

^ Commencement of Offering.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

^^ Effective January 4, 2016, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 1.75% for Class C shares. Prior to January 4, 2016, the maximum ratio was 1.85% for Class C shares.

§ Amount is less than 0.005%.

# Not Annualized.

* Annualized.

The accompanying notes are an integral part of the financial statements.
22

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

High Yield Portfolio

	Class IS
	Year Ended September 30,						Period from March 28, 2014^ to
Selected Per Share Data and Ratios	2016††			2015			September 30, 2014
Net Asset Value, Beginning of Period	$	9.79		$	10.74		$	10.98
Income (Loss) from Investment Operations:
Net Investment Income†		0.67			0.69			0.37
Net Realized and Unrealized Gain (Loss)		0.14			(0.92	)		(0.27	)
Total from Investment Operations		0.81			(0.23	)		0.10
Distributions from and/or in Excess of:
Net Investment Income		(0.68	)		(0.66	)		(0.34	)
Net Realized Gain		—			(0.06	)		—
Total Distributions		(0.68	)		(0.72	)		(0.34	)
Net Asset Value, End of Period	$	9.92		$	9.79		$	10.74
Total Return++		8.75	%		(2.17	)%		0.89	%#
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	13,789		$	574		$	10
Ratio of Expenses to Average Net Assets ⁽¹⁾		0.62	%+^^		0.72	%+		0.72	%+*
Ratio of Net Investment Income to Average Net Assets ⁽¹⁾		7.05	%+^^		6.75	%+		6.66	%+*
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.00	%§		0.00	%§		0.00	%§*
Portfolio Turnover Rate		74	%		62	%		96	%#
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		0.93	%		1.57	%		15.70	%*
Net Investment Income (Loss) to Average Net Assets		6.74	%		5.90	%		(8.32	)%*

†† Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class IS shares. The Ratio of Expenses to Average Net Assets and the Ratio of Net Investment Income to Average Net Assets would be unchanged as the change to current period custodian fees was offset against current period expense waivers/reimbursements with no impact to net expenses or net investment income.

^ Commencement of Offering.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value as of the last business day of the period.

^^ Effective January 4, 2016, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 0.62% for Class IS shares. Prior to January 4, 2016, the maximum ratio was 0.72% for Class IS shares.

§ Amount is less than 0.005%.

# Not Annualized.

* Annualized.

The accompanying notes are an integral part of the financial statements.
23

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements

Morgan Stanley Institutional Fund Trust ("MSIFT" or the "Fund") is registered under the Investment Company Act of 1940, as amended (the "Act"), as an open-end management investment company. The Fund is comprised of nine separate, active portfolios (individually referred to as a "Portfolio", collectively as the "Portfolios"). The Fund applies investment company accounting and reporting guidance. All Portfolios are considered diversified for purposes of the Act.

The accompanying financial statements relate to the High Yield Portfolio. The Portfolio seeks total return. The Portfolio offers five classes of shares — Class I, Class A, Class L, Class C and Class IS.

On April 30, 2015, the Portfolio suspended offering Class L shares to all investors. Existing Class L shareholders may invest through reinvestment of dividends and distributions.

prices are available on the relevant exchanges; (3) all other equity portfolio securities for which over-the-counter ("OTC") market quotations are readily available are valued at the latest reported sales price (or at the market official closing price if such market reports an official closing price), and if there was no trading in the security on a given day and if there is no official closing price from relevant markets for that day, the security is valued at the mean between the last reported bid and asked prices if such bid and asked prices are available on the relevant markets. Listed equity securities not traded on the valuation date with no reported bid and asked prices available on the exchange are valued at the mean between the current bid and asked prices obtained from one or more reputable brokers or dealers. An unlisted equity security that does not trade on the valuation date and for which bid and asked prices from the relevant markets are unavailable is valued at the mean between the current bid and asked prices obtained from one or more reputable brokers or dealers. In cases where a security is traded on more than one exchange, the security is valued on the exchange designated as the primary market; (4) swaps are marked-to-market daily based upon quotations from market makers; (5) certain senior collateralized loans ("Senior Loans") are valued based on quotations received from an independent pricing service; (6) when market quotations are not readily available, including circumstances under which Morgan Stanley Investment Management Inc. (the "Adviser") determines that the closing price, last sale price or the mean between the last reported bid and asked prices are not reflective of a security's market value, portfolio securities are valued at their fair value as determined in good faith under procedures established by and under the general supervision of the Trustees. Occasionally, developments affecting the closing prices of securities and other assets may occur between the times at which valuations of such securities are determined (that is, close of the foreign market on which the securities trade) and the close of business of the New York Stock Exchange ("NYSE"). If developments occur during such periods that are expected to materially affect the value of such securities, such valuations may be adjusted to reflect the estimated fair value of such securities as of the close of the NYSE, as determined in good faith by the Trustees or by the Adviser using a pricing service and/or procedures approved by the Trustees; and (7) investments in mutual funds, including the Morgan

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

Stanley Institutional Liquidity Funds, are valued at the net asset value ("NAV") as of the close of each business day.

2. Fair Value Measurement: Financial Accounting Standards Board ("FASB") Accounting Standards Codification^TM

("ASC") 820, "Fair Value Measurement" ("ASC 820"), defines fair value as the value that the Fund would receive to sell an investment or pay to transfer a liability in a timely transaction with an independent buyer in the principal market, or in the absence of a principal market the most advantageous market for the investment or liability. ASC 820 establishes a three-tier hierarchy to distinguish between (1) inputs that reflect the assumptions market participants would use in valuing an asset or liability developed based on market data obtained from sources independent of the reporting entity (observable inputs) and (2) inputs that reflect the reporting entity's own assumptions about the assumptions market participants would use in valuing an asset or liability developed based on the best information available in the circumstances (unobservable inputs) and to establish classification of fair value measurements for disclosure purposes. Various inputs are used in determining the value of the Fund's investments. The inputs are summarized in the three broad levels listed below.

• Level 1 – unadjusted quoted prices in active markets for identical investments

• Level 2 – other significant observable inputs (including quoted prices for similar investments, interest rates, prepayment speeds, credit risk, etc.)

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

The following is a summary of the inputs used to value the Portfolio's investments as of September 30, 2016.

Investment Type	Level 1 Unadjusted quoted prices (000)		Level 2 Other significant observable inputs (000)		Level 3 Significant unobservable inputs (000)			Total (000)
Assets:
Fixed Income Securities
Corporate Bonds	$	—	$	119,455	$	—	†	$	119,455	†
Sovereign		—		1,137		—			1,137
Variable Rate Senior Loan Interests		—		5,596		—			5,596
Total Fixed Income Securities		—		126,188		—	†		126,188	†
Common Stocks
Auto Components		1		—		—			1
Energy Equipment & Services		453		—		—			453
Semiconductors & Semiconductor Equipment		—		77		—			77
Total Common Stocks		454		77		—			531
Participation Note		—		—		—†			—†
Short-Term Investment
Investment Company		399		—		—			399
Total Assets	$	853	$	126,265	$	—	†	$	127,118	†

† Includes securities which are valued at zero.

Following is a reconciliation of investments in which significant unobservable inputs (Level 3) were used in determining fair value.

	Corporate Bond (000)			Common Stock (000)			Participation Note (000)
Beginning Balance	$	—		$	—	@	$	—
Purchases		—			—			—	†
Sales		—			—			—
Amortization of discount		—			—			—
Transfers in		—	†		—			—
Transfers out		—			(1	)		—
Corporate actions		—			—			—
Change in unrealized appreciation (depreciation)		—			1			—
Realized gains (losses)		—			—			—

Corporate
Bond
(000)

Common
Stock
(000)

Participation
Note
(000)

Ending Balance

—

†

—

†

Net change in unrealized appreciation
(depreciation) from investments still
held as of September 30, 2016

—

† Includes securities which are valued at zero.

@ Value is less than $500.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

there is no assurance that the use of derivatives will achieve this result.

Following is a description of the derivative instruments and techniques that the Portfolio used during the period and their associated risks:

During the period swap agreements are open, payments are received from or made to the clearinghouse or counterparty based upon changes in the value of the contract (variation margin). The Dodd-Frank Wall Street Reform and Consumer Protection Act and related regulatory developments require the clearing and exchange-trading of certain standardized swap transactions. Mandatory exchange-trading and clearing is occurring on a phased-in basis.

The Portfolio's use of swaps during the period included those based on the credit of an underlying security

commonly referred to as "credit default swaps." The Portfolio may be either the buyer or seller in a credit default swap. Where the Portfolio is the buyer of a credit default swap contract, it would typically be entitled to receive the par (or other agreed-upon) value of a referenced debt obligation from the counterparty to the contract only in the event of a default or similar event by the issuer of the debt obligation. If no default occurs, the Portfolio would have paid to the counterparty a periodic stream of payments over the term of the contract and received no benefit from the contract. When the Portfolio is the seller of a credit default swap contract, it typically receives the stream of payments but is obligated to pay an amount equal to the par (or other agreed-upon) value of a referenced debt obligation upon the default or similar event by the issuer of the referenced debt obligation. The use of credit default swaps could result in losses to the Portfolio if the Adviser fails to correctly evaluate the creditworthiness of the issuer of the referenced debt obligation.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

recovery value is determined by a facilitated auction whereby a minimum number of allowable broker bids, together with a specified valuation method, are used to calculate the settlement value. The Portfolio's maximum risk of loss from counterparty risk, either as the protection seller or as the protection buyer, is the fair value of the swap agreement.

The following table sets forth by primary risk exposure the Portfolio's realized gains (losses) by type of derivative contract for the year ended September 30, 2016 in accordance with ASC 815.

Realized Gain (Loss)
Primary Risk Exposure	Derivative Type	Value (000)
Credit Risk	Swap Agreement	$	43

5. Structured Investments: The Portfolio invested a portion of its assets in structured investments. A structured investment is a derivative security designed to offer a return linked to a particular underlying security, currency, commodity or market. Structured investments may come in various forms including notes (such as exchange-traded notes), warrants and options to purchase securities. The Portfolio will typically use structured investments to gain exposure to a permitted underlying security, currency, commodity or market when direct access to a market is limited or inefficient from a tax or cost standpoint. There can be no assurance that structured investments will trade at the same price or have the same value as the underlying security, currency, commodity or market. Investments in

structured investments involve risks including issuer risk, counterparty risk and market risk. Holders of structured investments bear risks of the underlying investment and are subject to issuer or counterparty risk because the Portfolio is relying on the creditworthiness of such issuer or counterparty and has no rights with respect to the underlying investment. Certain structured investments may be thinly traded or have a limited trading market and may have the effect of increasing the Portfolio's illiquidity to the extent that the Portfolio, at a particular time, may be unable to find qualified buyers for these securities.

7. Restricted Securities: The Portfolio invests in unregistered or otherwise restricted securities. The term "restricted securities" refers to securities that are unregistered or are held by control persons of the issuer and securities that are subject to contractual restrictions on their resale. As a result, restricted securities may be more difficult to value and the Portfolio may have difficulty disposing of such assets either in a timely manner or for a reasonable price. In order to dispose of an unregistered security, the Portfolio, where it has contractual rights to do so, may have to cause such security to be registered. A considerable period may elapse between the time the decision is made to sell the security and the time the security is registered so that the Portfolio could sell it.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

Contractual restrictions on the resale of securities vary in length and scope and are generally the result of a negotiation between the issuer and acquirer of the securities. The Portfolio would, in either case, bear market risks during that period. Restricted securities are identified in the Portfolio of Investments.

8. Indemnifications: The Fund enters into contracts that contain a variety of indemnifications. The Fund's maximum exposure under these arrangements is unknown. However, the Fund has not had prior claims or losses pursuant to these contracts and expects the risk of loss to be remote.

9. Dividends and Distributions to Shareholders: Dividend income and distributions to shareholders are recorded on the ex-dividend date. Dividends from net investment income, if any, are declared and paid monthly. Net realized capital gains, if any, are distributed at least annually.

10. Security Transactions, Income and Expenses: Security transactions are accounted for on the trade date (date the order to buy or sell is executed). Realized gains and losses on the sale of investment securities are determined on the specific identified cost method. When the Portfolio buys an interest in a Senior Loan, it may receive a commitment fee which is paid to lenders on an ongoing basis based upon the undrawn portion committed by the lenders of the underlying Senior Loan. The Portfolio accrues the commitment fee over the expected term of the loan. When the Portfolio sells interest in a Senior Loan, it may be required to pay fees or commissions to the purchaser of the interest. Fees received in connection with loan amendments are accrued as earned. Dividend income and other distributions are recorded on the ex-dividend date (except for certain foreign dividends which may be recorded as soon as the Portfolio is informed of such dividends) net of applicable withholding taxes. Interest income is recognized on the accrual basis except where collection is in doubt. Discounts are accreted and premiums are amortized over the life of the respective securities. Most expenses of the Fund can be directly attributed to a particular Portfolio. Expenses which cannot be directly attributed are apportioned among the Portfolios based upon relative net assets or other appropriate methods. Income, expenses (other than class specific expenses — distribution and shareholder services, transfer agency and sub transfer agency fees) and realized and unrealized gains or losses are

allocated to each class of shares based upon their relative net assets.

The Adviser has agreed to reduce its advisory fee and/or reimburse the Portfolio so that total annual portfolio operating expenses, excluding certain investment related expenses, taxes, interest and other extraordinary expenses (including litigation), will not exceed 0.75% for Class I shares, 1.10% for Class A shares, 1.35% for Class L shares, 1.85% for Class C shares and 0.72% for Class IS shares. Effective January 4, 2016, the Adviser has agreed to reduce its advisory fee and/or reimburse the Portfolio so that total annual portfolio operating expenses will not exceed 0.65% for Class I shares, 1.00% for Class A shares, 1.25% for Class L shares, 1.75% for Class C shares and 0.62% for Class IS shares. The fee waivers and/or expense reimbursements will continue for at least one year from the date of the Portfolio's prospectus or until such time as the Trustees act to discontinue all or a portion of such waivers and/or reimbursements when they deem such action is appropriate. For the year ended September 30, 2016, approximately $255,000 of advisory fees were waived and approximately $43,000 of other expenses were reimbursed by the Adviser pursuant to this arrangement.

C. Administration Fees: The Adviser also serves as Administrator to the Fund and provides administrative services pursuant to an Administration Agreement for an annual fee, accrued daily and paid monthly, of 0.08% of the Portfolio's average daily net assets. Under a Sub-Administration Agreement between the Administrator and State Street Bank and Trust Company ("State Street"), State Street provides certain administrative services to the Fund. For such services, the Administrator pays State Street a portion of the fee the Administrator receives from the Portfolio.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

pays the Distributor a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Portfolio's average daily net assets attributable to Class A shares.

was reflected as "Reimbursement of Custodian Fees" in the Statement of Operations. Pursuant to the expense limitations described in Note B, the Portfolio has experienced investment advisory fee waivers during the current period. Accordingly, the reimbursement of out-of-pocket expenses in the current period resulted in the reduction in the current period waiver of advisory fees.

G. Security Transactions and Transactions with Affiliates: For the year ended September 30, 2016, purchases and sales of investment securities for the Portfolio, other than long-term U.S. Government securities and short-term investments, were approximately $124,237,000 and $73,164,000, respectively. There were no purchases and sales of long-term U.S. Government securities for the year ended September 30, 2016.

The Portfolio invests in the Institutional Class of the Morgan Stanley Institutional Liquidity Funds (the "Liquidity Funds"), an open-end management investment company managed by the Adviser. Advisory fees paid by the Portfolio are reduced by an amount equal to its pro-rata share of the advisory and administration fees paid by the Portfolio due to its investment in the Liquidity Funds. For the year ended September 30, 2016, advisory fees paid were reduced by approximately $1,000 relating to the Portfolio's investment in the Liquidity Funds.

A summary of the Portfolio's transactions in shares of the Liquidity Funds during the year ended September 30, 2016 is as follows:

Value September 30, 2015 (000)				Purchases at Cost (000)				Sales (000)				Dividend Income (000)				Value September 30, 2016 (000)
$	991			$	60,106			$	60,698			$	4			$	399

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

the Morgan Stanley funds that are offered as investment options under the Compensation Plan. Appreciation/depreciation and distributions received from these investments are recorded with an offsetting increase/decrease in the deferred compensation obligation and do not affect the NAV of the Portfolio.

FASB ASC 740-10, "Income Taxes — Overall", sets forth a minimum threshold for financial statement recognition of the benefit of a tax position taken or expected to be taken in a tax return. Management has concluded there are no significant uncertain tax positions that would require recognition in the financial statements. If applicable, the Portfolio recognizes interest accrued related to unrecognized tax benefits in "Interest Expense" and penalties in "Other Expenses" in the Statement of Operations. The Portfolio files tax returns with the U.S. Internal Revenue Service, New York and various states. Each of the tax years in the four-year period ended September 30, 2016, remains subject to examination by taxing authorities.

2016 Distributions Paid From:				2015 Distributions Paid From:
Ordinary Income (000)		Long-Term Capital Gain (000)		Ordinary Income (000)		Long-Term Capital Gain (000)
$	6,619	$	—	$	3,836	$	94

Permanent differences, primarily due to basis adjustments for swap transactions, paydown adjustments and adjustments on bonds sold, resulted in the following reclassifications among the components of net assets at September 30, 2016:

Accumulated Undistributed Net Investment Income (000)				Accumulated Net Realized Loss (000)				Paid-in- Capital (000)
$	1			$	(1	)		$	—

At September 30, 2016, the components of distributable earnings for the Portfolio on a tax basis were as follows:

Undistributed Ordinary Income (000)				Undistributed Long-Term Capital Gain (000)
$	1,007			$	—

At September 30, 2016, the Portfolio had available for federal income tax purposes unused short term and long term capital losses of approximately $204,000 and $2,214,000, respectively, that do not have an expiration date.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Report of Independent Registered Public Accounting Firm

To the Shareholders and Board of Trustees of
Morgan Stanley Institutional Fund Trust —
High Yield Portfolio

We have audited the accompanying statement of assets and liabilities, including the portfolio of investments, of High Yield Portfolio (one of the portfolios constituting Morgan Stanley Institutional Fund Trust) (the "Portfolio") as of September 30, 2016, and the related statement of operations for the year then ended, the statements changes in net assets for each of the two years in the period then ended and the financial highlights for each of the years or periods indicated therein. These financial statements and financial highlights are the responsibility of the Portfolio's management. Our responsibility is to express an opinion on these financial statements and financial highlights based on our audits.

In our opinion, the financial statements and financial highlights referred to above present fairly, in all material respects, the financial position of High Yield Portfolio (one of the portfolios constituting Morgan Stanley Institutional Fund Trust) at September 30, 2016, the results of its operations for the year then ended, the changes in its net assets for each of the two years in the period then ended and the financial highlights for each of the years or periods indicated therein, in conformity with U.S. generally accepted accounting principles.

Boston, Massachusetts
November 22, 2016

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Advisory Agreement Approval (unaudited)

Nature, Extent and Quality of Services

Performance, Fees and Expenses of the Portfolio

The Board reviewed the performance, fees and expenses of the Portfolio compared to its peers, as determined by Broadridge, and to appropriate benchmarks where applicable. The Board discussed with the Adviser the performance goals and the actual results achieved in managing the Portfolio. When considering a fund's performance, the Board and the Adviser place emphasis on trends and longer-term returns (focusing on one-year, three-year and five-year performance, as of December 31, 2015, or since inception, as applicable). When a fund underperforms its benchmark and/or its peer group average, the Board and the Adviser discuss the causes of such underperformance and, where necessary, they discuss specific changes to investment strategy or investment personnel. The Board noted that the Portfolio's performance was better than its peer group average for the one- and three-year periods and the period since the end of February 2012, the month of the Portfolio's inception. The Board discussed with the Adviser the level of the advisory and administration fees (together, the "management fee") for this Portfolio relative to comparable funds and/or other accounts advised by the Adviser and/or compared to its peers as determined by Broadridge. In addition to the management fee, the Board also reviewed the Portfolio's total expense ratio. The Board noted that the Portfolio's management fee and total expense ratio were lower than its peer group averages. After discussion, the Board concluded that the Portfolio's (i) performance was competitive with its peer group average; and (ii) management fee and total expense ratio were competitive with its peer group averages.

Economies of Scale

The Board considered the size and growth prospects of the Portfolio and how that relates to the Portfolio's total expense ratio and particularly the Portfolio's management fee rate, which does not include breakpoints. In conjunction with its review of the Adviser's profitability, the Board discussed with the Adviser how a change in assets can affect the efficiency or effectiveness of managing the Portfolio and whether the management fee level is appropriate relative to current and projected asset levels and/or whether the management fee structure reflects economies of scale as asset levels change. The Board has determined that its review of the actual and/or potential economies of scale of the Portfolio supports its decision to approve the Management Agreement.

Profitability of the Adviser and Affiliates

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Advisory Agreement Approval (unaudited) (cont'd)

Other Benefits of the Relationship

Resources of the Adviser and Historical Relationship Between the Portfolio and the Adviser

Other Factors and Current Trends

General Conclusion

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Privacy Notice (unaudited)

MORGAN STANLEY INVESTMENT MANAGEMENT INC.
AN IMPORTANT NOTICE CONCERNING OUR U.S. PRIVACY POLICY

WE RESPECT YOUR PRIVACY

1. WHAT PERSONAL INFORMATION DO WE COLLECT ABOUT YOU?

For example:

• We may obtain information about your creditworthiness and credit history from consumer reporting agencies.

• We may collect background information from and through third-party vendors to verify representations you have made and to comply with various regulatory requirements.

2. WHEN DO WE DISCLOSE PERSONAL INFORMATION WE COLLECT ABOUT YOU?

We may disclose personal information we collect about you to other Morgan Stanley companies and to non-affiliated third parties.

a. Information We Disclose to Other Morgan Stanley Companies.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Privacy Notice (unaudited) (cont'd)

b. Information We Disclose to Non-affiliated Third Parties.

3. HOW DO WE PROTECT THE SECURITY AND CONFIDENTIALITY OF PERSONAL INFORMATION WE COLLECT ABOUT YOU?

4. HOW CAN YOU LIMIT THE SHARING OF CERTAIN TYPES OF PERSONAL INFORMATION WITH OTHER MORGAN STANLEY COMPANIES?

5. HOW CAN YOU LIMIT THE USE OF CERTAIN TYPES OF PERSONAL INFORMATION BY OTHER MORGAN STANLEY COMPANIES FOR MARKETING?

6. HOW CAN YOU SEND US AN OPT-OUT INSTRUCTION?

• Calling us at (800) 548-7786
Monday–Friday between 8a.m. and 6p.m.(EST)

• Writing to us at the following address:

Boston Financial Data Services, Inc.
c/o Privacy Coordinator
P.O. Box 219804
Kansas City, Missouri 64121

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Privacy Notice (unaudited) (cont'd)

7. WHAT IF AN AFFILIATED COMPANY BECOMES A NON-AFFILIATED THIRD PARTY?

SPECIAL NOTICE TO RESIDENTS OF VERMONT

If you wish to receive offers for investment products and services offered by or through other Morgan Stanley companies, please notify us in writing at the following address:

Boston Financial Data Services, Inc.
c/o Privacy Coordinator
P.O. Box 219804
Kansas City, Missouri 64121

SPECIAL NOTICE TO RESIDENTS OF CALIFORNIA

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited)

Independent Trustees:

Name, Age and Address of
Independent Trustee

Position(s)
Held with
Registrant

Length of Time
Served*

Principal Occupation(s) During Past 5 Years
and Other Relevant Professional Experience

Number of
Portfolios in
Fund Complex
Overseen by
Independent
Trustee**

Other Directorships
Held by Independent
Trustee***

Frank L. Bowman (71)
c/o Perkins Coie LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
August
2006

Kathleen A. Dennis (63)
c/o Perkins Coie LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
August
2006

Director of various non-profit organizations.

Nancy C. Everett (61)
c/o Perkins Coie LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
January
2015

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Age and Address of
Independent Trustee

Position(s)
Held with
Registrant

Length of Time
Served*

Principal Occupation(s) During Past 5 Years
and Other Relevant Professional Experience

Number of
Portfolios in
Fund Complex
Overseen by
Independent
Trustee**

Other Directorships
Held by Independent
Trustee***

Jakki L. Haussler (59)
c/o Perkins Coie LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
January
2015

Dr. Manuel H. Johnson (67)
c/o Johnson Smick
International, Inc.
220 I Street, N.E. —
Suite 200
Washington, D.C. 20002

Trustee

Since
July
1991

100

Director of NVR, Inc. (home construction).

Joseph J. Kearns (74)
c/o Kearns & Associates LLC
23823 Malibu Road
S-50-440
Malibu, CA 90265

Trustee

Since
August
1994

101

Director of Electro Rent Corporation (equipment leasing). Prior to December 31, 2013, Director of The Ford Family Foundation.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Age and Address of
Independent Trustee

Position(s)
Held with
Registrant

Length of Time
Served*

Principal Occupation(s) During Past 5 Years
and Other Relevant Professional Experience

Number of
Portfolios in
Fund Complex
Overseen by
Independent
Trustee**

Other Directorships
Held by Independent
Trustee***

Michael F. Klein (57)
c/o Perkins Coie LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
August
2006

Director of certain investment funds managed or sponsored by Aetos Capital, LLC; Director of Sanitized AG and Sanitized Marketing AG (specialty chemicals).

Michael E. Nugent (80)
522 Fifth Avenue
New York, NY 10036

Chair of the
Board and
Trustee

Chair of the
Boards since
July 2006 and
Trustee since
July 1991

100

None.

W. Allen Reed (69)
c/o Perkins Coie LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
August
2006

Director of Legg Mason, Inc.; formerly, Director of the Auburn University Foundation (2010-2015).

Fergus Reid (84)
c/o Joe Pietryka, Inc.
85 Charles Colman Blvd.
Pawling, NY 12564

Trustee

Since
June
1992

Chairman, Joe Pietryka, Inc.; Chairperson of the Governance Committee and Director or Trustee of various Morgan Stanley Funds (since June 1992).

100

Formerly, Trustee and Director of certain investment companies in the JP Morgan Fund Complex managed by JP Morgan Investment Management Inc. (1987-2012).

* This is the earliest date the Trustee began serving the Morgan Stanley Funds. Each Trustee serves an indefinite term, until his or her successor is elected.

*** This includes any directorships at public companies and registered investment companies held by the Trustee at any time during the past five years.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited) (cont'd)

Executive Officers:

Name, Age and Address of Executive Officer

Position(s) Held
with
Registrant

Length of
Time Served*

Principal Occupation(s) During Past 5 Years

John H. Gernon (53)
522 Fifth Avenue
New York, NY 10036

President and
Principal
Executive
Officer

Since
September
2013

Stefanie V. Chang Yu (49)
522 Fifth Avenue
New York, NY 10036

Chief
Compliance
Officer

Since
December
1997

Joseph C. Benedetti (51)
522 Fifth Avenue
New York, NY 10036

Vice President

Since
January
2014

Francis J. Smith (51)
522 Fifth Avenue
New York, NY 10036

Treasurer and
Principal
Financial
Officer

Treasurer
since July
2003 and
Principal
Financial
Officer since
September
2002

Executive Director of the Adviser and various entities affiliated with the Adviser; Treasurer (since July 2003) and Principal Financial Officer of various Morgan Stanley Funds (since September 2002).

Mary E. Mullin (49)
522 Fifth Avenue
New York, NY 10036

Secretary

Since
June
1999

Executive Director of the Adviser; Secretary of various Morgan Stanley Funds (since June 1999).

* This is the earliest date the officer began serving the Morgan Stanley Funds. Each officer serves a one-year term, until his or her successor is elected and has qualified.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Adviser and Administrator

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

Distributor

Morgan Stanley Distribution, Inc.
522 Fifth Avenue
New York, New York 10036

Dividend Disbursing and Transfer Agent

Boston Financial Data Services, Inc.
2000 Crown Colony Drive
Quincy, Massachusetts 02169

Custodian

State Street Bank and Trust Company
One Lincoln Street
Boston, Massachusetts 02111

Legal Counsel

Dechert LLP
1095 Avenue of the Americas
New York, New York 10036

Counsel to the Independent Trustees

Perkins Coie LLP
30 Rockefeller Plaza
New York, New York 10112

Independent Registered Public Accounting Firm

Ernst & Young LLP
200 Clarendon Street
Boston, Massachusetts 02116

Reporting to Shareholders

Proxy Voting Policies and Procedures and Proxy Voting Record

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable Portfolio of Morgan Stanley Institutional Funds Trust, which describes in detail the Portfolio's investment policies, risks, fees and expenses. Please read the prospectus carefully before you invest or send money. For additional information, including information regarding the investments comprising the Portfolio, please visit our website at www.morganstanley.com/im or call toll free 1 (800) 548-7786.

(This Page has been left blank intentionally.)

Printed in U.S.A.
This Report has been prepared for shareholders and may be distributed to others only if preceded or accompanied by a current prospectus.

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

IFTHYANN
1627761 EXP. 11.30.17

INVESTMENT MANAGEMENT

Morgan Stanley Institutional Fund Trust

Mid Cap Growth Portfolio

Annual Report

September 30, 2016

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Table of Contents

Shareholders' Letter					2
Expense Example					3
Investment Overview					4
Portfolio of Investments					6
Statement of Assets and Liabilities					8
Statement of Operations					10
Statements of Changes in Net Assets					11
Financial Highlights					12
Notes to Financial Statements					16
Report of Independent Registered Public Accounting Firm					27
Investment Advisory Agreement Approval					28
Federal Tax Notice					30
Privacy Notice					31
Trustee and Officer Information					34

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Shareholders' Letter (unaudited)

Dear Shareholders,

We are pleased to provide this Annual report, in which you will learn how your investment in Mid Cap Growth Portfolio (the "Portfolio") performed during the latest twelve-month period.

As always, we thank you for selecting Morgan Stanley Investment Management, and look forward to working with you in the months and years ahead.

Sincerely,

John H. Gernon
President and Principal Executive Officer

October 2016

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Expense Example (unaudited)

Mid Cap Growth Portfolio

This example is based on an investment of $1,000 invested at the beginning of the six-month period ended September 30, 2016 and held for the entire six-month period (unless otherwise noted).

Actual Expenses

Hypothetical Example for Comparison Purposes

	Beginning Account Value 4/1/16		Actual Ending Account Value 9/30/16		Hypothetical Ending Account Value		Actual Expenses Paid During Period*		Hypothetical Expenses Paid During Period*		Net Expense Ratio During Period**
Mid Cap Growth Portfolio Class I	$	1,000.00	$	1,075.70	$	1,021.95	$	3.17	$	3.08		0.61	%***
Mid Cap Growth Portfolio Class A		1,000.00		1,073.70		1,020.60		4.56		4.45		0.88	***
Mid Cap Growth Portfolio Class L		1,000.00		1,069.70		1,016.90		8.38		8.17		1.62	***
Mid Cap Growth Portfolio Class IS		1,000.00		1,075.40		1,021.95		3.16		3.08		0.61	***

** Annualized.

*** Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Overview (unaudited)

Mid Cap Growth Portfolio

The Portfolio seeks long-term capital growth.

Performance

For the fiscal year ended September 30, 2016, the Portfolio's Class I shares had a total return based on net asset value and reinvestment of distributions per share of 0.19%, net of fees. The Portfolio's Class I shares underperformed against the Portfolio's benchmark, the Russell Midcap® Growth Index (the "Index"), which returned 11.24%.

Factors Affecting Performance

• Despite mixed economic data and some notable spikes in market volatility, U.S. stocks advanced over the 12-month period ended September 30, 2016. After raising its main policy interest rate in December 2015 based on improvements in the labor market, the Federal Reserve (Fed) left rates on hold for the next six meetings. The Fed's non-action (combined with accommodative policy from the European Central Bank and Bank of Japan), low global interest rates, an easing in the U.S. dollar's relative strength and a recovery in oil prices continued to bolster investor confidence in stocks. Although stocks sold-off sharply early in 2016 on a combination of concerns, including the pacing of the Fed's rate hikes, weak data in China and a new low in oil prices, and were roiled again in late June by the surprise outcome of the Brexit vote, losses were reversed in the subsequent rallies.

• Stock selection drove the Fund's underperformance relative to the Index. The information technology sector was the largest relative detractor, with particular weakness in the software subsector.

• The consumer discretionary sector was also disadvantageous to relative performance. A small relative gain from an underweight to the sector was offset by weak stock selection, primarily in internet and catalog retail holdings.

• The health care sector posted disappointing results, pressured by negative performance from holdings in the health care technology and pharmaceuticals subsectors.

• The only positive contributor to relative performance at the sector level was consumer staples. Holdings in two food products companies added to relative returns during the period.

Management Strategies

• As a team, we believe having a market outlook can be an anchor. Our focus is on assessing company prospects over three to five years, and owning a portfolio of what we believe are high quality companies with diverse business drivers not tied to a particular market environment.

• We look for high-quality growth companies that we believe have these attributes: sustainable competitive advantages, above-average business visibility, rising return on invested capital, strong free cash flow generation and a favorable risk/reward profile. We find these companies through intense fundamental research. Our emphasis is on secular growth, and as a result, short-term market events are not as meaningful in the stock selection process.

* Minimum Investment

In accordance with SEC regulations, the Portfolio's performance shown assumes that all recurring fees (including management fees) were deducted and all dividends and distributions were reinvested. The performance of Class A, Class L and Class IS shares will vary from the performance of Class I shares based upon their different inception dates and will be negatively impacted by additional fees assessed to those classes (where applicable).

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Overview (unaudited) (cont'd)

Mid Cap Growth Portfolio

Performance Compared to the Russell Midcap^® Growth Index⁽¹⁾ and the Lipper Multi-Cap Growth Funds Index⁽²⁾

	Period Ended September 30, 2016 Total Returns⁽³⁾
				Average Annual
	One Year			Five Years			Ten Years			Since Inception⁽⁸⁾
Portfolio — Class I Shares w/o sales charges⁽⁴⁾		0.19	%		7.75	%		6.98	%		11.65	%
Portfolio — Class A Shares w/o sales charges⁽⁵⁾		–0.12			7.47			6.70			8.82
Portfolio — Class A Shares with maximum 5.25% sales charges⁽⁵⁾		–5.37			6.32			6.13			8.52
Portfolio — Class L Shares w/o sales charges⁽⁶⁾		–0.73			—			—			6.48
Portfolio — Class IS Shares w/o sales charges⁽⁷⁾		0.25			—			—			0.77
Russell Midcap^® Growth Index		11.24			15.85			8.51			10.17
Lipper Multi-Cap Growth Funds Index		9.58			15.04			7.68			8.93

⁽¹⁾ The Russell Midcap^® Growth Index measures the performance of the mid-cap growth segment of the U.S. equity universe. It includes those Russell Midcap^® Index companies with higher price-to-book ratios and higher forecasted growth values. The Russell Midcap^® Index is a subset of the Russell 1000^® Index and includes approximately 800 of the smallest securities in the Russell 1000^® Index, which in turn consists of approximately 1,000 of the largest U.S. securities based on a combination of market capitalization and current index membership. The Index is unmanaged and its returns do not include any sales charges or fees. Such costs would lower performance. It is not possible to invest directly in an index.

⁽²⁾ The Lipper Multi-Cap Growth Funds Index is an equally weighted performance index of the largest qualifying funds (based on net assets) in the Lipper Multi-Cap Growth Funds classification. The index, which is adjusted for capital gains distributions and income dividends, is unmanaged and should not be considered an investment. There are currently 30 funds represented in this Index. As of the date of this report, the Portfolio was in the Lipper Multi-Cap Growth Funds classification.

⁽³⁾ Total returns for the Portfolio reflect expenses waived and/or reimbursed, if applicable, by the Adviser. Without such waivers and/or reimbursements, total returns would have been lower.

⁽⁴⁾ Commenced operations on March 30, 1990.

⁽⁵⁾ Commenced operations on January 31, 1997.

⁽⁶⁾ Commenced operations on June 14, 2012.

⁽⁷⁾ Commenced operations on September 13, 2013.

⁽⁸⁾ For comparative purposes, average annual since inception returns listed for the Indexes refer to the inception date of Class I of the Portfolio, not the inception of the Indexes.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments

Mid Cap Growth Portfolio

	Shares		Value (000)
Common Stocks (94.0%)
Aerospace & Defense (1.5%)
TransDigm Group, Inc. (a)		64,562	$	18,666
Air Freight & Logistics (0.7%)
XPO Logistics, Inc. (a)		229,502		8,416
Automobiles (4.4%)
Tesla Motors, Inc. (a)(b)		272,940		55,688
Biotechnology (1.0%)
Alnylam Pharmaceuticals, Inc. (a)		72,742		4,931
Intrexon Corp. (a)(b)		182,619		5,117
Juno Therapeutics, Inc. (a)(b)		76,516		2,296
				12,344
Capital Markets (8.1%)
Affiliated Managers Group, Inc. (a)		78,083		11,299
MSCI, Inc.		383,507		32,191
S&P Global, Inc.		472,328		59,778
				103,268
Communications Equipment (0.8%)
Palo Alto Networks, Inc. (a)		66,457		10,589
Consumer Finance (0.7%)
LendingClub Corp. (a)		1,475,488		9,118
Food Products (2.9%)
Mead Johnson Nutrition Co.		457,607		36,156
Health Care Equipment & Supplies (6.1%)
DexCom, Inc. (a)		191,508		16,788
Intuitive Surgical, Inc. (a)		84,307		61,108
				77,896
Health Care Technology (4.8%)
athenahealth, Inc. (a)		488,537		61,614
Hotels, Restaurants & Leisure (6.3%)
Chipotle Mexican Grill, Inc. (a)		12,752		5,400
Dunkin' Brands Group, Inc.		814,796		42,435
Marriott International, Inc., Class A		488,041		32,860
				80,695
Information Technology Services (3.8%)
FleetCor Technologies, Inc. (a)		207,866		36,113
Gartner, Inc. (a)		143,810		12,720
				48,833
Internet & Direct Marketing Retail (1.4%)
TripAdvisor, Inc. (a)		85,886		5,426
Zalando SE (Germany) (a)(c)		286,475		11,953
				17,379
Internet Software & Services (16.9%)
Dropbox, Inc. (a)(d)(e)(f) (acquisition cost — $33,909; acquired 5/1/12)		3,747,173		50,699
LinkedIn Corp., Class A (a)		55,954		10,694
MercadoLibre, Inc. (Brazil)		135,231		25,014
Pandora Media, Inc. (a)		633,317		9,075

	Shares		Value (000)
Survey Monkey, Inc. (a)(d)(e)(f) (acquisition cost — $28,952; acquired 11/25/14)		1,760,030	$	17,864
Twitter, Inc. (a)		1,981,595		45,676
Yelp, Inc. (a)		241,561		10,073
Zillow Group, Inc., Class A (a)		440,541		15,177
Zillow Group, Inc., Class C (a)(b)		875,304		30,329
				214,601
Life Sciences Tools & Services (6.6%)
Illumina, Inc. (a)		465,132		84,496
Multi-line Retail (0.9%)
Dollar Tree, Inc. (a)		136,814		10,799
Pharmaceuticals (2.8%)
Zoetis, Inc.		693,706		36,080
Professional Services (6.0%)
IHS Markit Ltd. (a)		994,866		37,357
Verisk Analytics, Inc. (a)		483,441		39,294
				76,651
Semiconductors & Semiconductor Equipment (1.0%)
NVIDIA Corp.		179,031		12,267
Software (12.7%)
Atlassian Corp., PLC, Class A (United Kingdom) (a)		205,073		6,146
FireEye, Inc. (a)		342,220		5,041
Mobileye N.V. (a)(b)		168,263		7,163
NetSuite, Inc. (a)		115,406		12,774
ServiceNow, Inc. (a)		422,792		33,464
Splunk, Inc. (a)		563,453		33,063
Tableau Software, Inc., Class A (a)		133,250		7,365
Workday, Inc., Class A (a)		619,840		56,833
				161,849
Tech Hardware, Storage & Peripherals (0.4%)
3D Systems Corp. (a)(b)		194,960		3,500
Stratasys Ltd. (a)		66,302		1,597
				5,097
Textiles, Apparel & Luxury Goods (3.3%)
Lululemon Athletica, Inc. (Canada) (a)		178,549		10,888
Michael Kors Holdings Ltd. (a)		382,816		17,912
Under Armour, Inc., Class C (a)		405,086		13,716
				42,516
Trading Companies & Distributors (0.9%)
Fastenal Co.		270,948		11,320
Total Common Stocks (Cost $874,824)				1,196,338
Convertible Preferred Stock (0.4%)
Internet Software & Services (0.4%)
Dropbox, Inc. Series A (a)(d)(e)(f) (acquisition cost — $3,365; acquired 5/25/12) (Cost $3,365)		371,814		5,031

The accompanying notes are an integral part of the financial statements.
6

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Mid Cap Growth Portfolio

	Shares		Value (000)
Preferred Stock (2.3%)
Internet & Direct Marketing Retail (2.3%)
Flipkart Online Services Pvt Ltd. Series D (a)(d)(e)(f) (acquisition cost — $13,007; acquired 10/4/13) (Cost $13,007)		566,827	$	29,549
	Notional Amount (000)
Call Option Purchased (0.0%)
Foreign Currency Option (0.0%)
USD/CNY December 2016 @ CNY 7.60, Royal Bank of Scotland (Cost $1,044)	$	225,859		10
	Shares
Short-Term Investments (7.3%)
Securities held as Collateral on Loaned Securities (4.8%)
Investment Company (4.1%)
Morgan Stanley Institutional Liquidity Funds — Treasury Securities Portfolio — Institutional Class (See Note G)		52,110,823		52,111
	Face Amount (000)
Repurchase Agreement (0.7%)
Merrill Lynch & Co., Inc., (0.50%, dated 9/30/16, due 10/3/16; proceeds $9,105; fully collateralized by a U.S. Government agency security; 4.00% due 12/1/45; valued at $9,287)	$	9,105		9,105
Total Securities held as Collateral on Loaned Securities (Cost $61,216)				61,216
	Shares
Investment Company (2.5%)
Morgan Stanley Institutional Liquidity Funds — Treasury Securities Portfolio — Institutional Class (See Note G) (Cost $31,493)		31,493,194		31,493
Total Short-Term Investments (Cost $92,709)				92,709
Total Investments (104.0%) (Cost $984,949) Including $73,901 of Securities Loaned (g)(h)				1,323,637
Liabilities in Excess of Other Assets (–4.0%)				(50,623	)
Net Assets (100.0%)			$	1,273,014

(a) Non-income producing security.

(b) All or a portion of this security was on loan at September 30, 2016.

(c) 144A security — Certain conditions for public sale may exist. Unless otherwise noted, these securities are deemed to be liquid.

(d) Security has been deemed illiquid at September 30, 2016.

(e) Security cannot be offered for public resale without first being registered under the Securities Act of 1933 and related rules ("restricted security"). Acquisition date represents the day on which an enforceable right to acquire such security is obtained and is presented along with related cost in the security description. The Portfolio has registration rights for certain restricted securities. Any costs related to such registration are borne by the issuer. The aggregate value of restricted securities (excluding 144A holdings) at September 30, 2016, amounts to approximately $103,143,000 and represents 8.1% of net assets.

(f) At September 30, 2016, the Portfolio held fair valued securities valued at approximately $103,143,000, representing 8.1% of net assets. These securities have been fair valued as determined in good faith under procedures established by and under the general supervision of the Fund's Trustees.

(g) The approximate fair value and percentage of net assets, $11,953,000 and 0.9%, respectively, represent the securities that have been fair valued under the fair valuation policy for international investments as described in Note A-1 within the Notes to the Financial Statements.

(h) At September 30, 2016, the aggregate cost for federal income tax purposes is approximately $1,032,774,000. The aggregate gross unrealized appreciation is approximately $361,871,000 and the aggregate gross unrealized depreciation is approximately $71,008,000 resulting in net unrealized appreciation of approximately $290,863,000.

CNY — Chinese Yuan Renminbi

USD — United States Dollar

Portfolio Composition*

Classification	Percentage of Total Investments
Other**		36.3	%
Internet Software & Services		17.4
Software		12.8
Capital Markets		8.2
Life Sciences Tools & Services		6.7
Hotels, Restaurants & Leisure		6.4
Health Care Equipment & Supplies		6.1
Professional Services		6.1
Total Investments		100.0	%

* Percentages indicated are based upon total investments (excluding Securities held as Collateral on Loaned Securities) as of September 30, 2016.

** Industries and/or investment types representing less than 5% of total investments.

The accompanying notes are an integral part of the financial statements.
7

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Mid Cap Growth Portfolio

Statement of Assets and Liabilities	September 30, 2016 (000)
Assets:
Investments in Securities of Unaffiliated Issuers, at Value⁽¹⁾ (Cost $901,345)	$	1,240,033
Investment in Security of Affiliated Issuer, at Value (Cost $83,604)		83,604
Total Investments in Securities, at Value (Cost $984,949)		1,323,637
Cash		27,884
Receivable for Investments Sold		25,804
Dividends Receivable		2,750
Receivable for Portfolio Shares Sold		399
Receivable from Affiliate		2
Other Assets		281
Total Assets		1,380,757
Liabilities:
Collateral on Securities Loaned, at Value		65,380
Payable for Portfolio Shares Redeemed		31,953
Payable for Investments Purchased		7,006
Payable for Advisory Fees		1,953
Payable for Sub Transfer Agency Fees — Class I		271
Payable for Sub Transfer Agency Fees — Class A		189
Payable for Sub Transfer Agency Fees — Class L		4
Due to Broker		200
Payable for Shareholder Services Fees — Class A		102
Payable for Distribution and Shareholder Services Fees — Class L		6
Payable for Administration Fees		88
Payable for Trustees' Fees and Expenses		49
Payable for Transfer Agency Fees — Class I		12
Payable for Transfer Agency Fees — Class A		20
Payable for Transfer Agency Fees — Class L		1
Payable for Transfer Agency Fees — Class IS		1
Payable for Professional Fees		24
Payable for Custodian Fees		11
Other Liabilities		473
Total Liabilities		107,743
Net Assets	$	1,273,014
Net Assets Consist of:
Paid-in-Capital	$	703,478
Accumulated Net Investment Loss		(23,543	)
Accumulated Undistributed Net Realized Gain		254,391
Unrealized Appreciation (Depreciation) on:
Investments		338,688
Net Assets	$	1,273,014

The accompanying notes are an integral part of the financial statements.
8

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Mid Cap Growth Portfolio

Statement of Assets and Liabilities (cont'd)	September 30, 2016 (000)
CLASS I:
Net Assets	$	563,397
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		17,688,977
Net Asset Value, Offering and Redemption Price Per Share	$	31.85
CLASS A:
Net Assets	$	480,488
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		16,093,179
Net Asset Value, Redemption Price Per Share	$	29.86
Maximum Sales Load		5.25	%
Maximum Sales Charge	$	1.65
Maximum Offering Price Per Share	$	31.51
CLASS L:
Net Assets	$	9,874
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		340,416
Net Asset Value, Offering and Redemption Price Per Share	$	29.01
CLASS IS:
Net Assets	$	219,255
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		6,864,234
Net Asset Value, Offering and Redemption Price Per Share	$	31.94
⁽¹⁾ Including: Securities on Loan, at Value:	$	73,901

The accompanying notes are an integral part of the financial statements.
9

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Mid Cap Growth Portfolio

Statement of Operations	Year Ended September 30, 2016 (000)
Investment Income:
Income from Securities Loaned — Net	$	11,013
Dividends from Securities of Unaffiliated Issuers		10,507
Dividends from Security of Affiliated Issuer (Note G)		230
Total Investment Income		21,750
Expenses:
Advisory Fees (Note B)		13,170
Sub Transfer Agency Fees — Class I		1,544
Sub Transfer Agency Fees — Class A		864
Sub Transfer Agency Fees — Class L		21
Administration Fees (Note C)		2,107
Shareholder Services Fees — Class A (Note D)		1,698
Distribution and Shareholder Services Fees — Class L (Note D)		80
Shareholder Reporting Fees		355
Registration Fees		190
Transfer Agency Fees — Class I (Note E)		41
Transfer Agency Fees — Class A (Note E)		68
Transfer Agency Fees — Class L (Note E)		5
Transfer Agency Fees — Class IS (Note E)		5
Custodian Fees (Note F)		105
Professional Fees		91
Trustees' Fees and Expenses		75
Pricing Fees		5
Other Expenses		92
Total Expenses		20,516
Rebate from Morgan Stanley Affiliate (Note G)		(99	)
Reimbursement of Custodian Fees (Note F)		(52	)
Net Expenses		20,365
Net Investment Income		1,385
Realized Gain:
Investments Sold		298,769
Foreign Currency Transactions		4
Net Realized Gain		298,773
Change in Unrealized Appreciation (Depreciation):
Investments		(417,181	)
Foreign Currency Translations		—	@
Net Change in Unrealized Appreciation (Depreciation)		(417,181	)
Net Realized Gain and Change in Unrealized Appreciation (Depreciation)		(118,408	)
Net Decrease in Net Assets Resulting from Operations	$	(117,023	)

@ Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
10

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Mid Cap Growth Portfolio

Statements of Changes in Net Assets	Year Ended September 30, 2016 (000)			Year Ended September 30, 2015 (000)
Increase (Decrease) in Net Assets:
Operations:
Net Investment Income (Loss)	$	1,385		$	(27,971	)
Net Realized Gain		298,773			462,448
Net Change in Unrealized Appreciation (Depreciation)		(417,181	)		(616,480	)
Net Decrease in Net Assets Resulting from Operations		(117,023	)		(182,003	)
Distributions from and/or in Excess of:
Class I:
Net Investment Income		—			(9,202	)
Net Realized Gain		(213,404	)		(622,473	)
Class A:
Net Realized Gain		(107,999	)		(246,534	)
Class L:
Net Realized Gain		(1,556	)		(2,378	)
Class IS:
Net Investment Income		—			(2,208	)
Net Realized Gain		(132,809	)		(89,011	)
Total Distributions		(455,768	)		(971,806	)
Capital Share Transactions:⁽¹⁾
Class I:
Subscribed		99,014			388,442
Distributions Reinvested		195,833			591,126
Redeemed		(1,632,976	)		(2,845,084	)
Class A:
Subscribed		46,654			96,465
Distributions Reinvested		104,817			243,008
Redeemed		(546,761	)		(908,512	)
Class L:
Subscribed		—			265
Distributions Reinvested		1,516			2,327
Redeemed		(2,529	)		(3,574	)
Class IS:
Subscribed		206,340			840,659
Distributions Reinvested		123,359			90,604
Redeemed		(1,010,792	)		(327,990	)
Net Decrease in Net Assets Resulting from Capital Share Transactions		(2,415,525	)		(1,832,264	)
Total Decrease in Net Assets		(2,988,316	)		(2,986,073	)
Net Assets:
Beginning of Period		4,261,330			7,247,403
End of Period (Including Accumulated Net Investment Loss of $(23,543) and $(32,212))	$	1,273,014		$	4,261,330
(1) Capital Share Transactions:
Class I:
Shares Subscribed		3,169			9,353
Shares Issued on Distributions Reinvested		5,943			15,709
Shares Redeemed		(51,617	)		(70,154	)
Net Decrease in Class I Shares Outstanding		(42,505	)		(45,092	)
Class A:
Shares Subscribed		1,631			2,466
Shares Issued on Distributions Reinvested		3,386			6,803
Shares Redeemed		(18,183	)		(23,545	)
Net Decrease in Class A Shares Outstanding		(13,166	)		(14,276	)
Class L:
Shares Subscribed		—			6
Shares Issued on Distributions Reinvested		50			66
Shares Redeemed		(87	)		(94	)
Net Decrease in Class L Shares Outstanding		(37	)		(22	)
Class IS:
Shares Subscribed		6,353			21,050
Shares Issued on Distributions Reinvested		3,735			2,405
Shares Redeemed		(33,413	)		(8,054	)
Net Increase (Decrease) in Class IS Shares Outstanding		(23,325	)		15,401

The accompanying notes are an integral part of the financial statements.
11

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Mid Cap Growth Portfolio

	Class I
	Year Ended September 30,
Selected Per Share Data and Ratios	2016††			2015			2014			2013			2012
Net Asset Value, Beginning of Period	$	35.96		$	44.73		$	44.24		$	35.34		$	33.65
Income (Loss) from Investment Operations:
Net Investment Income (Loss)†		0.03			(0.16	)		0.09			0.10			0.17
Net Realized and Unrealized Gain (Loss)		0.18			(2.33	)		3.04			10.10			3.35
Total from Investment Operations		0.21			(2.49	)		3.13			10.20			3.52
Distributions from and/or in Excess of:
Net Investment Income		—			(0.09	)		—			(0.12	)		—
Net Realized Gain		(4.32	)		(6.19	)		(2.64	)		(1.18	)		(1.83	)
Total Distributions		(4.32	)		(6.28	)		(2.64	)		(1.30	)		(1.83	)
Net Asset Value, End of Period	$	31.85		$	35.96		$	44.73		$	44.24		$	35.34
Total Return++		0.19	%		(6.18	)%		7.25	%		29.92	%		10.91	%
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	563,397		$	2,164,565		$	4,708,900		$	5,174,440		$	4,219,528
Ratio of Expenses to Average Net Assets		0.73	%+		0.74	%+		0.75	%+		0.70	%+^		0.71	%+
Ratio of Expenses to Average Net Assets Excluding Non Operating Expenses		N/A			N/A			N/A			0.71	%+^		N/A
Ratio of Net Investment Income (Loss) to Average Net Assets		0.09	%+		(0.39	)%+		0.19	%+		0.27	%+^		0.48	%+
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.00	%§		0.00	%§		0.00	%§		0.00	%§		0.00	%§
Portfolio Turnover Rate		23	%		27	%		45	%		52	%		26	%
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		0.74	%		N/A			N/A			N/A			N/A
Investment Income to Average Net Assets		0.08	%		N/A			N/A			N/A			N/A

†† Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class I shares. The Ratio of Expenses to Average Net Assets would have been less than 0.005% higher and the Ratio of Net Investment Income (Loss) to Average Net Assets would have been less than 0.005% lower had the custodian not reimbursed the Portfolio.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value as of the last business day of the period.

^ Effective September 16, 2013, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 0.80% for Class I shares.

§ Amount is less than 0.005%.

The accompanying notes are an integral part of the financial statements.
12

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Mid Cap Growth Portfolio

	Class A
	Year Ended September 30,
Selected Per Share Data and Ratios	2016††			2015			2014			2013			2012
Net Asset Value, Beginning of Period	$	34.06		$	42.70		$	42.46		$	34.03		$	32.55
Income (Loss) from Investment Operations:
Net Investment Income (Loss)†		(0.05	)		(0.26	)		(0.03	)		0.01			0.06
Net Realized and Unrealized Gain (Loss)		0.17			(2.19	)		2.91			9.70			3.25
Total from Investment Operations		0.12			(2.45	)		2.88			9.71			3.31
Distributions from and/or in Excess of:
Net Investment Income		—			—			—			(0.10	)		—
Net Realized Gain		(4.32	)		(6.19	)		(2.64	)		(1.18	)		(1.83	)
Total Distributions		(4.32	)		(6.19	)		(2.64	)		(1.28	)		(1.83	)
Net Asset Value, End of Period	$	29.86		$	34.06		$	42.70		$	42.46		$	34.03
Total Return++		(0.12	)%		(6.40	)%		6.95	%		29.60	%		10.62	%
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	480,488		$	996,553		$	1,859,126		$	2,171,493		$	1,832,003
Ratio of Expenses to Average Net Assets		0.99	%+		1.00	%+		1.00	%+		0.95	%+^		0.96	%+
Ratio of Expenses to Average Net Assets Excluding Non Operating Expenses		N/A			N/A			N/A			0.96	%+^		N/A
Ratio of Net Investment Income (Loss) to Average Net Assets		(0.17	)%+		(0.65	)%+		(0.07	)%+		0.02	%+^		0.17	%+
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.00	%§		0.00	%§		0.00	%§		0.00	%§		0.00	%§
Portfolio Turnover Rate		23	%		27	%		45	%		52	%		26	%
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		1.00	%		N/A			N/A			N/A			N/A
Net Investment Loss to Average Net Assets		(0.18	)%		N/A			N/A			N/A			N/A

†† Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class A shares. The Ratio of Expenses to Average Net Assets would have been less than 0.005% higher and the Ratio of Net Investment Income (Loss) to Average Net Assets would have been less than 0.005% lower had the custodian not reimbursed the Portfolio.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

^ Effective September 16, 2013, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 1.15% for Class A shares.

§ Amount is less than 0.005%.

The accompanying notes are an integral part of the financial statements.
13

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Mid Cap Growth Portfolio

	Class L
	Year Ended September 30,												Period from June 14, 2012^ to
Selected Per Share Data and Ratios	2016††			2015			2014			2013			September 30, 2012
Net Asset Value, Beginning of Period	$	33.39		$	42.20		$	42.20		$	33.97		$	32.87
Income (Loss) from Investment Operations:
Net Investment Income (Loss)†		(0.22	)		(0.46	)		(0.26	)		(0.15	)		0.05
Net Realized and Unrealized Gain (Loss)		0.16			(2.16	)		2.90			9.63			1.05
Total from Investment Operations		(0.06	)		(2.62	)		2.64			9.48			1.10
Distributions from and/or in Excess of:
Net Investment Income		—			—			—			(0.07	)		—
Net Realized Gain		(4.32	)		(6.19	)		(2.64	)		(1.18	)		—
Total Distributions		(4.32	)		(6.19	)		(2.64	)		(1.25	)		—
Net Asset Value, End of Period	$	29.01		$	33.39		$	42.20		$	42.20		$	33.97
Total Return++		(0.73	)%		(6.94	)%		6.40	%		28.92	%		3.35	%#
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	9,874		$	12,600		$	16,817		$	17,190		$	10
Ratio of Expenses to Average Net Assets		1.60	%+		1.55	%+		1.55	%+		1.46	%+^^		1.50	%+*
Ratio of Expenses to Average Net Assets Excluding Non Operating Expenses		N/A			N/A			N/A			1.46	%+^^		N/A
Ratio of Net Investment Income (Loss) to Average Net Assets		(0.76	)%+		(1.20	)%+		(0.60	)%+		(0.41	)%+^^		0.46	%+*
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.00	%§		0.00	%§		0.00	%§		0.00	%§		0.00	%§*
Portfolio Turnover Rate		23	%		27	%		45	%		52	%		26	%#
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		1.61	%		N/A			N/A			N/A			N/A
Investment Loss to Average Net Assets		(0.77	)%		N/A			N/A			N/A			N/A

†† Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class L shares. The Ratio of Expenses to Average Net Assets would have been less than 0.005% higher and the Ratio of Net Investment Income (Loss) to Average Net Assets would have been less than 0.005% lower had the custodian not reimbursed the Portfolio.

^ Commencement of Offering.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value as of the last business day of the period.

^^ Effective September 16, 2013, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 1.65% for Class L shares.

§ Amount is less than 0.005%.

# Not Annualized.

* Annualized.

The accompanying notes are an integral part of the financial statements.
14

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Mid Cap Growth Portfolio

	Class IS
	Year Ended September 30,									Period from September 13, 2013^ to
Selected Per Share Data and Ratios	2016††			2015			2014			September 30, 2013
Net Asset Value, Beginning of Period	$	36.03		$	44.80		$	44.25		$	43.74
Income (Loss) from Investment Operations:
Net Investment Income (Loss)†		0.07			(0.10	)		0.18			(0.00	)‡
Net Realized and Unrealized Gain (Loss)		0.16			(2.33	)		3.01			0.51
Total from Investment Operations		0.23			(2.43	)		3.19			0.51
Distributions from and/or in Excess of:
Net Investment Income		—			(0.15	)		—			—
Net Realized Gain		(4.32	)		(6.19	)		(2.64	)		—
Total Distributions		(4.32	)		(6.34	)		(2.64	)		—
Net Asset Value, End of Period	$	31.94		$	36.03		$	44.80		$	44.25
Total Return++		0.25	%		(6.02	)%		7.39	%		1.17	%#
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	219,255		$	1,087,612		$	662,560		$	10
Ratio of Expenses to Average Net Assets		0.61	%+		0.61	%+		0.61	%+		0.49	%+^^*
Ratio of Expenses to Average Net Assets Excluding Non Operating Expenses		N/A			N/A			N/A			0.58	%+^^*
Ratio of Net Investment Income (Loss) to Average Net Assets		0.22	%+		(0.25	)%+		0.41	%+		(0.22	)%+^^*
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.00	%§		0.00	%§		0.00	%§		0.01	%*
Portfolio Turnover Rate		23	%		27	%		45	%		52	%#
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		0.62	%		N/A			N/A			N/A
Net Investment Income to Average Net Assets		0.21	%		N/A			N/A			N/A

†† Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class IS shares. The Ratio of Expenses to Average Net Assets would have been less than 0.005% higher and the Ratio of Net Investment Income (Loss) to Average Net Assets would have been less than 0.005% lower had the custodian not reimbursed the Portfolio.

^ Commencement of Offering.

† Per share amount is based on average shares outstanding.

‡ Amount is less than $0.005 per share.

++ Calculated based on the net asset value as of the last business day of the period.

^^ Effective September 16, 2013, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 0.73% for Class IS shares.

§ Amount is less than 0.005%.

# Not Annualized.

* Annualized.

The accompanying notes are an integral part of the financial statements.
15

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements

The accompanying financial statements relate to the Mid Cap Growth Portfolio. The Portfolio seeks long-term capital growth. The Portfolio offers four classes of shares — Class I, Class A, Class L and Class IS.

The Portfolio's Class I, Class A, Class L and Class IS shares are currently closed to new investors with certain exceptions.

1. Security Valuation: (1) An equity portfolio security listed or traded on an exchange is valued at its latest reported sales price (or at the exchange official closing price if such exchange reports an official closing price), and if there were no sales on a given day and if there is no official exchange closing price for that day, the security is valued at the mean between the last reported bid and asked prices if such bid and asked prices are available on the relevant exchanges; (2) all other equity portfolio securities for which over-the-counter ("OTC") market quotations are readily available are valued at the latest reported sales price (or at the market official closing price if such market reports an official closing price), and if there was no trading in the security on a given day and if there is no official closing price from relevant markets for that day, the security is valued at the mean between the last reported bid and asked prices if such bid and asked prices are available on the relevant markets. Listed equity securities not traded on the valuation date with no reported bid and asked prices available on the exchange are valued at the mean between the current bid and asked prices obtained from one or more reputable brokers or dealers. An unlisted equity security that does not trade on the valuation date and for

which bid and asked prices from the relevant markets are unavailable is valued at the mean between the current bid and asked prices obtained from one or more reputable brokers or dealers. In cases where a security is traded on more than one exchange, the security is valued on the exchange designated as the primary market; (3) listed options are valued at the last reported sales price on the exchange on which they are listed (or at the exchange official closing price if such exchange reports an official closing price). If an official closing price or last reported sales price is unavailable, the listed option should be fair valued at the mean between their latest bid and asked price. Unlisted options and swaps are valued by an outside pricing service approved by the Fund's Board of Trustees (the "Trustees") or quotes from a broker or dealer; (4) certain portfolio securities may be valued by an outside pricing service/vendor approved by the Trustees. The pricing service/vendor may employ a pricing model that takes into account, among other things, bids, yield spreads, and/or other market data and specific security characteristics. Alternatively, if a valuation is not available from an outside pricing service/vendor, and the security trades on an exchange, the security may be valued at its latest reported sale price (or at the exchange official closing price if such exchange reports an official closing price), prior to the time when assets are valued. If there are no sales on a given day and if there is no official exchange closing price for that day, the security is valued at the mean between the last reported bid and asked prices if such bid and asked prices are available in the relevant exchanges; (5) when market quotations are not readily available, including circumstances under which Morgan Stanley Investment Management Inc. (the "Adviser") determines that the closing price, last sale price or the mean between the last reported bid and asked prices are not reflective of a security's market value, portfolio securities are valued at their fair value as determined in good faith under procedures established by and under the general supervision of the Trustees. Occasionally, developments affecting the closing prices of securities and other assets may occur between the times at which valuations of such securities are determined (that is, close of the foreign market on which the securities trade) and the close of business of the New York Stock Exchange ("NYSE"). If developments occur during such periods that are expected to materially affect the value of such securities, such valuations may be adjusted to reflect the estimated fair value of such securities as of the close of

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

the NYSE, as determined in good faith by the Trustees or by the Adviser using a pricing service and/or procedures approved by the Trustees; (6) quotations of foreign portfolio securities, other assets and liabilities and forward contracts stated in foreign currency are translated into U.S. dollar equivalents at the prevailing market rates prior to the close of the NYSE; and (7) investments in mutual funds, including the Morgan Stanley Institutional Liquidity Funds, are valued at the net asset value ("NAV") as of the close of each business day.

• Level 1 – unadjusted quoted prices in active markets for identical investments

• Level 2 – other significant observable inputs (including quoted prices for similar investments, interest rates, prepayment speeds, credit risk, etc.)

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

The following is a summary of the inputs used to value the Portfolio's investments as of September 30, 2016.

Investment Type	Level 1 Unadjusted quoted prices (000)		Level 2 Other significant observable inputs (000)		Level 3 Significant unobservable inputs (000)		Total (000)
Assets:
Common Stocks
Aerospace & Defense	$	18,666	$	—	$	—	$	18,666
Air Freight & Logistics		8,416		—		—		8,416
Automobiles		55,688		—		—		55,688
Biotechnology		12,344		—		—		12,344
Capital Markets		103,268		—		—		103,268
Communications Equipment		10,589		—		—		10,589
Consumer Finance		9,118		—		—		9,118
Food Products		36,156		—		—		36,156
Health Care Equipment & Supplies		77,896		—		—		77,896
Health Care Technology		61,614		—		—		61,614
Hotels, Restaurants & Leisure		80,695		—		—		80,695
Information Technology Services		48,833		—		—		48,833
Internet & Direct Marketing Retail		5,426		11,953		—		17,379
Internet Software & Services		146,038		—		68,563		214,601
Life Sciences Tools & Services		84,496		—		—		84,496
Multi-line Retail		10,799		—		—		10,799
Pharmaceuticals		36,080		—		—		36,080
Professional Services		76,651		—		—		76,651
Semiconductors & Semiconductor Equipment		12,267		—		—		12,267
Software		161,849		—		—		161,849
Tech Hardware, Storage & Peripherals		5,097		—		—		5,097
Textiles, Apparel & Luxury Goods		42,516		—		—		42,516
Trading Companies & Distributors		11,320		—		—		11,320
Total Common Stocks		1,115,822		11,953		68,563		1,196,338

Investment Type	Level 1 Unadjusted quoted prices (000)		Level 2 Other significant observable inputs (000)		Level 3 Significant unobservable inputs (000)		Total (000)
Convertible Preferred Stock	$	—	$	—	$	5,031	$	5,031
Preferred Stock		—		—		29,549		29,549
Call Option Purchased		—		10		—		10
Short-Term Investments
Investment Company		83,604		—		—		83,604
Repurchase Agreement		—		9,105		—		9,105
Total Short-Term Investments		83,604		9,105		—		92,709
Total Assets	$	1,199,426	$	21,068	$	103,143	$	1,323,637

Transfers between investment levels may occur as the markets fluctuate and/or the availability of data used in an investment's valuation changes. The Portfolio recognizes transfers between the levels as of the end of the period. As of September 30, 2016, the Portfolio did not have any investments transfer between investment levels. At September 30, 2016, the fair value of certain securities were adjusted due to developments which occurred between the time of the close of the foreign markets on which they trade and the close of business on the NYSE which resulted in their Level 2 classification.

Following is a reconciliation of investments in which significant unobservable inputs (Level 3) were used in determining fair value.

	Common Stocks (000)			Convertible Preferred Stocks (000)			Preferred Stocks (000)
Beginning Balance	$	165,222		$	7,132		$	252,754
Purchases		—			—			—
Sales		(60,467	)		—			(112,699	)
Amortization of discount		—			—			—
Transfers in		—			—			—
Transfers out		—			—			—
Corporate actions		—			(18,817	)		—
Change in unrealized appreciation (depreciation)		(57,847	)		16,716			(156,630	)
Realized gains (losses)		21,655			—			46,124
Ending Balance	$	68,563		$	5,031		$	29,549
Net change in unrealized appreciation (depreciation) from investments still held as of September 30, 2016	$	(29,787	)	$	(1,855	)	$	(47,438	)

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

The following table presents additional information about valuation techniques and inputs used for investments that are measured at fair value and categorized within Level 3 as of September 30, 2016. Various valuation techniques were used in the valuation of certain investments and weighted based on the level of significance.

	Fair Value at September 30, 2016 (000)		Valuation Technique	Unobservable Input	Range					Selected Value			Impact to Valuation from an increase in input
Internet & Direct Marketing Retail
Preferred Stock	$	29,549	Discounted Cash Flow	Weighted Average Cost of Capital		17.0	%	19.0	%		18.0	%	Decrease
				Perpetual Growth Rate		3.5	%	4.5	%		4.0	%	Increase
			Market Comparable Companies	Enterprise Value/Revenue		1.1	x	3.1	x		2.2	x	Increase
				Discount for Lack of Marketability		20.0	%	20.0	%		20.0	%	Decrease
Internet Software & Services
Common Stock	$	50,699	Discounted Cash Flow	Weighted Average Cost of Capital		18.0	%	20.0	%		19.0	%	Decrease
Convertible Preferred Stock	$	5,031		Perpetual Growth Rate		2.5	%	3.5	%		3.0	%	Increase
			Market Comparable Companies	Enterprise Value/Revenue		6.3	x	17.8	x		8.1	x	Increase
				Discount for Lack of Marketability		20.0	%	20.0	%		20.0	%	Decrease
Common Stock	$	17,864	Discounted Cash Flow	Weighted Average Cost of Capital		16.5	%	18.5	%		17.5	%	Decrease
				Perpetual Growth Rate		3.0	%	4.0	%		3.5	%	Increase
			Market Comparable Companies	Enterprise Value/Revenue		6.0	x	8.2	x		7.0	x	Increase
				Discount for Lack of Marketability		20.0	%	20.0	%		20.0	%	Decrease

3. Repurchase Agreements: The Portfolio may enter into repurchase agreements under which the Portfolio lends cash and takes possession of securities with an agreement that the counterparty will repurchase such securities. In connection with transactions in repurchase agreements, a bank as custodian for the Portfolio takes possession of the underlying securities which are held as collateral, with a market value at least equal to the amount of the repurchase transaction, including principal and accrued interest. To the extent that any repurchase transaction exceeds one business day, the value of the collateral is marked-to-market on a daily basis to determine that the value of the collateral does not decrease below the repurchase price plus accrued interest as earned. If such a decrease occurs, additional collateral will be requested and, when received, will be added to the account to maintain full collateralization. In the event of default on the obligation to repurchase, the Portfolio has the right to liquidate the collateral and apply the proceeds in satisfaction of the obligation. In

the event of default or bankruptcy by the counterparty to the agreement, realization of the collateral proceeds may be subject to cost and delays. The Portfolio, along with other affiliated investment companies, may utilize a joint trading account for the purpose of entering into repurchase agreements.

4. Foreign Currency Translation and Foreign Investments: The books and records of the Portfolio are maintained in U.S. dollars. Foreign currency amounts are translated into U.S. dollars as follows:

– investments, other assets and liabilities at the prevailing rate of exchange on the valuation date;

– investment transactions and investment income at the prevailing rates of exchange on the dates of such transactions.

Although the net assets of the Portfolio are presented at the foreign exchange rates and market values at the close

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

of the period, the Portfolio does not isolate that portion of the results of operations arising as a result of changes in the foreign exchange rates from the fluctuations arising from changes in the market prices of securities held at period end. Similarly, the Portfolio does not isolate the effect of changes in foreign exchange rates from the fluctuations arising from changes in the market prices of securities sold during the period. Accordingly, realized and unrealized foreign currency gains (losses) on investments in securities are included in the reported net realized and unrealized gains (losses) on investment transactions and balances. However, pursuant to U.S. federal income tax regulations, gains and losses from certain foreign currency transactions and the foreign currency portion of gains and losses realized on sales and maturities of foreign denominated debt securities are treated as ordinary income for U.S. federal income tax purposes.

subject to limitation in other countries. Foreign ownership limitations also may be imposed by the charters of individual companies to prevent, among other concerns, violations of foreign investment limitations. As a result, an additional class of shares (identified as "Foreign" in the Portfolio of Investments) may be created and offered for investment. The "local" and "foreign shares" market values may differ. In the absence of trading of the foreign shares in such markets, the Portfolio values the foreign shares at the closing exchange price of the local shares.

5. Derivatives: The Portfolio may, but is not required to, use derivative instruments for a variety of purposes, including hedging, risk management, portfolio management or to earn income. Derivatives are financial instruments whose value is based, in part, on the value of an underlying asset, interest rate, index or financial instrument. Prevailing interest rates and volatility levels, among other things, also affect the value of derivative instruments. A derivative instrument often has risks similar to its underlying asset and may have additional risks, including imperfect correlation between the value of the derivative and the underlying asset, risks of default by the counterparty to certain transactions, magnification of losses incurred due to changes in the market value of the securities, instruments, indices or interest rates to which the derivative instrument relates, risks that the transactions may not be liquid and risks arising from margin requirements. The use of derivatives involves risks that are different from, and possibly greater than, the risks associated with other portfolio investments. Derivatives may involve the use of highly specialized instruments that require investment techniques and risk analyses different from those associated with other portfolio investments. All of the Portfolio's holdings, including derivative instruments, are marked-to-market each day with the change in value reflected in unrealized appreciation (depreciation). Upon disposition, a realized gain or loss is recognized.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

may cause the Portfolio to be more volatile than if the Portfolio had not been leveraged. Although the Adviser seeks to use derivatives to further the Portfolio's investment objectives, there is no assurance that the use of derivatives will achieve this result.

Following is a description of the derivative instruments and techniques that the Portfolio used during the period and their associated risks:

Options: With respect to options, the Portfolio is subject to equity risk, interest rate risk and foreign currency exchange risk in the normal course of pursuing its investment objectives. If the Portfolio buys an option, it buys a legal contract giving it the right to buy or sell a specific amount of the underlying instrument or foreign currency, or futures contract on the underlying instrument or foreign currency, at an agreed-upon price typically in exchange for a premium paid by the Portfolio. The Portfolio may purchase and/or sell put and call options. Purchasing call options tends to increase the Portfolio's exposure to the underlying (or similar) instrument. Purchasing put options tends to decrease the Portfolio's exposure to the underlying (or similar) instrument. When entering into purchased option contracts, the Portfolio bears the risk of interest or exchange rates or securities prices moving unexpectedly, in which case, the Portfolio may not achieve the anticipated benefits of the purchased option contracts; however the risk of loss is limited to the premium paid. Purchased options are reported as part of "Total Investments in Securities" in the Statement of Assets and Liabilities. Premium paid for purchasing options which expired are treated as realized losses. If the Portfolio sells an option, it sells to another party the right to buy from or sell to the Portfolio a specific amount of the underlying instrument or foreign currency, or futures contract on the underlying instrument or foreign currency, at an agreed-upon price typically in exchange for a premium received by the Portfolio. When options are purchased OTC, the Portfolio bears the risk that the counterparty that wrote the option will be unable or unwilling to perform its obligations under the option contract. Options may also be illiquid and the Portfolio may have difficulty closing out its position. A decision as to whether, when and how to use options involves the exercise of skill and judgment and even a well-conceived option transaction may be unsuccessful because of market

behavior or unexpected events. The prices of options can be highly volatile and the use of options can lower total returns.

The following table sets forth the fair value of the Portfolio's derivative contracts by primary risk exposure as of September 30, 2016.

Asset Derivatives
Statement of Assets and
Liabilities Location

Primary Risk
Exposure

Value
(000)

Option Purchased

Investments, at Value
(Option Purchased)

Currency Risk

(a)

(a) Amounts are included in Investments in Securities in the Statement of Assets and Liabilities.

Realized Gain (Loss)
Primary Risk Exposure	Derivative Type	Value (000)
Currency Risk	Investments (Option Purchased)	$	(6,849	)(b)

(b) Amounts are included in Investments Sold in the Statement of Operations.

Change in Unrealized Appreciation (Depreciation)
Primary Risk Exposure	Derivative Type	Value (000)
Currency Risk	Investments (Options Purchased)	$	(7,249	)(c)

At September 30, 2016, the Portfolio's derivative assets and liabilities are as follows:

Gross Amounts of Assets and Liabilities Presented in the Statement of Assets and Liabilities
Derivatives	Assets(d) (000)			Liabilities (000)
Option Purchased	$	10	(a)	$	—

(a) Amounts are included in Investments in Securities in the Statement of Assets and Liabilities.

(d) Absent an event of default or early termination, OTC derivative assets and liabilities are presented gross and not offset in the Statement of Assets and Liabilities.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

The following tables present derivative financial instruments that are subject to enforceable netting arrangements as of September 30, 2016.

Gross Amounts Not Offset in the Statement of Assets and Liabilities
Counterparty	Gross Asset Derivatives Presented in Statement of Assets and Liabilities (000)		Financial Instrument (000)		Collateral Received(e) (000)			Net Amount (not less than $0) (000)
Royal Bank of Scotland	$	10	$	—	$	(10	)	$	0

(e) In some instances, the actual collateral received may be more than the amount shown here due to overcollateralization.

For the year ended September 30, 2016, the approximate average monthly amount outstanding for each derivative type is as follows:

Options Purchased:
Average monthly notional amount					723,720,000

6. Securities Lending: The Portfolio lends securities to qualified financial institutions, such as broker-dealers, to earn additional income. Any increase or decrease in the fair value of the securities loaned that might occur and any interest earned or dividends declared on those securities during the term of the loan would remain in the Portfolio. The Portfolio would receive cash or securities as collateral in an amount equal to or exceeding 100% of the current fair value of the loaned securities. The collateral is marked-to-market daily by State Street Bank and Trust Company ("State Street"), the securities lending agent, to ensure that a minimum of 100% collateral coverage is maintained.

The Portfolio has the right under the lending agreement to recover the securities from the borrower on demand.

The following table presents financial instruments that are subject to enforceable netting arrangements as of September 30, 2016.

Gross Amounts Not Offset in the Statement of Assets and Liabilities
Gross Asset Amounts Presented in Statement of Assets and Liabilities (000)			Financial Instrument (000)		Collateral Received (000)			Net Amount (not less than $0) (000)
$	73,901	(f)	$	—	$	(73,901	)(g)(h)	$	0

(f) Represents market value of loaned securities at period end.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

(g) The Portfolio received cash collateral of approximately $65,380,000, of which approximately $61,216,000 was subsequently invested in a Repurchase Agreement and Morgan Stanley Institutional Liquidity Funds as reported in the Portfolio of Investments. As of September 30, 2016, there was uninvested cash of approximately $4,164,000, which is not reflected in the Portfolio of Investments. In addition, the Portfolio received non-cash collateral of approximately $9,362,000 in the form of U.S. Government obligations, which the Portfolio cannot sell or repledge, and accordingly are not reflected in the Portfolio of Investments.

(h) The actual collateral received is greater than the amount shown here due to overcollateralization.

Remaining Contractual Maturity of the Agreements
	Overnight and Continuous (000)		<30 days (000)		Between 30 & 90 days (000)		>90 days (000)		Total (000)
Securities Lending Transactions
Common Stocks	$	65,380	$	—	$	—	$	—	$	65,380
Total Borrowings	$	65,380	$	—	$	—	$	—	$	65,380
Gross amount of recognized liabilities for securities lending transactions									$	65,380

the resale of securities vary in length and scope and are generally the result of a negotiation between the issuer and acquirer of the securities. The Portfolio would, in either case, bear market risks during that period. Restricted securities are identified in the Portfolio of Investments.

9. Dividends and Distributions to Shareholders: Dividend income and distributions to shareholders are recorded on the ex-dividend date. Dividends from net investment income, if any, are declared and paid annually. Net realized capital gains, if any, are distributed at least annually.

10. Security Transactions, Income and Expenses: Security transactions are accounted for on the trade date (date the order to buy or sell is executed). Realized gains and losses on the sale of investment securities are determined on the specific identified cost method. Dividend income and other distributions are recorded on the ex-dividend date (except for certain foreign dividends which may be recorded as soon as the Portfolio is informed of such dividends) net of applicable withholding taxes. Interest income is recognized on the accrual basis except where collection is in doubt. Discounts are accreted and premiums are amortized over the life of the respective securities. Most expenses of the Fund can be directly attributed to a particular Portfolio. Expenses which cannot be directly attributed are apportioned among the Portfolios based upon relative net assets or other appropriate methods. Income, expenses (other than class specific expenses — distribution and shareholder services, transfer agency and sub transfer agency fees) and realized and unrealized gains or losses are allocated to each class of shares based upon their relative net assets.

The Adviser has agreed to reduce its advisory fee and/or reimburse the Portfolio so that total annual portfolio operating

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

expenses, excluding certain investment related expenses, taxes, interest and other extraordinary expenses (including litigation), will not exceed 0.80% for Class I shares, 1.15% for Class A shares, 1.65% for Class L shares and 0.73% for Class IS shares. The fee waivers and/or expense reimbursements will continue for at least one year from the date of the Portfolio's prospectus or until such time as the Trustees act to discontinue all or a portion of such waivers and/or reimbursements when they deem such action is appropriate. This arrangement had no effect during the most recent reporting period.

The Fund has adopted a Distribution and Shareholder Services Plan with respect to Class L shares pursuant to Rule 12b-1 under the Act. Under the Distribution and Shareholder Services Plan, the Portfolio pays the Distributor a distribution fee, accrued daily and paid monthly, at an annual rate of 0.50% and a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Portfolio's average daily net assets attributable to Class L shares.

G. Security Transactions and Transactions with Affiliates: For the year ended September 30, 2016, purchases and sales of investment securities for the Portfolio, other than long-term U.S. Government securities and short-term investments, were approximately $603,037,000 and $3,521,057,000, respectively. There were no purchases and sales of long-term U.S. Government securities for the year ended September 30, 2016.

The Portfolio invests in the Institutional Class of the Morgan Stanley Institutional Liquidity Funds (the "Liquidity Funds"), an open-end management investment company managed by the Adviser, both directly and as a portion of the securities held as collateral on loaned securities. Advisory fees paid by the Portfolio are reduced by an amount equal to its pro-rata share of the advisory and administration fees paid by the Portfolio due to its investment in the Liquidity Funds. For the year ended September 30, 2016, advisory fees paid were reduced by approximately $99,000 relating to the Portfolio's investment in the Liquidity Funds.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

A summary of the Portfolio's transactions in shares of the Liquidity Funds during the year ended September 30, 2016 is as follows:

Value September 30, 2015 (000)				Purchases at Cost (000)				Sales (000)				Dividend Income (000)				Value September 30, 2016 (000)
$	210,142			$	2,262,235			$	2,388,773			$	230			$	83,604

During the year ended September 30, 2016, the Portfolio incurred approximately $17,000 in brokerage commissions with Morgan Stanley & Co., LLC, an affiliate of the Adviser/Administrator and Distributor, for portfolio transactions executed on behalf of the Portfolio.

and are accrued based on the value of investments denominated in such currency.

FASB ASC 740-10, "Income Taxes — Overall", sets forth a minimum threshold for financial statement recognition of the benefit of a tax position taken or expected to be taken in a tax return. Management has concluded there are no significant uncertain tax positions that would require recognition in the financial statements. If applicable, the Portfolio recognizes interest accrued related to unrecognized tax benefits in "Interest Expense" and penalties in "Other Expenses" in the Statement of Operations. The Portfolio files tax returns with the U.S. Internal Revenue Service, New York and various states. Each of the tax years in the four-year period ended September 30, 2016, remains subject to examination by taxing authorities.

2016 Distributions Paid From:				2015 Distributions Paid From:
Ordinary Income (000)		Long-Term Capital Gain (000)		Ordinary Income (000)		Long-Term Capital Gain (000)
$	—	$	455,768	$	69,051	$	902,755

Permanent differences, primarily due to differing treatments of gains (losses) related to foreign currency transactions, tax adjustments on partnership investments held and sold by the Portfolio and a net operating loss, resulted in the following reclassifications among the components of net assets at September 30, 2016:

Accumulated Net Investment Loss (000)				Accumulated Undistributed Net Realized Gain (000)				Paid-in- Capital (000)
$	7,284			$	26,992			$	(34,276	)

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

At September 30, 2016, the components of distributable earnings for the Portfolio on a tax basis were as follows:

Undistributed Ordinary Income (000)				Undistributed Long-Term Capital Gain (000)
$	—			$	302,213

Post-October Currency and Specified Ordinary Losses (000)				Post-October Capital Losses (000)
$	23,275			$	—

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Report of Independent Registered Public Accounting Firm

To the Shareholders and Board of Trustees of
Morgan Stanley Institutional Fund Trust —
Mid Cap Growth Portfolio

We have audited the accompanying statement of assets and liabilities, including the portfolio of investments, of Mid Cap Growth Portfolio (one of the portfolios constituting Morgan Stanley Institutional Fund Trust) (the "Portfolio") as of September 30, 2016, and the related statement of operations for the year then ended, the statements of changes in net assets for each of the two years in the period then ended and the financial highlights for each of the years or periods indicated therein. These financial statements and financial highlights are the responsibility of the Portfolio's management. Our responsibility is to express an opinion on these financial statements and financial highlights based on our audits.

We conducted our audits in accordance with the standards of the Public Company Accounting Oversight Board (United States). Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements and financial highlights are free of material misstatement. We were not engaged to perform an audit of the Portfolio's internal control over financial reporting. Our audits included consideration of internal control over financial reporting as a basis for designing audit procedures that are appropriate in the circumstances, but not for the purpose of expressing an opinion on the effectiveness of the Portfolio's internal control over financial reporting. Accordingly, we express no such opinion. An audit also includes examining, on a test basis, evidence supporting the amounts and disclosures in the financial statements and financial highlights, assessing the accounting principles used and significant estimates made by management, and evaluating the overall financial statement presentation. Our procedures included confirmation of securities owned as of September 30, 2016, by correspondence with the custodian and others or by other appropriate auditing procedures where replies from others were not obtained. We believe that our audits provide a reasonable basis for our opinion.

In our opinion, the financial statements and financial highlights referred to above present fairly, in all material respects, the financial position of Mid Cap Growth Portfolio (one of the portfolios constituting Morgan Stanley Institutional Fund Trust) at September 30, 2016, the results of its operations for the year then ended, the changes in its net assets for each of the two years in the period then ended and the financial highlights for each of the years or periods indicated therein, in conformity with U.S. generally accepted accounting principles.

Boston, Massachusetts
November 22, 2016

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Advisory Agreement Approval (unaudited)

Nature, Extent and Quality of Services

Performance, Fees and Expenses of the Portfolio

The Board reviewed the performance, fees and expenses of the Portfolio compared to its peers, as determined by Broadridge, and to appropriate benchmarks where applicable. The Board discussed with the Adviser the performance goals and the actual results achieved in managing the Portfolio. When considering a fund's performance, the Board and the Adviser place emphasis on trends and longer-term returns (focusing on one-year, three-year and five-year performance, as of December 31, 2015, or since inception, as applicable). When a fund underperforms its benchmark and/or its peer group average, the Board and the Adviser discuss the causes of such underperformance and, where necessary, they discuss specific changes to investment strategy or investment personnel. The Board noted that the Portfolio's performance was below its peer group average for the one-, three- and five-year periods. The Board discussed with the Adviser the level of the advisory and administration fees (together, the "management fee") for this Portfolio relative to comparable funds and/or other accounts advised by the Adviser and/or compared to its peers as determined by Broadridge. In addition to the management fee, the Board also reviewed the Portfolio's total expense ratio. The Board noted that the Portfolio's management fee and total expense ratio were lower than its peer group averages. After discussion, the Board concluded that the Portfolio's (i) performance was acceptable; and (ii) management fee and total expense ratio were competitive with its peer group averages.

Economies of Scale

The Board considered the size and growth prospects of the Portfolio and how that relates to the Portfolio's total expense ratio and particularly the Portfolio's management fee rate, which does not include breakpoints. In conjunction with its review of the Adviser's profitability, the Board discussed with the Adviser how a change in assets can affect the efficiency or effectiveness of managing the Portfolio and whether the management fee level is appropriate relative to current and projected asset levels and/or whether the management fee structure reflects economies of scale as asset levels change. The Board has determined that its review of the actual and/or potential economies of scale of the Portfolio supports its decision to approve the Management Agreement.

Profitability of the Adviser and Affiliates

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Advisory Agreement Approval (unaudited) (cont'd)

Other Benefits of the Relationship

Resources of the Adviser and Historical Relationship Between the Portfolio and the Adviser

Other Factors and Current Trends

General Conclusion

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Federal Tax Notice (unaudited)

For federal income tax purposes, the following information is furnished with respect to the distributions paid by the Portfolio during its taxable year ended September 30, 2016.

The Portfolio designated and paid approximately $455,768,000 as a long-term capital gain distribution.

In January, the Portfolio provides tax information to shareholders for the preceding calendar year.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Privacy Notice (unaudited)

MORGAN STANLEY INVESTMENT MANAGEMENT INC.
AN IMPORTANT NOTICE CONCERNING OUR U.S. PRIVACY POLICY

WE RESPECT YOUR PRIVACY

1. WHAT PERSONAL INFORMATION DO WE COLLECT ABOUT YOU?

For example:

• We may obtain information about your creditworthiness and credit history from consumer reporting agencies.

• We may collect background information from and through third-party vendors to verify representations you have made and to comply with various regulatory requirements.

2. WHEN DO WE DISCLOSE PERSONAL INFORMATION WE COLLECT ABOUT YOU?

We may disclose personal information we collect about you to other Morgan Stanley companies and to non-affiliated third parties.

a. Information We Disclose to Other Morgan Stanley Companies.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Privacy Notice (unaudited) (cont'd)

b. Information We Disclose to Non-affiliated Third Parties.

3. HOW DO WE PROTECT THE SECURITY AND CONFIDENTIALITY OF PERSONAL INFORMATION WE COLLECT ABOUT YOU?

4. HOW CAN YOU LIMIT THE SHARING OF CERTAIN TYPES OF PERSONAL INFORMATION WITH OTHER MORGAN STANLEY COMPANIES?

5. HOW CAN YOU LIMIT THE USE OF CERTAIN TYPES OF PERSONAL INFORMATION BY OTHER MORGAN STANLEY COMPANIES FOR MARKETING?

6. HOW CAN YOU SEND US AN OPT-OUT INSTRUCTION?

• Calling us at (800) 548-7786
Monday–Friday between 8a.m. and 6p.m.(EST)

• Writing to us at the following address:

Boston Financial Data Services, Inc.
c/o Privacy Coordinator
P.O. Box 219804
Kansas City, Missouri 64121

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Privacy Notice (unaudited) (cont'd)

7. WHAT IF AN AFFILIATED COMPANY BECOMES A NON-AFFILIATED THIRD PARTY?

SPECIAL NOTICE TO RESIDENTS OF VERMONT

If you wish to receive offers for investment products and services offered by or through other Morgan Stanley companies, please notify us in writing at the following address:

Boston Financial Data Services, Inc.
c/o Privacy Coordinator
P.O. Box 219804
Kansas City, Missouri 64121

SPECIAL NOTICE TO RESIDENTS OF CALIFORNIA

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited)

Independent Trustees:

Name, Age and Address of
Independent Trustee

Position(s)
Held with
Registrant

Length of Time
Served*

Principal Occupation(s)
During Past 5 Years
and Other Relevant
Professional Experience

Number of
Portfolios in
Fund Complex
Overseen by
Independent
Trustee**

Other Directorships
Held by Independent
Trustee***

Frank L. Bowman (71)
c/o Perkins Coie LLP
Counsel to the Independent Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since August 2006

Kathleen A. Dennis (63)
c/o Perkins Coie LLP
Counsel to the Independent Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since August 2006

Director of various non-profit organizations.

Nancy C. Everett (61)
c/o Perkins Coie LLP
Counsel to the Independent Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since January 2015

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Age and Address of
Independent Trustee

Position(s)
Held with
Registrant

Length of Time
Served*

Principal Occupation(s)
During Past 5 Years
and Other Relevant
Professional Experience

Number of
Portfolios in
Fund Complex
Overseen by
Independent
Trustee**

Other Directorships
Held by Independent
Trustee***

Jakki L. Haussler (59)
c/o Perkins Coie LLP
Counsel to the Independent Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since January 2015

Dr. Manuel H. Johnson (67)
c/o Johnson Smick International, Inc.
220 I Street, N.E. — Suite 200
Washington, D.C. 20002

Trustee

Since July 1991

100

Director of NVR, Inc. (home construction).

Joseph J. Kearns (74)
c/o Kearns & Associates LLC
23823 Malibu Road
S-50-440
Malibu, CA 90265

Trustee

Since August 1994

101

Director of Electro Rent Corporation (equipment leasing). Prior to December 31, 2013, Director of The Ford Family Foundation.

Michael F. Klein (57)
c/o Perkins Coie LLP
Counsel to the Independent Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since August 2006

Director of certain investment funds managed or sponsored by Aetos Capital, LLC; Director of Sanitized AG and Sanitized Marketing AG (specialty chemicals).

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Age and Address of
Independent Trustee

Position(s)
Held with
Registrant

Length of Time
Served*

Principal Occupation(s)
During Past 5 Years
and Other Relevant
Professional Experience

Number of
Portfolios in
Fund Complex
Overseen by
Independent
Trustee**

Other Directorships
Held by Independent
Trustee***

Michael E. Nugent (80)
522 Fifth Avenue
New York, NY 10036

Chair of the Board and Trustee

Chair of the Boards since July 2006 and Trustee since July 1991

100

None.

W. Allen Reed (69)
c/o Perkins Coie LLP
Counsel to the Independent Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since August 2006

Director of Legg Mason, Inc.; formerly, Director of the Auburn University Foundation (2010-2015).

Fergus Reid (84)
c/o Joe Pietryka, Inc.
85 Charles Colman Blvd.
Pawling, NY 12564

Trustee

Since June 1992

Chairman, Joe Pietryka, Inc.; Chairperson of the Governance Committee and Director or Trustee of various Morgan Stanley Funds (since June 1992).

100

Formerly, Trustee and Director of certain investment companies in the JP Morgan Fund Complex managed by JP Morgan Investment Management Inc. (1987-2012).

* This is the earliest date the Trustee began serving the Morgan Stanley Funds. Each Trustee serves an indefinite term, until his or her successor is elected.

*** This includes any directorships at public companies and registered investment companies held by the Trustee at any time during the past five years.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited) (cont'd)

Executive Officers:

Name, Age and Address of Executive Officer

Position(s) Held
with
Registrant

Length of Time
Served*

Principal Occupation(s) During Past 5 Years

John H. Gernon (53)
522 Fifth Avenue
New York, NY 10036

President and Principal Executive Officer

Since September 2013

Stefanie V. Chang Yu (49)
522 Fifth Avenue
New York, NY 10036

Chief Compliance Officer

Since December 1997

Joseph C. Benedetti (51)
522 Fifth Avenue
New York, NY 10036

Vice President

Since January 2014

Francis J. Smith (51)
522 Fifth Avenue
New York, NY 10036

Treasurer and Principal Financial Officer

Treasurer since July 2003 and Principal Financial Officer since September 2002

Executive Director of the Adviser and various entities affiliated with the Adviser; Treasurer (since July 2003) and Principal Financial Officer of various Morgan Stanley Funds (since September 2002).

Mary E. Mullin (49)
522 Fifth Avenue
New York, NY 10036

Secretary

Since June 1999

Executive Director of the Adviser; Secretary of various Morgan Stanley Funds (since June 1999).

* This is the earliest date the officer began serving the Morgan Stanley Funds. Each officer serves a one-year term, until his or her successor is elected and has qualified.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Adviser and Administrator

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

Distributor

Morgan Stanley Distribution, Inc.
522 Fifth Avenue
New York, New York 10036

Dividend Disbursing and Transfer Agent

Boston Financial Data Services, Inc.
2000 Crown Colony Drive
Quincy, Massachusetts 02169

Custodian

State Street Bank and Trust Company
One Lincoln Street
Boston, Massachusetts 02111

Legal Counsel

Dechert LLP
1095 Avenue of the Americas
New York, New York 10036

Counsel to the Independent Trustees

Perkins Coie LLP
30 Rockefeller Plaza
New York, New York 10112

Independent Registered Public Accounting Firm

Ernst & Young LLP
200 Clarendon Street
Boston, Massachusetts 02116

Reporting to Shareholders

Proxy Voting Policies and Procedures and Proxy Voting Record

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable Portfolio of Morgan Stanley Institutional Funds Trust, which describes in detail the Portfolio's investment policies, risks, fees and expenses. Please read the prospectus carefully before you invest or send money. For additional information, including information regarding the investments comprising the Portfolio, please visit our website at www.morganstanley.com/im or call toll free 1 (800) 548-7786.

(This Page has been left blank intentionally.)

Printed in U.S.A.
This Report has been prepared for shareholders and may be distributed to others only if preceded or accompanied by a current prospectus.

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

IFTMCGANN
1627711 EXP. 11.30.17

INVESTMENT MANAGEMENT

Morgan Stanley Institutional Fund Trust

Short Duration Income Portfolio

(formerly Limited Duration Portfolio)

Annual Report

September 30, 2016

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Table of Contents

Shareholders' Letter					2
Expense Example					3
Investment Overview					4
Portfolio of Investments					7
Statement of Assets and Liabilities					14
Statement of Operations					16
Statements of Changes in Net Assets					17
Financial Highlights					19
Notes to Financial Statements					24
Report of Independent Registered Public Accounting Firm					35
Investment Advisory Agreement Approval					36
Privacy Notice					38
Trustee and Officer Information					41

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Shareholders' Letter (unaudited)

Dear Shareholders,

We are pleased to provide this Annual report, in which you will learn how your investment in Short Duration Income Portfolio (the "Portfolio") performed during the latest twelve-month period.

As always, we thank you for selecting Morgan Stanley Investment Management, and look forward to working with you in the months and years ahead.

Sincerely,

John H. Gernon
President and Principal Executive Officer

October 2016

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Expense Example (unaudited)

Short Duration Income Portfolio

This example is based on an investment of $1,000 invested at the beginning of the six-month period ended September 30, 2016 and held for the entire six-month period (unless otherwise noted).

Actual Expenses

Hypothetical Example for Comparison Purposes

	Beginning Account Value 4/1/16		Actual Ending Account Value 9/30/16		Hypothetical Ending Account Value		Actual Expenses Paid During Period*		Hypothetical Expenses Paid During Period*		Net Expense Ratio During Period**
Short Duration Income Portfolio Class I	$	1,000.00	$	1,043.00	$	1,023.50	$	1.53	$	1.52		0.30	%***
Short Duration Income Portfolio Class A		1,000.00		1,040.50		1,022.40		2.65		2.63		0.52	***
Short Duration Income Portfolio Class L		1,000.00		1,039.00		1,021.00		4.08		4.04		0.80	***
Short Duration Income Portfolio Class C		1,000.00		1,036.50		1,018.50		6.62		6.56		1.30	***
Short Duration Income Portfolio Class IS		1,000.00		1,042.00		1,023.75		1.28		1.26		0.25	***

** Annualized.

*** Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Overview (unaudited)

Short Duration Income Portfolio

The Portfolio seeks above-average total return over a market cycle of three to five years.

Performance

On January 11, 2016, Morgan Stanley ("MS") Limited Duration U.S. Government Trust merged into Morgan Stanley Institutional Fund Trust ("MSIFT") Limited Duration Portfolio. In conjunction with the Reorganization, MSIFT Limited Duration Portfolio (the Portfolio) was renamed MSIFT Short Duration Income Portfolio and changed its principal investment policy. In addition, the Portfolio changed its benchmark from the Bloomberg Barclays 1-3 Year Government/Credit Index to the Bank of America/Merrill Lynch 1-Year U.S. Treasury Note Index.

For the fiscal year ended September 30, 2016, the Portfolio's Class I shares had a total return based on net asset value and reinvestment of distributions per share of 7.43%, net of fees. The Portfolio's Performance Linked benchmark, which reflects the performance of the Bloomberg Barclays 1-3 Year Government/Credit Index from the beginning of the fiscal period to January 8, 2016 and the performance of the Bank of America/Merrill Lynch 1-Year U.S. Treasury Note Index for periods thereafter through September 30, 2016, returned 0.49%.

During calendar year 2016, the Portfolio received monies related to certain nonrecurring litigation settlements. If these monies were not received, any period returns which include these settlement monies would have been lower. For example, the 2016 fiscal year total return would have been 1.46% for Class I Shares as of September 30, 2016. The returns on the other Share Classes would also have been similarly impacted. These were one-time settlements, and as a result, the impact on the net asset value and consequently the performance will not likely be repeated in the future. Please call 1-800-548-7786 for additional information.

Factors Affecting Performance

For the full 12 months ended September 30, 2016, the Bloomberg Barclays 1-3 Year Government/Credit Index posted a 1.31% return and the Bank of America/Merrill Lynch 1-Year U.S. Treasury Note Index posted a 0.54% return. The Portfolio's Performance Linked benchmark (represented by performance of the Bloomberg Barclays 1-3 Year Government/Credit Index for periods from the beginning of the fiscal year to January 8, 2016 and the Bank of America/Merrill Lynch 1-Year U.S. Treasury Note Index for periods thereafter through September 30, 2016) returned 0.49%.

• The rise in risk premia and increase in correlations across asset classes that began when China devalued its currency in the third quarter of 2015 have continued to dominate asset prices over the 12-month period. The devaluation of the Chinese currency and ensuing fall in Chinese equity prices was followed by a substantial move lower in oil prices, which continued through February 2016. Oil prices were at the epicenter of market volatility, with investor concerns about Chinese economic performance and a broader emerging markets slowdown reflected in lower commodity prices. Weaker expectations for oil demand, combined with fears of new supply coming on line, pushed oil prices down to levels not seen in a decade. Volatility in the energy market put pressure on all the major risk markets, and correlations between crude oil prices and equities, credit, inflation expectations and even government bond yields were extremely high. The market has since been calmed by a stabilization in oil prices and continued global central bank policy coordination, which has led to a recovery in risk asset prices and the start of a rise in global government bond yields, mainly at the back-end (or, longer maturity range) of yield curves.

• Global government bond yields fell during the period. Yields on the 10-year U.S. Treasury fell to as low as 1.36% and returned 5.6% over the period.^(iv)

Management Strategies

• Throughout the period, the Portfolio was positioned with an overweight to investment grade credit, particularly in financials, as we believe valuations relative to fundamentals have been attractive. Additionally, the yield offered by the investment-grade credit sector has been attractive, in our view. This positioning added to relative performance.

• The Portfolio has also been positioned with an allocation to short-maturity, high-quality asset-backed securities. This position is primarily in credit card, auto, and business and construction equipment securities. The position had a small positive effect on relative performance during the period.

• Until the principal investment strategy changed in January 2016, the Portfolio had allocations to riskier segments of the market, such as BB-rated high-yield corporates and non-agency mortgage

(iv) Source: Bloomberg L.P. Data as of September 30, 2016

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Overview (unaudited) (cont'd)

Short Duration Income Portfolio

securities, and these positions detracted from relative performance early in the period as sectors with credit risk underperformed due to declines in energy prices and concerns over a global recession. However, we note that energy prices have since recovered and concerns over a global recession have since been removed.

• In conjunction with the January 11, 2016 Reorganization and renaming of the Portfolio (as described in the Performance discussion), the Portfolio changed its principal investment policy such that under normal circumstances, it seeks to achieve its investment objective of above-average total return over a market cycle of three to five years by investing substantially all of its assets in investment grade fixed income securities denominated in U.S. dollars, while seeking to maintain an overall duration of its portfolio of approximately one year or less. In addition, the Portfolio changed its benchmark from the from the Bloomberg Barclays 1-3 Year Government/Credit Index to the Bank of America/Merrill Lynch 1-Year U.S. Treasury Note Index.

* Minimum Investment

In accordance with SEC regulations, the Portfolio's performance shown assumes that all recurring fees (including management fees) were deducted and all dividends and distributions were reinvested. The performance of Class A, Class L, Class C and Class IS shares will vary from the performance of Class I shares based upon their different inception dates and will be negatively impacted by additional fees assessed to those classes (where applicable).

Performance Compared to the Short Duration Income Blend Index⁽¹⁾, the Bank of America/Merrill Lynch 1-Year U.S. Treasury Note Index⁽²⁾, the Bloomberg Barclays 1-3 Year U.S. Government/Credit Index⁽³⁾ and the Lipper Short Investment Grade Debt Funds Index⁽⁴⁾

	Period Ended September 30, 2016 Total Returns⁽⁵⁾
				Average Annual
	One Year			Five Years			Ten Years			Since Inception⁽¹¹⁾
Portfolio — Class I Shares w/o sales charges⁽⁶⁾		7.43	%		2.77	%		0.46	%		3.16	%
Portfolio — Class A Shares w/o sales charges⁽⁷⁾		7.15			2.48			—			–0.21
Portfolio — Class L Shares w/o sales charges⁽⁸⁾		6.79			—			—			2.01
Portfolio — Class C Shares w/o sales charges⁽⁹⁾		6.24			—			—			3.68
Portfolio — Class C Shares with maximum 1.00% deferred sales charges⁽⁹⁾		5.24			—			—			3.68
Portfolio — Class IS Shares w/o sales charges⁽¹⁰⁾		—			—			—			7.42
Short Duration Income Blend Index		0.49			0.89			2.50			4.15
Bank of America/Merrill Lynch 1-Year U.S. Treasury Note Index		0.54			0.33			1.53			2.86
Bloomberg Barclays 1-3 year U.S. Government/Credit Index		1.31			1.05			2.59			4.18
Lipper Short Investment Grade Debt Funds Index		2.06			1.73			2.55			3.95

Performance data quoted represents past performance, which is no guarantee of future results, and current performance may be lower or higher than the figures shown. Performance assumes that all dividends and distributions, if any, were reinvested. Returns for period less than one year are not annualized. For the most recent month-end performance figures, please visit www.morganstanley.com/im. Investment returns and principal value will fluctuate so that Portfolio shares, when redeemed, may be worth more or less than their original cost. Total returns do not reflect the deduction of taxes that a shareholder would pay on Portfolio distributions or the redemption of Portfolio shares. Performance of share classes will vary due to differences in sales charge and expenses.

⁽¹⁾ The Short Duration Income Blend Index is a performance linked benchmark of the old and new benchmark of the Portfolio, the old represented by Bloomberg Barclays 1-3 Year U.S. Government/Credit Index from the Portfolio's inception to January 8, 2016, and the new represented by Bank of America/Merrill Lynch 1-Year U.S. Treasury Note Index for periods thereafter. The Index is unmanaged and its returns do not include any sales charges or fees. Such costs would lower performance. It is not possible to invest directly in an index.

⁽²⁾ The Bank of America/Merrill Lynch 1-year U.S. Treasury note Index tracks one-year U.S. government securities. The Index is unmanaged and its returns do not include any sales charges or fees. Such costs would lower performance. It is not possible to invest directly in an index. The Portfolio's primary benchmark was changed to the Bank of America/Merrill Lynch 1-Year U.S. Treasury Note Index to more accurately reflect the Portfolio's new investible universe following the Reorganization.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Overview (unaudited) (cont'd)

Short Duration Income Portfolio

⁽³⁾ The Bloomberg Barclays 1-3 Year U.S. Government/Credit Index tracks the securities in the 1-3 year maturity range of the Bloomberg Barclays U.S. Government/Credit Index which tracks investment-grade (BBB-/Baa3) or higher publicly traded fixed rate U.S. government, U.S. agency, and corporate issues. The Index is unmanaged and its returns do not include any sales charges or fees. Such costs would lower performance. It is not possible to invest directly in an index.

⁽⁴⁾ The Lipper Short Investment Grade Debt Funds Index is an equally weighted performance index of the largest qualifying funds (based on net assets) in the Lipper Short Investment Grade Debt Funds classification. The Index, which is adjusted for capital gains distributions and income dividends, is unmanaged and should not be considered an investment. There are currently 30 funds represented in this Index. As of the date of this report, the Portfolio was in the Lipper Short Investment Grade Debt Funds classification.

⁽⁵⁾ Total returns for the Portfolio reflect expenses waived and/or reimbursed, if applicable, by the Adviser. Without such waivers and/or reimbursements, total returns would have been lower.

⁽⁶⁾ Commenced operations on March 31, 1992.

⁽⁷⁾ Commenced operations on September 28, 2007.

⁽⁸⁾ Commenced operations on April 27, 2012.

⁽⁹⁾ Commenced operations on April 30, 2015.

⁽¹⁰⁾ Commenced operations on January 11, 2016.

⁽¹¹⁾ For comparative purposes, average annual since inception returns listed for the Indexes refer to the inception date of Class I of the Portfolio, not the inception of the Indexes.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments

	Face Amount (000)		Value (000)
Fixed Income Securities (93.1%)
Agency Adjustable Rate Mortgages (4.3%)
Federal Home Loan Mortgage Corporation,
Conventional Pools:
2.69%, 6/1/38	$	495	$	524
2.76%, 1/1/36 - 7/1/38		2,062		2,186
2.81%, 5/1/40		559		594
3.12%, 6/1/37		240		254
Federal National Mortgage Association,
Conventional Pools:
2.36%, 9/1/37		752		773
2.80%, 9/1/38		555		579
2.82%, 9/1/38 - 5/1/39		1,139		1,202
2.95%, 10/1/35		691		728
3.04%, 9/1/39		232		246
				7,086
Agency Bond — Consumer Discretionary (U.S. Government Guaranteed) (0.4%)
Safina Ltd.
2.00%, 12/30/23		621		627
Agency Fixed Rate Mortgages (4.6%)
Federal Home Loan Mortgage Corporation,
Gold Pools:
4.50%, 12/1/24		622		669
6.50%, 9/1/19 - 4/1/24		3		3
7.50%, 11/1/19 - 5/1/35		39		50
8.00%, 8/1/32		23		28
8.50%, 8/1/31		24		30
Federal National Mortgage Association,
Conventional Pools:
4.50%, 6/1/24 - 1/1/44		2,522		2,750
5.00%, 12/1/23 - 11/1/44		1,776		1,952
6.00%, 2/1/37 - 9/1/37		437		500
6.50%, 2/1/28 - 10/1/32		279		324
7.00%, 7/1/29 - 3/1/37		373		445
7.50%, 8/1/37		53		64
8.00%, 4/1/33		98		122
8.50%, 10/1/32		42		54
Government National Mortgage Association,
Various Pools:
6.00%, 11/15/38		193		221
7.50%, 11/15/32		273		321
8.50%, 7/15/30		110		125
9.00%, 11/15/16		1		1
				7,659
Asset-Backed Securities (10.0%)
Ally Auto Receivables Trust
1.47%, 4/15/20		650		653
CAM Mortgage LLC
3.50%, 7/15/64 (a)		66		66

	Face Amount (000)		Value (000)
Capital One Multi-Asset Execution Trust,
1.33%, 6/15/22	$	1,250	$	1,249
1.45%, 8/16/21		474		477
Chase Issuance Trust
1.06%, 9/16/19		725		725
Citibank Credit Card Issuance Trust
2.88%, 1/23/23		450		477
Colony American Homes
1.68%, 5/17/31 (a)(b)		402		402
Ford Credit Auto Owner Trust
2.26%, 11/15/25 (a)		1,165		1,188
Green Tree Agency Advance Funding Trust I,
2.38%, 10/15/48 (a)		600		600
3.09%, 10/15/48 (a)		227		227
Honda Auto Receivables Owner Trust
1.01%, 10/18/18		550		550
Hyundai Auto Lease Securitization Trust,
0.00%, 3/15/19 (a)		825		825
1.07%, 7/16/18 (a)(b)		600		602
Invitation Homes Trust,
1.68%, 12/17/30 (a)(b)		584		584
1.88%, 6/17/32 (a)(b)		392		394
3.28%, 8/17/32 (a)(b)		666		674
Nationstar HECM Loan Trust,
2.24%, 6/25/26 (a)		399		399
2.88%, 11/25/25 (a)		192		193
2.98%, 2/25/26 (a)		332		332
Nissan Auto Receivables Owner Trust
1.07%, 5/15/19		620		620
North Carolina State Education Assistance Authority
1.51%, 7/25/25 (b)		484		481
Panhandle-Plains Higher Education Authority, Inc.
1.60%, 7/1/24 (b)		137		136
PRPM LLC
4.00%, 9/27/21 (a)		350		351
RMAT LLC
4.83%, 6/25/35 (a)		344		339
SBA Small Business Investment Cos.
2.25%, 9/10/22		578		586
SPS Servicer Advance Receivables Trust
2.92%, 7/15/47 (a)		350		351
Sunset Mortgage Loan Co., LLC
3.72%, 11/16/44 (a)		98		98
Vericrest Opportunity Loan Trust
4.25%, 3/26/46 (a)		396		402
Verizon Owner Trust
1.42%, 1/20/21 (a)		500		502
Volkswagen Credit Auto Master Trust
1.40%, 7/22/19 (a)		398		398
VOLT NPL X LLC
4.75%, 10/26/54 (a)		282		277

The accompanying notes are an integral part of the financial statements.
7

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

	Face Amount (000)		Value (000)
Asset-Backed Securities (cont'd)
VOLT XIX LLC,
3.88%, 4/25/55 (a)	$	285	$	286
5.00%, 4/25/55 (a)		200		197
VOLT XXII LLC
4.25%, 2/25/55 (a)		199		194
VOLT XXX LLC
4.75%, 10/25/57 (a)		200		195
VOLT XXXI LLC
4.50%, 2/25/55 (a)		200		195
VOLT XXXIII LLC
4.25%, 3/25/55 (a)		347		337
				16,562
Collateralized Mortgage Obligations — Agency Collateral Series (4.3%)
Federal Home Loan Mortgage Corporation,
1.44%, 1/25/19		360		361
1.56%, 10/25/18		158		158
1.62%, 9/25/18		382		384
1.66%, 11/25/16		113		112
1.78%, 10/25/20		447		451
1.88%, 5/25/19		843		855
2.06%, 10/25/20		534		541
2.09%, 3/25/19		265		270
2.26%, 10/25/20		280		284
2.30%, 9/25/18		320		326
2.32%, 10/25/18		285		291
3.03%, 10/25/20 (b)		483		512
REMIC
7.50%, 9/15/29		748		869
Federal National Mortgage Association,
0.73%, 6/25/18 (b)		216		216
1.55%, 4/25/18		250		251
1.63%, 2/25/18		273		274
2.17%, 9/25/19 (b)		587		599
Government National Mortgage Association,
IO
5.00%, 11/20/38		741		46
5.70%, 3/20/43 (b)		757		115
5.97%, 8/16/39 - 5/20/40(b)		1,696		237
6.07%, 1/16/40 (b)		535		88
				7,240
Commercial Mortgage-Backed Securities (1.1%)
BLCP Hotel Trust
1.47%, 8/15/29 (a)(b)		581		579
CDGJ Commercial Mortgage Trust
1.92%, 12/15/27 (a)(b)		506		507
Citigroup Commercial Mortgage Trust
2.11%, 1/12/30 (a)		162		163
Hilton USA Trust
1.52%, 11/5/30 (a)(b)		154		154
Hudsons Bay Simon JV Trust
2.10%, 8/5/34 (a)(b)		185		185

	Face Amount (000)		Value (000)
JP Morgan Chase Commercial Mortgage Securities Trust
1.50%, 7/15/31 (a)(b)	$	177	$	177
				1,765
Corporate Bonds (64.4%)
Finance (28.2%)
ABN Amro Bank N.V.
2.50%, 10/30/18 (a)		630		642
American Express Credit Corp.,
Series G
1.80%, 7/31/18		425		428
2.25%, 8/15/19		675		689
Bank of America Corp.,
MTN
2.63%, 10/19/20		780		797
Bank of Montreal,
MTN
1.50%, 7/18/19		375		374
Bank of New York Mellon Corp. (The),
MTN
2.45%, 11/27/20		525		539
Bank of Nova Scotia (The),
1.70%, 6/11/18		550		553
1.95%, 1/15/19		725		733
BB&T Corp.,
MTN
2.25%, 2/1/19		580		591
Berkshire Hathaway Finance Corp.
1.70%, 3/15/19		500		505
BNP Paribas SA,
MTN
2.70%, 8/20/18		1,560		1,590
BNZ International Funding Ltd.
2.35%, 3/4/19 (a)		650		661
BPCE SA,
MTN
2.25%, 1/27/20		600		610
Capital One Financial Corp.
2.45%, 4/24/19		1,005		1,028
Citigroup, Inc.,
2.05%, 12/7/18 - 6/7/19		1,575		1,588
Commonwealth Bank of Australia,
1.38%, 9/6/18 (a)		900		899
2.50%, 9/20/18		600		612
Compass Bank
1.85%, 9/29/17		600		599
Credit Agricole SA
2.13%, 4/17/18 (a)		775		781
Credit Suisse AG,
Series G
2.30%, 5/28/19		650		658
Danske Bank A/S
1.65%, 9/6/19 (a)		825		824

The accompanying notes are an integral part of the financial statements.
8

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

	Face Amount (000)		Value (000)
Finance (cont'd)
DBS Group Holdings Ltd.
2.25%, 7/16/19 (a)	$	650	$	662
Discover Bank
2.00%, 2/21/18		665		667
DNB Bank ASA
3.20%, 4/3/17 (a)		610		616
ERP Operating LP
2.38%, 7/1/19		550		562
Goldman Sachs Group, Inc. (The),
2.38%, 1/22/18		880		890
2.63%, 1/31/19		790		807
HSBC USA, Inc.,
1.63%, 1/16/18		725		726
2.25%, 6/23/19		659		666
ING Bank N.V.
2.05%, 8/17/18 (a)		1,075		1,083
Intesa Sanpaolo SpA
3.88%, 1/16/18		355		362
Jackson National Life Global Funding
1.88%, 10/15/18 (a)		275		278
JPMorgan Chase & Co.,
1.85%, 3/22/19		1,170		1,177
2.20%, 10/22/19		325		330
KeyBank NA
1.60%, 8/22/19		300		300
LeasePlan Corp. N.V.
2.88%, 1/22/19 (a)		500		505
Macquarie Bank Ltd.,
2.35%, 1/15/19 (a)		725		733
2.60%, 6/24/19 (a)		605		616
Manufacturers & Traders Trust Co.
2.10%, 2/6/20		560		565
Metropolitan Life Global Funding I,
1.35%, 9/14/18 (a)		1,120		1,120
2.00%, 4/14/20 (a)		550		556
Mizuho Bank Ltd.
1.85%, 3/21/18 (a)		645		647
National Australia Bank Ltd.,
1.25%, 3/17/17 (a)		400		400
1.38%, 7/12/19		1,220		1,212
New York Life Global Funding
1.55%, 11/2/18 (a)		375		377
Nordea Bank AB,
1.63%, 9/30/19 (a)		900		898
1.88%, 9/17/18 (a)		800		806
PNC Bank NA
1.95%, 3/4/19		875		887
Principal Financial Group, Inc.
1.85%, 11/15/17		725		729
Protective Life Global Funding,
1.72%, 4/15/19 (a)		700		702
2.70%, 11/25/20 (a)		525		540

	Face Amount (000)		Value (000)
QBE Insurance Group Ltd.
2.40%, 5/1/18 (a)	$	200	$	201
Royal Bank of Canada,
Series G
1.80%, 7/30/18		1,300		1,309
Santander Holdings USA, Inc.
2.70%, 5/24/19		675		684
Santander UK Group Holdings PLC
2.88%, 10/16/20		200		202
Skandinaviska Enskilda Banken AB
1.75%, 3/19/18 (a)		380		382
Standard Chartered PLC
1.50%, 9/8/17 (a)		900		898
Sumitomo Mitsui Banking Corp.
2.45%, 1/10/19		630		641
Suncorp-Metway Ltd.
2.10%, 5/3/19 (a)		275		278
Swedbank AB
1.75%, 3/12/18 (a)		305		307
Synchrony Financial
3.00%, 8/15/19		800		819
Toronto-Dominion Bank (The),
MTN
1.95%, 1/22/19		1,450		1,467
UBS AG,
MTN
2.38%, 8/14/19		925		944
UnitedHealth Group, Inc.
2.70%, 7/15/20		500		520
WEA Finance LLC/Westfield UK & Europe Finance PLC
2.70%, 9/17/19 (a)		600		616
Wells Fargo & Co.
2.15%, 1/15/19		360		365
Westpac Banking Corp.,
1.65%, 5/13/19		625		628
1.95%, 11/23/18		375		378
				46,759
Industrials (34.0%)
AbbVie, Inc.
2.50%, 5/14/20		575		587
Actavis Funding SCS
3.00%, 3/12/20		835		863
Altera Corp.
2.50%, 11/15/18		300		308
Amazon.com, Inc.
2.60%, 12/5/19		525		545
American Honda Finance Corp.,
MTN
1.20%, 7/12/19		530		527
2.45%, 9/24/20		550		566
Amgen, Inc.
2.20%, 5/22/19		790		805

The accompanying notes are an integral part of the financial statements.
9

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

	Face Amount (000)		Value (000)
Industrials (cont'd)
Anheuser-Busch InBev Finance, Inc.
1.90%, 2/1/19	$	775	$	783
AstraZeneca PLC
1.75%, 11/16/18		1,495		1,507
AT&T, Inc.
2.45%, 6/30/20		1,225		1,249
AutoZone, Inc.
1.63%, 4/21/19		740		743
Baidu, Inc.
3.25%, 8/6/18		225		231
BAT International Finance PLC
2.75%, 6/15/20 (a)		450		466
Baxalta, Inc.
2.88%, 6/23/20		550		564
Bayer US Finance LLC
2.38%, 10/8/19 (a)		600		609
Becton Dickinson and Co.,
1.80%, 12/15/17		815		819
2.68%, 12/15/19		300		310
Biogen, Inc.
2.90%, 9/15/20		525		546
BMW US Capital LLC
1.50%, 4/11/19 (a)		700		701
Boston Scientific Corp.
2.65%, 10/1/18		570		583
Caterpillar Financial Services Corp.,
MTN
1.35%, 5/18/19		790		790
1.80%, 11/13/18		300		303
CBS Corp.
2.30%, 8/15/19		625		634
Celgene Corp.,
2.13%, 8/15/18		755		763
2.88%, 8/15/20		525		544
Chevron Corp.
1.79%, 11/16/18		300		303
Comcast Corp.
5.70%, 5/15/18		1,485		1,591
CVS Health Corp.
1.90%, 7/20/18		550		556
Daimler Finance North America LLC,
1.50%, 7/5/19 (a)		500		497
2.38%, 8/1/18 (a)		750		761
Deutsche Telekom International Finance BV
6.00%, 7/8/19		650		728
Dominion Gas Holdings LLC
2.50%, 12/15/19		825		848
EMD Finance LLC
2.40%, 3/19/20 (a)		575		585
Enbridge, Inc.
1.29%, 6/2/17 (b)		175		175

	Face Amount (000)		Value (000)
Energy Transfer Partners LP
2.50%, 6/15/18	$	575	$	579
Enterprise Products Operating LLC
2.55%, 10/15/19		325		331
Experian Finance PLC
2.38%, 6/15/17 (a)		600		603
Exxon Mobil Corp.
1.71%, 3/1/19		775		784
Ford Motor Credit Co., LLC
5.00%, 5/15/18		825		866
General Motors Financial Co., Inc.
3.15%, 1/15/20		600		612
Gilead Sciences, Inc.
2.55%, 9/1/20		500		517
Goldcorp, Inc.
2.13%, 3/15/18		520		522
Home Depot, Inc.
2.25%, 9/10/18		795		813
Hutchison Whampoa International 14 Ltd.
1.63%, 10/31/17 (a)		240		240
Hyundai Capital America,
2.00%, 3/19/18 (a)		525		528
2.50%, 3/18/19 (a)		775		788
2.60%, 3/19/20 (a)		325		332
Ingersoll-Rand Global Holding Co., Ltd.
2.88%, 1/15/19		335		344
Intel Corp.
2.45%, 7/29/20		550		569
JM Smucker Co. (The)
2.50%, 3/15/20		225		231
John Deere Capital Corp.,
MTN
1.95%, 1/8/19		1,590		1,617
Kinder Morgan, Inc.
3.05%, 12/1/19		650		665
Kroger Co. (The)
2.00%, 1/15/19		750		760
L-3 Communications Corp.
1.50%, 5/28/17		275		275
Lockheed Martin Corp.,
1.85%, 11/23/18		555		562
2.50%, 11/23/20		225		232
LVMH Moet Hennessy Louis Vuitton SE
1.63%, 6/29/17 (a)		525		526
Marathon Petroleum Corp.
2.70%, 12/14/18		725		741
McDonald's Corp.,
MTN
2.20%, 5/26/20		550		561
McKesson Corp.
2.28%, 3/15/19		790		804
Mead Johnson Nutrition Co.
3.00%, 11/15/20		175		182

The accompanying notes are an integral part of the financial statements.
10

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

	Face Amount (000)		Value (000)
Industrials (cont'd)
Medtronic, Inc.
2.50%, 3/15/20	$	550	$	569
Microsoft Corp.
1.10%, 8/8/19		425		424
Molson Coors Brewing Co.
1.45%, 7/15/19		775		773
Nissan Motor Acceptance Corp.,
2.00%, 3/8/19 (a)		575		580
2.65%, 9/26/18 (a)		720		735
Orange SA
2.75%, 2/6/19		625		643
Reynolds American, Inc.
2.30%, 6/12/18		525		533
Ryder System, Inc.,
MTN
2.65%, 3/2/20		125		128
5.85%, 11/1/16		475		477
Scripps Networks Interactive, Inc.
2.75%, 11/15/19		575		591
Shell International Finance BV
1.38%, 9/12/19		700		698
Siemens Financieringsmaatschappij N.V.,
1.30%, 9/13/19 (a)		900		896
2.15%, 5/27/20 (a)		550		560
Southwest Airlines Co.
2.75%, 11/6/19		600		620
Teva Pharmaceutical Finance Netherlands III BV
1.40%, 7/20/18		810		808
Thomson Reuters Corp.,
1.30%, 2/23/17		325		325
1.65%, 9/29/17		150		150
Time Warner Cable, Inc.
6.75%, 7/1/18		400		435
Toyota Motor Credit Corp.,
MTN
1.40%, 5/20/19		625		626
1.70%, 2/19/19		725		731
TSMC Global Ltd.
1.63%, 4/3/18 (a)		800		802
Tyson Foods, Inc.
2.65%, 8/15/19		600		616
Union Pacific Corp.
2.25%, 6/19/20		550		564
Verizon Communications, Inc.
2.55%, 6/17/19		1,250		1,287
Viacom, Inc.
2.50%, 9/1/18		625		632
Visa, Inc.
2.20%, 12/14/20		500		513
Vodafone Group PLC
1.50%, 2/19/18		750		750

	Face Amount (000)		Value (000)
Volkswagen Group of America Finance LLC
2.40%, 5/22/20 (a)	$	550	$	554
Walgreens Boots Alliance, Inc.
1.75%, 5/30/18		790		795
Wm Wrigley Jr. Co.
1.40%, 10/21/16 (a)		600		600
				56,389
Utilities (2.2%)
Dominion Resources, Inc.,
Series B
1.60%, 8/15/19		225		225
DTE Energy Co.
1.50%, 10/1/19 (c)		425		425
Engie SA
1.63%, 10/10/17 (a)		650		651
Eversource Energy
1.45%, 5/1/18		525		526
Origin Energy Finance Ltd.
3.50%, 10/9/18 (a)		200		204
Sempra Energy
2.40%, 3/15/20		600		612
Southern Co. (The)
2.15%, 9/1/19		725		734
Xcel Energy, Inc.
1.20%, 6/1/17		275		275
				3,652
				106,800
Mortgages — Other (2.2%)
CHL Mortgage Pass-Through Trust
5.50%, 5/25/34		239		245
Fannie Mae Connecticut Avenue Securities,
1.68%, 5/25/25 (b)		110		110
1.98%, 1/25/29 (b)		297		299
2.73%, 10/25/28 (b)		388		393
FDIC Guaranteed Notes Trust
1.07%, 2/25/48 (a)(b)		1		1
Freddie Mac Structured Agency Credit Risk Debt Notes,
1.43%, 10/25/27 (b)		191		192
1.53%, 2/25/24 (b)		89		89
1.63%, 12/25/28 (b)		245		245
1.78%, 10/25/28 (b)		240		240
1.98%, 7/25/28 (b)		472		474
2.28%, 9/25/28 (b)		334		336
New Residential Mortgage Loan Trust,
3.75%, 5/28/52 - 8/25/55 (a)(b)		627		658
Sequoia Mortgage Trust
1.15%, 8/20/34 (b)		462		437
				3,719

The accompanying notes are an integral part of the financial statements.
11

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

	Face Amount (000)		Value (000)
Sovereign (0.4%)
Korea Development Bank (The)
1.50%, 1/22/18	$	690	$	691
U.S. Agency Security (1.4%)
Private Export Funding Corp.
1.45%, 8/15/19		2,300		2,320
Total Fixed Income Securities (Cost $152,844)				154,469
	Shares
Short-Term Investments (7.3%)
Investment Company (3.6%)
Morgan Stanley Institutional Liquidity Funds — Government Portfolio — Institutional Class (See Note G) (Cost $5,928)		5,928,392		5,928
	Face Amount (000)
U.S. Treasury Security (0.8%)
U.S. Treasury Bill
0.41%, 3/23/17 (d)(e) (Cost $1,348)	$	1,350		1,347
Certificates of Deposit (2.5%)
International Banks (2.5%)
Bank of Montreal
1.23%, 5/3/17		450		450
Credit Suisse AG
1.65%, 9/12/17		760		761
Prudential PLC
1.08%, 4/21/17		1,500		1,491
Skandinaviska Enskilda Banken AB
1.26%, 5/26/17		1,520		1,521
				4,223

	Face Amount (000)		Value (000)
Commercial Paper (0.4%)
International Bank (0.4%)
Credit Agricole SA
1.25%, 2/9/17 (f)	$	700	$	697
Total Short-Term Investments (Cost $12,194)				12,195
Total Investments (100.4%) (Cost $165,038) (g)(h)				166,664
Liabilities in Excess of Other Assets (–0.4%)				(731	)
Net Assets (100.0%)			$	165,933

(a) 144A security — Certain conditions for public sale may exist. Unless otherwise noted, these securities are deemed to be liquid.

(b) Variable/Floating Rate Security — Interest rate changes on these instruments are based on changes in a designated base rate. The rates shown are those in effect on September 30, 2016.

(d) Rate shown is the yield to maturity at September 30, 2016.

(e) All or a portion of the security was pledged to cover margin requirements for futures contracts.

(f) The rates shown are the effective yields at the date of purchase.

(g) Securities are available for collateral in connection with open futures contracts.

(h) At September 30, 2016, the aggregate cost for federal income tax purposes is approximately $165,040,000. The aggregate gross unrealized appreciation is approximately $1,799,000 and the aggregate gross unrealized depreciation is approximately $175,000 resulting in net unrealized appreciation of approximately $1,624,000.

FDIC Federal Deposit Insurance Corporation.

IO Interest Only.

MTN Medium Term Note.

REMIC Real Estate Mortgage Investment Conduit.

Futures Contracts:

The Portfolio had the following futures contracts open at September 30, 2016:

	Number of Contracts		Value (000)			Expiration Date	Unrealized Appreciation (Depreciation) (000)
Short:
U.S. Treasury 5 yr. Note		266	$	(32,323	)	Dec-16	$	(3	)
U.S. Treasury 2 yr. Note		80		(17,477	)	Dec-16		(—	@)
U.S. Treasury 10 yr. Ultra Long Bond		4		(577	)	Dec-16		—	@
							$	(3	)

The accompanying notes are an integral part of the financial statements.
12

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Portfolio Composition

Classification	Percentage of Total Investments
Industrials		33.8	%
Finance		28.1
Other*		20.9
Asset-Backed Securities		9.9
Short-Term Investments		7.3
Total Investments		100.0	%**

* Industries and/or investment types representing less than 5% of total investments.

** Does not include open short futures contracts with an underlying face amount of approximately $50,377,000 with total unrealized depreciation of approximately $3,000.

The accompanying notes are an integral part of the financial statements.
13

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Short Duration Income Portfolio

Statement of Assets and Liabilities	September 30, 2016 (000)
Assets:
Investments in Securities of Unaffiliated Issuers, at Value (Cost $159,110)	$	160,736
Investment in Security of Affiliated Issuer, at Value (Cost $5,928)		5,928
Total Investments in Securities, at Value (Cost $165,038)		166,664
Cash		23
Receivable for Investments Sold		4,809
Interest Receivable		765
Receivable for Portfolio Shares Sold		267
Receivable for Variation Margin on Futures Contracts		66
Receivable from Affiliate		1
Other Assets		48
Total Assets		172,643
Liabilities:
Payable for Investments Purchased		6,223
Payable for Portfolio Shares Redeemed		225
Payable for Reorganization Expense		50
Payable for Advisory Fees		46
Payable for Professional Fees		32
Payable for Sub Transfer Agency Fees — Class I		7
Payable for Sub Transfer Agency Fees — Class A		6
Payable for Sub Transfer Agency Fees — Class L		—	@
Payable for Sub Transfer Agency Fees — Class C		—	@
Payable for Shareholder Services Fees — Class A		12
Payable for Distribution and Shareholder Services Fees — Class L		—	@
Payable for Distribution and Shareholder Services Fees — Class C		—	@
Payable for Administration Fees		10
Payable for Trustees' Fees and Expenses		7
Payable for Custodian Fees		4
Payable for Transfer Agency Fees — Class I		1
Payable for Transfer Agency Fees — Class A		2
Payable for Transfer Agency Fees — Class L		—	@
Payable for Transfer Agency Fees — Class C		1
Payable for Transfer Agency Fees — Class IS		—	@
Other Liabilities		84
Total Liabilities		6,710
Net Assets	$	165,933
Net Assets Consist of:
Paid-in-Capital	$	404,250
Accumulated Undistributed Net Investment Income		474
Accumulated Net Realized Loss		(240,414	)
Unrealized Appreciation (Depreciation) on:
Investments		1,626
Futures Contracts		(3	)
Foreign Currency Translations		—	@
Net Assets	$	165,933

The accompanying notes are an integral part of the financial statements.
14

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Short Duration Income Portfolio

Statement of Assets and Liabilities (cont'd)	September 30, 2016 (000)
CLASS I:
Net Assets	$	98,603
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		12,149,602
Net Asset Value, Offering and Redemption Price Per Share	$	8.12
CLASS A:
Net Assets	$	66,821
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		8,215,885
Net Asset Value, Redemption Price Per Share	$	8.13
CLASS L:
Net Assets	$	403
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		49,703
Net Asset Value, Offering and Redemption Price Per Share	$	8.11
CLASS C:
Net Assets	$	95
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		11,768
Net Asset Value, Offering and Redemption Price Per Share	$	8.09
CLASS IS:
Net Assets	$	11
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		1,307
Net Asset Value, Offering and Redemption Price Per Share	$	8.11

@ Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
15

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Short Duration Income Portfolio

Statement of Operations	Year Ended September 30, 2016 (000)
Investment Income:
Interest from Securities of Unaffiliated Issuers	$	3,176
Dividends from Security of Affiliated Issuer (Note G)		8
Total Investment Income		3,184
Expenses:
Advisory Fees (Note B)		301
Professional Fees		155
Administration Fees (Note C)		109
Shareholder Services Fees — Class A (Note D)		94
Distribution and Shareholder Services Fees — Class L (Note D)		2
Distribution and Shareholder Services Fees — Class C (Note D)		1
Sub Transfer Agency Fees — Class I		74
Sub Transfer Agency Fees — Class A		5
Sub Transfer Agency Fees — Class L		—	@
Sub Transfer Agency Fees — Class C		—	@
Registration Fees		67
Shareholder Reporting Fees		62
Pricing Fees		31
Transfer Agency Fees — Class I (Note E)		7
Transfer Agency Fees — Class A (Note E)		1
Transfer Agency Fees — Class L (Note E)		3
Transfer Agency Fees — Class C (Note E)		2
Transfer Agency Fees — Class IS (Note E)		1
Custodian Fees (Note F)		13
Trustees' Fees and Expenses		—	@
Other Expenses		24
Total Expenses		952
Waiver of Advisory Fees (Note B)		(216	)
Reimbursement of Class Specific Expenses — Class I (Note B)		(46	)
Reimbursement of Class Specific Expenses — Class A (Note B)		(1	)
Reimbursement of Class Specific Expenses — Class L (Note B)		(3	)
Reimbursement of Class Specific Expenses — Class C (Note B)		(2	)
Reimbursement of Class Specific Expenses — Class IS (Note B)		(1	)
Rebate from Morgan Stanley Affiliate (Note G)		(3	)
Reimbursement of Custodian Fees (Note F)		(125	)
Net Expenses		555
Net Investment Income		2,629
Realized Gain (Loss):
Investments Sold		8,255
Foreign Currency Forward Exchange Contracts		2
Foreign Currency Transactions		—	@
Futures Contracts		(1,065	)
Swap Agreements		(65	)
Net Realized Gain		7,127
Change in Unrealized Appreciation (Depreciation):
Investments		833
Foreign Currency Forward Exchange Contracts		(2	)
Foreign Currency Translations		—	@
Futures Contracts		189
Swap Agreements		73
Net Change in Unrealized Appreciation (Depreciation)		1,093
Net Realized Gain and Change in Unrealized Appreciation (Depreciation)		8,220
Net Increase in Net Assets Resulting from Operations	$	10,849

@ Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
16

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Short Duration Income Portfolio

Statements of Changes in Net Assets	Year Ended September 30, 2016 (000)			Year Ended September 30, 2015 (000)
Increase (Decrease) in Net Assets:
Operations:
Net Investment Income	$	2,629		$	1,904
Net Realized Gain (Loss)		7,127			(804	)
Net Change in Unrealized Appreciation (Depreciation)		1,093			(1,030	)
Net Increase in Net Assets Resulting from Operations		10,849			70
Distributions from and/or in Excess of:
Class I:
Net Investment Income		(1,953	)		(1,478	)
Class A:
Net Investment Income		(590	)		(14	)
Class L:
Net Investment Income		(6	)		(2	)
Class C:
Net Investment Income		(1	)		(—	@)*
Class IS:
Net Investment Income		(—	@)**		—
Total Distributions		(2,550	)		(1,494	)
Capital Share Transactions:⁽¹⁾
Class I:
Subscribed		8,502			6,678
Issued due to a tax-free reorganization		604			—
Distributions Reinvested		1,951			1,477
Redeemed		(20,237	)		(23,006	)
Class A:
Subscribed		23,263			2,156
Issued due to a tax-free reorganization		47,269			—
Distributions Reinvested		585			14
Redeemed		(9,355	)		(1,330	)
Class L:
Exchanged		167			—
Subscribed		—			367
Issued due to a tax-free reorganization		112			—
Distributions Reinvested		3			1
Redeemed		(339	)		(124	)
Class C:
Exchanged		32			—
Subscribed		—			72	*
Distributions Reinvested		1			—	@*
Redeemed		(13	)		(1	)*
Class IS:
Subscribed		10	**		—
Net Increase (Decrease) in Net Assets Resulting from Capital Share Transactions		52,555			(13,696	)
Total Increase (Decrease) in Net Assets		60,854			(15,120	)
Net Assets:
Beginning of Period		105,079			120,199
End of Period (Including Accumulated Undistributed Net Investment Income of $474 and $506)	$	165,933		$	105,079

The accompanying notes are an integral part of the financial statements.
17

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Short Duration Income Portfolio

Statements of Changes in Net Assets (cont'd)	Year Ended September 30, 2016 (000)			Year Ended September 30, 2015 (000)
(1) Capital Share Transactions:
Class I:
Shares Subscribed	$	1,090		$	859
Shares Issued due to a tax-free reorganization		79			—
Shares Issued on Distributions Reinvested		252			190
Shares Redeemed		(2,604	)		(2,959	)
Net Decrease in Class I Shares Outstanding		(1,183	)		(1,910	)
Class A:
Shares Subscribed		2,949			277
Shares Issued due to a tax-free reorganization		6,163			—
Shares Issued on Distributions Reinvested		75			2
Shares Redeemed		(1,199	)		(171	)
Net Increase in Class A Shares Outstanding		7,988			108
Class L:
Shares Exchanged		22			—
Shares Subscribed		—			47
Shares Issued due to a tax-free reorganization		15			—
Shares Issued on Distributions Reinvested		—	@@		—	@@
Shares Redeemed		(44	)		(16	)
Net Increase (Decrease) in Class L Shares Outstanding		(7	)		31
Class C:
Shares Exchanged		5			—
Shares Subscribed		—			9	*
Shares Issued on Distributions Reinvested		—	@@		—	@@*
Shares Redeemed		(2	)		(—	@@)*
Net Increase in Class C Shares Outstanding		3			9
Class IS:
Shares Subscribed		1	**		—

* For the period April 30, 2015 through September 30, 2015.

** For the period January 11, 2016 through September 30, 2016.

@ Amount is less than $500.

@@ Amount is less than 500 shares.

The accompanying notes are an integral part of the financial statements.
18

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Short Duration Income Portfolio

	Class I
	Year Ended September 30,
Selected Per Share Data and Ratios	2016††			2015			2014			2013			2012
Net Asset Value, Beginning of Period	$	7.71		$	7.81		$	7.76		$	7.80		$	7.71
Income (Loss) from Investment Operations:
Net Investment Income†		0.15			0.13			0.12			0.11			0.15
Net Realized and Unrealized Gain (Loss)		0.41			(0.12	)		0.04			(0.03	)		0.11
Total from Investment Operations		0.56			0.01			0.16			0.08			0.26
Distributions from and/or in Excess of:
Net Investment Income		(0.15	)		(0.11	)		(0.11	)		(0.12	)		(0.17	)
Net Asset Value, End of Period	$	8.12		$	7.71		$	7.81		$	7.76		$	7.80
Total Return++		7.43	%**		0.06	%		2.06	%		1.09	%		3.35	%
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	98,603		$	102,808		$	119,059		$	122,958		$	145,387
Ratio of Expenses to Average Net Assets⁽¹⁾		0.36	%+^^		0.53	%+		0.53	%+		0.71	%+^		0.63	%+
Ratio of Net Investment Income to Average Net Assets⁽¹⁾		1.97	%+^^		1.72	%+		1.49	%+		1.45	%+^		1.92	%+
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.00	%§		0.00	%§		0.00	%§		0.00	%§		0.00	%§
Portfolio Turnover Rate		66	%		41	%		60	%		66	%		51	%
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		0.65	%		0.63	%		0.78	%		0.72	%		N/A
Net Investment Income to Average Net Assets		1.68	%		1.62	%		1.24	%		1.44	%		N/A

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value as of the last business day of the period.

** Performance was positively impacted by approximately 5.97% due to the receipt of proceeds from the settlement of class action suits involving the Portfolio's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class I shares would have been approximately 1.46%.

^ Effective September 16, 2013, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 0.53% for Class I shares.

^^ Effective January 11, 2016, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 0.30% for Class I shares. Prior to January 11, 2016, the maximum ratio was 0.53% for Class I shares.

§ Amount is less than 0.005%.

The accompanying notes are an integral part of the financial statements.
19

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Short Duration Income Portfolio

	Class A
	Year Ended September 30,
Selected Per Share Data and Ratios	2016††			2015			2014			2013			2012
Net Asset Value, Beginning of Period	$	7.72		$	7.83		$	7.77		$	7.80		$	7.71
Income (Loss) from Investment Operations:
Net Investment Income†		0.14			0.11			0.09			0.09			0.13
Net Realized and Unrealized Gain (Loss)		0.40			(0.14	)		0.05			(0.01	)		0.11
Total from Investment Operations		0.54			(0.03	)		0.14			0.08			0.24
Distributions from and/or in Excess of:
Net Investment Income		(0.13	)		(0.08	)		(0.08	)		(0.11	)		(0.15	)
Net Asset Value, End of Period	$	8.13		$	7.72		$	7.83		$	7.77		$	7.80
Total Return++		7.15	%**		(0.41	)%		1.78	%		0.84	%		3.22	%
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	66,821		$	1,761		$	940		$	749		$	145
Ratio of Expenses to Average Net Assets⁽¹⁾		0.52	%+^^		0.88	%+		0.88	%+		0.97	%+^		0.88	%+
Ratio of Net Investment Income to Average Net Assets⁽¹⁾		1.83	%+^^		1.40	%+		1.14	%+		1.15	%+^		1.70	%+
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.00	%§		0.00	%§		0.00	%§		0.00	%§		0.00	%§
Portfolio Turnover Rate		66	%		41	%		60	%		66	%		51	%
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		0.80	%		1.22	%		1.10	%		1.00	%		N/A
Net Investment Income to Average Net Assets		1.55	%		1.06	%		0.92	%		1.12	%		N/A

†† Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class A shares. The Ratio of Expenses to Average Net Assets and the Ratio of Net Investment Income to Average Net Assets would be unchanged as the change to current period custodian fees was offset against current period expense waivers/reimbursements with no impact to net expenses or net investment income.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value as of the last business day of the period.

** Performance was positively impacted by approximately 5.94% due to the receipt of proceeds from the settlement of class action suits involving the Portfolio's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class A shares would have been approximately 1.21%.

^ Effective September 16, 2013, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 0.88% for Class A shares.

^^ Effective January 11, 2016, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 0.55% for Class A shares. Prior to January 11, 2016, the maximum ratio was 0.88% for Class A shares.

§ Amount is less than 0.005%.

The accompanying notes are an integral part of the financial statements.
20

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Short Duration Income Portfolio

	Class L
	Year Ended September 30,												Period from April 27, 2012^ to
Selected Per Share Data and Ratios	2016††			2015			2014			2013			September 30, 2012
Net Asset Value, Beginning of Period	$	7.70		$	7.80		$	7.75		$	7.80		$	7.76
Income (Loss) from Investment Operations:
Net Investment Income†		0.11			0.08			0.06			0.07			0.04
Net Realized and Unrealized Gain (Loss)		0.41			(0.13	)		0.05			(0.03	)		0.04
Total from Investment Operations		0.52			(0.05	)		0.11			0.04			0.08
Distributions from and/or in Excess of:
Net Investment Income		(0.11	)		(0.05	)		(0.06	)		(0.09	)		(0.04	)
Net Asset Value, End of Period	$	8.11		$	7.70		$	7.80		$	7.75		$	7.80
Total Return++		6.79	%**		(0.68	)%		1.38	%		0.48	%		1.06	%#
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	403		$	439		$	200		$	95		$	10
Ratio of Expenses to Average Net Assets⁽¹⁾		0.92	%+^^^		1.23	%+		1.23	%+		1.24	%+^^		1.21	%+*
Ratio of Net Investment Income to Average Net Assets⁽¹⁾		1.42	%+^^^		1.05	%+		0.79	%+		0.85	%+^^		1.14	%+*
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.00	%§		0.00	%§		0.00	%§		0.00	%§		0.00	%§*
Portfolio Turnover Rate		66	%		41	%		60	%		66	%		51	%#
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		1.83	%		1.80	%		3.48	%		1.34	%		N/A
Net Investment Income (Loss) to Average Net Assets		0.51	%		0.48	%		(1.46	)%		0.75	%		N/A

†† Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class L shares. The Ratio of Expenses to Average Net Assets and the Ratio of Net Investment Income to Average Net Assets would be unchanged as the change to current period custodian fees was offset against current period expense waivers/reimbursements with no impact to net expenses or net investment income.

^ Commencement of Offering.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value as of the last business day of the period.

** Performance was positively impacted by approximately 5.92% due to the receipt of proceeds from the settlement of class action suits involving the Portfolio's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class L shares would have been approximately 0.87%.

^^ Effective September 16, 2013, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 1.23% for Class L shares.

^^^ Effective January 11, 2016, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 0.80% for Class L shares. Prior to January 11, 2016, the maximum ratio was 1.23% for Class L shares.

§ Amount is less than 0.005%.

# Not Annualized.

* Annualized.

The accompanying notes are an integral part of the financial statements.
21

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Short Duration Income Portfolio

	Class C
Selected Per Share Data and Ratios	Year Ended September 30, 2016††			Period from April 30, 2015^ to September 30, 2015
Net Asset Value, Beginning of Period	$	7.69		$	7.78
Income (Loss) from Investment Operations:
Net Investment Income†		0.07			0.02
Net Realized and Unrealized Gain (Loss)		0.41			(0.09	)
Total from Investment Operations		0.48			(0.07	)
Distributions from and/or in Excess of:
Net Investment Income		(0.08	)		(0.02	)
Net Asset Value, End of Period	$	8.09		$	7.69
Total Return++		6.24	%**		(0.92	)%#
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	95		$	71
Ratio of Expenses to Average Net Assets⁽¹⁾		1.39	%+^^		1.63	%+*
Ratio of Net Investment Income to Average Net Assets⁽¹⁾		0.93	%+^^		0.73	%+*
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.00	%§		0.00	%§*
Portfolio Turnover Rate		66	%		41	%#
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		3.95	%		6.73	%*
Net Investment Loss to Average Net Assets		(1.63	)%		(4.37	)%*

†† Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class C shares. The Ratio of Expenses to Average Net Assets and the Ratio of Net Investment Income to Average Net Assets would be unchanged as the change to current period custodian fees was offset against current period expense waivers/reimbursements with no impact to net expenses or net investment income.

^ Commencement of Offering.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

** Performance was positively impacted by approximately 5.77% due to the receipt of proceeds from the settlement of class action suits involving the Portfolio's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class C shares would have been approximately 0.47%.

^^ Effective January 11, 2016, the Adviser has agreed to limit the ratio of expenses to average net assets to the maximum ratio of 1.30% for Class C shares. Prior to January 11, 2016, the maximum ratio was 1.63% for Class C shares.

§ Amount is less than 0.005%.

# Not Annualized.

* Annualized.

The accompanying notes are an integral part of the financial statements.
22

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Short Duration Income Portfolio

	Class IS
Selected Per Share Data and Ratios	Period from January 11, 2016^ to September 30, 2016††
Net Asset Value, Beginning of Period	$	7.65
Income from Investment Operations:
Net Investment Income†		0.17
Net Realized and Unrealized Gain		0.39
Total from Investment Operations		0.56
Distributions from and/or in Excess of:
Net Investment Income		(0.10	)
Net Asset Value, End of Period	$	8.11
Total Return++		7.42	%**#
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	11
Ratio of Expenses to Average Net Assets⁽¹⁾		0.25	%+*
Ratio of Net Investment Income to Average Net Assets⁽¹⁾		2.20	%+*
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.00	%§*
Portfolio Turnover Rate		66	%#
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		17.12	%*
Net Investment Loss to Average Net Assets		(14.67	)%*

†† Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class IS shares. The Ratio of Expenses to Average Net Assets and the Ratio of Net Investment Income to Average Net Assets would be unchanged as the change to current period custodian fees was offset against current period expense waivers/reimbursements with no impact to net expenses or net investment income.

^ Commencement of Offering.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value as of the last business day of the period.

** Performance was positively impacted by approximately 5.96% due to the receipt of proceeds from the settlement of class action suits involving the Portfolio's past holdings. These were one-time settlements, and as a result, the impact on the NAV and consequently the performance will not likely be repeated in the future. Had these settlements not occurred, the total return for Class IS shares would have been approximately 1.46%.

§ Amount is less than 0.005%.

# Not Annualized.

* Annualized.

The accompanying notes are an integral part of the financial statements.
23

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements

The accompanying financial statements relate to the Short Duration Income Portfolio (name changed on January 11, 2016, formerly Limited Duration Portfolio). The Portfolio seeks above-average total return over a market cycle of three to five years. The Portfolio offers five classes of shares — Class I, Class A, Class L, Class C and Class IS.

The Portfolio has suspended offering Class L and Class C shares to all investors. Class L and Class C shareholders of the Portfolio do not have the option of purchasing additional Class L and Class C shares, respectively. However, existing Class L and Class C shareholders may invest through reinvestment of dividends and distributions.

On January 11, 2016, the Portfolio commenced offering Class IS shares.

On January 11, 2016, the Portfolio acquired the net assets of Morgan Stanley Limited Duration U.S. Government Trust ("Limited Duration U.S. Government Trust"), an open-end investment company, based on the respective valuations as of the close of business on January 8, 2016, pursuant to a Plan of Reorganization approved by the shareholders of Limited Duration U.S. Government Trust on June 9, 2015 ("Reorganization"). The purpose of the transaction was to combine two portfolios managed by Morgan Stanley Investment Management Inc. (the "Adviser") with comparable investment objectives and strategies. The acquisition was accomplished by a tax-free exchange of 78,397 Class I shares of the Portfolio at a net asset value of $7.65 for 68,223 Class I shares of Limited Duration U.S. Government Trust; 528 Class I shares of the Portfolio at a net asset value of $7.65 for 460 Advisor Class shares of Limited Duration U.S. Government Trust; 6,162,897 Class A shares of the Portfolio at a net asset value of $7.67 for 5,378,737 Advisor Class shares of Limited Duration U.S. Government Trust; and 14,702 Class L shares of the Portfolio at a net asset value of $7.65 for 12,798 Advisor Class shares of Limited Duration U.S. Government Trust. The net assets of Limited Duration U.S. Government Trust before the Reorganization were approximately

$47,986,000, including unrealized appreciation of approximately $462,000 at January 8, 2016. The investment portfolio of Limited Duration U.S. Government Trust, with a fair value of approximately $47,575,000 and identified cost of approximately $47,113,000 on January 8, 2016, was the principal asset acquired by the Portfolio. For financial reporting purposes, assets received and shares issued by the Portfolio were recorded at fair value; however, the cost basis of the investments received from Limited Duration U.S. Government Trust was carried forward to align ongoing reporting of the Portfolio's realized and unrealized gains and losses with amounts distributable to shareholders for tax purposes. Immediately prior to the Reorganization, the net assets of the Portfolio were approximately $100,541,000. Immediately after the Reorganization, the net assets of the Portfolio were approximately $148,527,000.

Upon closing of the Reorganization, shareholders of Limited Duration U.S. Government Trust received shares of the Portfolio as follows:

Limited Duration U.S. Government Trust				Short Duration Income Portfolio
Class I				Class I
Advisor Class				Class I
Advisor Class				Class A
Advisor Class				Class L

Assuming the acquisition had been completed on October 1, 2015, the beginning of the annual reporting period of the Portfolio, the Portfolio's pro forma results of operations for the period ended September 30, 2016, are as follows:

Net investment income⁽¹⁾	$	4,042,000
Net realized gain and unrealized gain⁽²⁾	$	7,755,000
Net increase in net assets resulting from operations	$	11,797,000

(1) Approximately $2,629,000 as reported, plus approximately $898,000 Limited Duration U.S. Government Trust prior to Reorganization, plus approximately $515,000 of estimated pro-forma eliminated expenses.

(2) Approximately $8,220,000 as reported, plus approximately $(465,000) Limited Duration U.S. Government Trust prior to Reorganization.

Because the combined investment portfolios have been managed as a single integrated portfolio since the acquisition was completed, it is not practicable to separate the amounts of revenue and earnings of Limited Duration U.S. Government Trust that have been included in the Portfolio's Statement of Operations since January 11, 2016.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

and disclosures in the financial statements. Actual results may differ from those estimates.

1. Security Valuation: (1) Certain portfolio securities may be valued by an outside pricing service/vendor approved by the Fund's Board of Trustees (the "Trustees"). The pricing service/vendor may employ a pricing model that takes into account, among other things, bids, yield spreads, and/or other market data and specific security characteristics. Alternatively, if a valuation is not available from an outside pricing service/vendor, and the security trades on an exchange, the security may be valued at its latest reported sale price (or at the exchange official closing price if such exchange reports an official closing price), prior to the time when assets are valued. If there are no sales on a given day and if there is no official exchange closing price for that day, the security is valued at the mean between the last reported bid and asked prices if such bid and asked prices are available in the relevant exchanges; (2) futures are valued at the latest price published by the commodities exchange on which they trade; (3) swaps are marked-to-market daily based upon quotations from market makers; (4) when market quotations are not readily available, including circumstances under which the Adviser determines that the closing price, last sale price or the mean between the last reported bid and asked prices are not reflective of a security's market value, portfolio securities are valued at their fair value as determined in good faith under procedures established by and under the general supervision of the Trustees. Occasionally, developments affecting the closing prices of securities and other assets may occur between the times at which valuations of such securities are determined (that is, close of the foreign market on which the securities trade) and the close of business of the New York Stock Exchange ("NYSE"). If developments occur during such periods that are expected to materially affect the value of such securities, such valuations may be adjusted to reflect the estimated fair value of such securities as of the close of the NYSE, as determined in good faith by the Trustees or by the Adviser using a pricing service and/or procedures approved by the Trustees; (5) quotations of foreign portfolio securities, other assets and liabilities and forward contracts stated in foreign currency are translated into U.S. dollar equivalents at the prevailing market rates prior to the close of the NYSE; and (6) investments in mutual funds, including the Morgan Stanley

Institutional Liquidity Funds, are valued at the net asset value ("NAV") as of the close of each business day.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

• Level 1 – unadjusted quoted prices in active markets for identical investments

• Level 2 – other significant observable inputs (including quoted prices for similar investments, interest rates, prepayment speeds, credit risk, etc.)

measurement in its entirety requires judgment and considers factors specific to each security.

The following is a summary of the inputs used to value the Portfolio's investments as of September 30, 2016.

Investment Type	Level 1 Unadjusted quoted prices (000)			Level 2 Other significant observable inputs (000)		Level 3 Significant unobservable inputs (000)		Total (000)
Assets:
Fixed Income Securities
Agency Adjustable Rate Mortgages	$	—		$	7,086	$	—	$	7,086
Agency Bonds — Consumer Discretionary (U.S. Government Guaranteed)		—			627		—		627
Agency Fixed Rate Mortgages		—			7,659		—		7,659
Asset-Backed Securities		—			16,562		—		16,562
Collateralized Mortgage Obligations — Agency Collateral Series		—			7,240		—		7,240
Commercial Mortgage-Backed Securities		—			1,765		—		1,765
Corporate Bonds		—			106,800		—		106,800
Mortgages — Other		—			3,719		—		3,719
Sovereign		—			691		—		691
U.S. Agency Security		—			2,320		—		2,320
Total Fixed Income Securities		—			154,469		—		154,469
Short-Term Investments
Investment Company		5,928			—		—		5,928
U.S. Treasury Security		—			1,347		—		1,347
Certificates of Deposit		—			4,223		—		4,223
Commercial Paper		—			697		—		697
Total Short-Term Investments		5,928			6,267		—		12,195
Total Assets		5,928			160,736		—		166,664
Liabilities:
Futures Contracts		(3	)		—		—		(3	)
Total	$	5,925		$	160,736	$	—	$	166,661

3. Foreign Currency Translation and Foreign Investments: The books and records of the Portfolio are

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

maintained in U.S. dollars. Foreign currency amounts are translated into U.S. dollars as follows:

– investments, other assets and liabilities at the prevailing rate of exchange on the valuation date;

– investment transactions and investment income at the prevailing rates of exchange on the dates of such transactions.

Net realized gains (losses) on foreign currency transactions represent net foreign exchange gains (losses) from currency gains (losses) realized between the trade and settlement dates on securities transactions, and the difference between the amount of investment income and foreign withholding taxes recorded on the Portfolio's books and the U.S. dollar equivalent amounts actually received or paid. Net unrealized currency gains (losses) from valuing foreign currency denominated assets and liabilities at period end exchange rates are reflected as a component of unrealized appreciation (depreciation) in the Statement of Assets and Liabilities. The change in unrealized currency gains (losses) on foreign currency translations for the period is reflected in the Statement of Operations.

Foreign security and currency transactions may involve certain considerations and risks not typically associated with those of U.S. dollar denominated transactions as a

result of, among other factors, fluctuations of exchange rates in relation to the U.S. dollar, the possibility of lower levels of governmental supervision and regulation of foreign securities markets and the possibility of political or economic instability.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

Following is a description of the derivative instruments and techniques that the Portfolio used during the period and their associated risks:

Foreign Currency Forward Exchange Contracts: In connection with its investments in foreign securities, the Portfolio also entered into contracts with banks, brokers or dealers to purchase or sell securities or foreign currencies at a future date. A foreign currency forward exchange contract ("currency contract") is a negotiated agreement between the contracting parties to exchange a specified amount of currency at a specified future time at a specified rate. The rate can be higher or lower than the spot rate between the currencies that are the subject of the contract. Currency contracts may be used to protect against uncertainty in the level of future foreign currency exchange rates or to gain or modify exposure to a particular currency. To the extent hedged by the use of currency contracts, the precise matching of the currency contract amounts and the value of the securities involved will not generally be possible because the future value of such securities in foreign currencies will change as a consequence of market movements in the value of those securities between the date on which the contract is entered into and the date it matures. Furthermore, such transactions may reduce or preclude the opportunity for gain if the value of the currency should move in the direction opposite to the position taken. There is additional risk to the extent that currency contracts create exposure to currencies in which the Portfolio's securities are not denominated. Unanticipated changes in currency prices may result in poorer overall performance for the Portfolio than if it had not entered into such contracts. The use of currency contracts involves the risk of loss

from the insolvency or bankruptcy of the counterparty to the contract or the failure of the counterparty to make payments or otherwise comply with the terms of the contract. A currency contract is marked-to-market daily and the change in market value is recorded by the Portfolio as unrealized gain or loss. The Portfolio records realized gains (losses) when the currency contract is closed equal to the difference between the value of the currency contract at the time it was opened and the value at the time it was closed.

As of September 30, 2016, the Portfolio did not have any open foreign currency forward exchange contracts.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

other instruments. Typically swap agreements provide that when the period payment dates for both parties are the same, the payments are made on a net basis (i.e., the two payment streams are netted out, with only the net amount paid by one party to the other). The Portfolio's obligations or rights under a swap contract entered into on a net basis will generally be equal only to the net amount to be paid or received under the agreement, based on the relative values of the positions held by each party. Cleared swap transactions may help reduce counterparty credit risk. In a cleared swap, the Portfolio's ultimate counterparty is a clearinghouse rather than a swap dealer, bank or other financial institution. OTC swap agreements are not entered into or traded on exchanges and often there is no central clearing or guaranty function for OTC swaps. These OTC swaps are often subject to credit risk or the risk of default or non-performance by the counterparty. Both OTC and cleared swaps could result in losses if interest rates, foreign currency exchange rates or other factors are not correctly anticipated by the Portfolio or if the reference index, security or investments do not perform as expected. During the period swap agreements are open, payments are received from or made to the clearinghouse or counterparty based upon changes in the value of the contract (variation margin). The Dodd-Frank Wall Street Reform and Consumer Protection Act and related regulatory developments require the clearing and exchange-trading of certain standardized swap transactions. Mandatory exchange-trading and clearing is occurring on a phased-in basis.

amount equal to the par (or other agreed-upon) value of a referenced debt obligation upon the default or similar event by the issuer of the referenced debt obligation. The use of credit default swaps could result in losses to the Portfolio if the Adviser fails to correctly evaluate the creditworthiness of the issuer of the referenced debt obligation.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

applicable, cash collateral is included with "Due from (to) Broker" in the Statement of Assets and Liabilities.

As of September 30, 2016, the Portfolio did not have any open swap agreements.

The following tables set forth the fair value of the Portfolio's derivative contracts by primary risk exposure as of September 30, 2016.

Asset Derivatives
Statement of Assets and
Liabilities Location

Primary Risk
Exposure

Value
(000)

Futures Contract

Variation Margin on
Futures Contract

Interest Rate Risk

—

@(a)

Liability Derivatives
Statement of Assets and
Liabilities Location

Primary Risk
Exposure

Value
(000)

Futures Contracts

Variation Margin on
Futures Contracts

Interest Rate Risk

)(a)

@ Amount is less than $500.

Realized Gain (Loss)
Primary Risk Exposure	Derivative Type	Value (000)
Currency Risk	Foreign Currency Forward Exchange Contracts	$	2
Interest Rate Risk	Futures Contracts		(1,065	)
Credit Risk	Swap Agreements		(15	)
Interest Rate Risk	Swap Agreements		(50	)
	Total	$	(1,128	)

Change in Unrealized Appreciation (Depreciation)
Primary Risk Exposure	Derivative Type	Value (000)
Currency Risk	Foreign Currency Forward Exchange Contracts	$	(2	)
Interest Rate Risk	Futures Contracts		189
Credit Risk	Swap Agreements		22
Interest Rate Risk	Swap Agreements		51
	Total	$	260

For the year ended September 30, 2016, the approximate average monthly amount outstanding for each derivative type is as follows:

Foreign Currency Forward Exchange Contracts:
Average monthly principal amount	$	334,000
Futures Contracts:
Average monthly original value	$	56,525,000
Swap Agreements:
Average monthly notional amount	$	161,000

7. Dividends and Distributions to Shareholders: Dividend income and distributions to shareholders are

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

recorded on the ex-dividend date. Dividends from net investment income, if any, are declared and paid monthly. Net realized capital gains, if any, are distributed at least annually.

B. Advisory Fees: The Adviser, a wholly-owned subsidiary of Morgan Stanley, provides the Portfolio with advisory services under the terms of an Investment Advisory Agreement, paid quarterly, at an annual rate of 0.30% of the average daily net assets of the Portfolio. Effective January 11, 2016, the advisory fees were reduced to 0.20% of the average daily net assets of the Portfolio.

Class A shares, 0.80% for Class L shares, 1.30% for Class C shares and 0.25% for Class IS shares. The fee waivers and/or expense reimbursements will continue for at least two years from the date of the Reorganization or until such time as the Trustees act to discontinue all or a portion of such waivers and/or reimbursements when they deem such action is appropriate. For the year ended September 30, 2016, approximately $216,000 of advisory fees were waived and approximately $53,000 of other expenses were reimbursed by the Adviser pursuant to this arrangement.

C. Administration Fees: The Adviser also serves as Administrator to the Fund and provides administrative services pursuant to an Administration Agreement for an annual fee, accrued daily and paid monthly, of 0.08% of the Portfolio's average daily net assets. Under a Sub-Administration Agreement between the Administrator and State Street Bank and Trust Company ("State Street"), State Street provides certain administrative services to the Fund. For such services, the Administrator pays State Street a portion of the fee the Administrator receives from the Portfolio.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

an annual rate of 0.25% of the Portfolio's average daily net assets attributable to Class C shares.

E. Dividend Disbursing and Transfer/Co-Transfer Agent: The Fund's dividend disbursing and transfer agent is Boston Financial Data Services, Inc. ("BFDS"). Pursuant to a Transfer Agency Agreement, the Fund pays BFDS a fee based on the number of classes, accounts and transactions relating to the Portfolios of the Fund.

Morgan Stanley Services Company Inc. serves as Co-Transfer Agent and provides certain transfer agency services to the Portfolio with respect to certain direct transactions with the Portfolio.

G. Security Transactions and Transactions with Affiliates: For the year ended September 30, 2016, purchases and sales of investment securities for the Portfolio, other than long-term U.S. Government securities and short-term investments, were approximately $78,072,000 and $49,982,000, respectively. For the year ended September 30, 2016, purchases

and sales of long-term U.S. Government securities were approximately $20,255,000 and $35,947,000, respectively.

The Portfolio invests in the Institutional Class of the Morgan Stanley Institutional Liquidity Funds (the "Liquidity Funds"), an open-end management investment company managed by the Adviser. Advisory fees paid by the Portfolio are reduced by an amount equal to its pro-rata share of the advisory and administration fees paid by the Portfolio due to its investment in the Liquidity Funds. For the year ended September 30, 2016, advisory fees paid were reduced by approximately $3,000 relating to the Portfolio's investment in the Liquidity Funds.

A summary of the Portfolio's transactions in shares of the Liquidity Funds during the year ended September 30, 2016 is as follows:

Value September 30, 2015 (000)				Purchases at Cost (000)				Sales (000)				Dividend Income (000)				Value September 30, 2016 (000)
$	750			$	91,298			$	86,120			$	8			$	5,928

The Portfolio may be subject to taxes imposed by countries in which it invests. Such taxes are generally based on income

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

and/or capital gains earned or repatriated. Taxes are accrued based on net investment income, net realized gains and net unrealized appreciation as such income and/or gains are earned. Taxes may also be based on transactions in foreign currency and are accrued based on the value of investments denominated in such currency.

FASB ASC 740-10, "Income Taxes — Overall", sets forth a minimum threshold for financial statement recognition of the benefit of a tax position taken or expected to be taken in a tax return. Management has concluded there are no significant uncertain tax positions that would require recognition in the financial statements. If applicable, the Portfolio recognizes interest accrued related to unrecognized tax benefits in "Interest Expense" and penalties in "Other Expenses" in the Statement of Operations. The Portfolio files tax returns with the U.S. Internal Revenue Service, New York and various states. Each of the tax years in the four-year period ended September 30, 2016, remains subject to examination by taxing authorities.

2016 Distributions Paid From: Ordinary Income (000)				2015 Distributions Paid From: Ordinary Income (000)
$	2,550			$	1,494

following reclassifications among the components of net assets at September 30, 2016:

Accumulated Undistributed Net Investment Income (000)				Accumulated Net Realized Loss (000)				Paid-in- Capital (000)
$	(111	)		$	(12,199	)		$	12,310

At September 30, 2016, the components of distributable earnings for the Portfolio on a tax basis were as follows:

Undistributed Ordinary Income (000)				Undistributed Long-Term Capital Gain (000)
$	533			$	—

At September 30, 2016, the Portfolio had available for federal income tax purposes unused short term and long term capital losses of approximately $1,410,000* and $4,307,000*, respectively, that do not have an expiration date.

In addition, at September 30, 2016, the Portfolio had available for federal income tax purposes unused capital losses which will expire on the indicated dates:

Amount (000)*		Expiration
$	200,657	September 30, 2017
	34,040	September 30, 2018

* These amounts include capital losses acquired from Limited Duration U.S. Government Trust that may be subject to limitation under IRC Section 382 in future years.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Report of Independent Registered Public Accounting Firm

To the Shareholders and Board of Trustees of
Morgan Stanley Institutional Fund Trust —
Short Duration Income Portfolio

We have audited the accompanying statement of assets and liabilities, including the portfolio of investments, of Short Duration Income Portfolio (formerly Limited Duration Portfolio) (one of the portfolios constituting Morgan Stanley Institutional Fund Trust) (the "Portfolio") as of September 30, 2016, and the related statement of operations for the year then ended, the statements of changes in net assets for each of the two years in the period then ended and the financial highlights for each of the years or periods indicated therein. These financial statements and financial highlights are the responsibility of the Portfolio's management. Our responsibility is to express an opinion on these financial statements and financial highlights based on our audits.

In our opinion, the financial statements and financial highlights referred to above present fairly, in all material respects, the financial position of Short Duration Income Portfolio (one of the portfolios constituting Morgan Stanley Institutional Fund Trust) at September 30, 2016, the results of its operations for the year then ended, the changes in its net assets for each of the two years in the period then ended and the financial highlights for each of the years or periods indicated therein, in conformity with U.S. generally accepted accounting principles.

Boston, Massachusetts
November 22, 2016

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Advisory Agreement Approval (unaudited)

Nature, Extent and Quality of Services

Performance, Fees and Expenses of the Portfolio

The Board reviewed the performance, fees and expenses of the Portfolio compared to its peers, as determined by Broadridge, and to appropriate benchmarks where applicable. The Board discussed with the Adviser the performance goals and the actual results achieved in managing the Portfolio. When considering a fund's performance, the Board and the Adviser place emphasis on trends and longer-term returns (focusing on one-year, three-year and five-year performance, as of December 31, 2015, or since inception, as applicable). When a fund underperforms its benchmark and/or its peer group average, the Board and the Adviser discuss the causes of such underperformance and, where necessary, they discuss specific changes to investment strategy or investment personnel. The Board noted that the Portfolio's performance was better than its peer group average for the three- and five-year periods but below its peer group average for the one-year period. The Board discussed with the Adviser the level of the advisory and administration fees (together, the "management fee") for this Portfolio relative to comparable funds and/or other accounts advised by the Adviser and/or compared to its peers as determined by Broadridge. In addition to the management fee, the Board also reviewed the Portfolio's total expense ratio. When a fund's management fee and/or its total expense ratio are higher than its peers, the Board and the Adviser discuss the reasons for this and, where appropriate, they discuss possible waivers and/or caps. The Board noted that the Portfolio's management fee was lower than its peer group average and total expense ratio was higher than its peer group average. After discussion, the Board concluded that the Portfolio's (i) performance was competitive with its peer group average; (ii) management fee was competitive with its peer group average; and (iii) total expense ratio was acceptable.

Economies of Scale

The Board considered the size and growth prospects of the Portfolio and how that relates to the Portfolio's total expense ratio and particularly the Portfolio's management fee rate, which does not include breakpoints. In conjunction with its review of the Adviser's profitability, the Board discussed with the Adviser how a change in assets can affect the efficiency or effectiveness of managing the Portfolio and whether the management fee level is appropriate relative to current and projected asset levels and/or whether the management fee structure reflects economies of scale as asset levels change. The Board has determined that its review of the actual and/or potential economies of scale of the Portfolio supports its decision to approve the Management Agreement.

Profitability of the Adviser and Affiliates

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Advisory Agreement Approval (unaudited) (cont'd)

Other Benefits of the Relationship

Resources of the Adviser and Historical Relationship Between the Portfolio and the Adviser

Other Factors and Current Trends

General Conclusion

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Privacy Notice (unaudited)

MORGAN STANLEY INVESTMENT MANAGEMENT INC.
AN IMPORTANT NOTICE CONCERNING OUR U.S. PRIVACY POLICY

WE RESPECT YOUR PRIVACY

1. WHAT PERSONAL INFORMATION DO WE COLLECT ABOUT YOU?

For example:

• We may obtain information about your creditworthiness and credit history from consumer reporting agencies.

• We may collect background information from and through third-party vendors to verify representations you have made and to comply with various regulatory requirements.

2. WHEN DO WE DISCLOSE PERSONAL INFORMATION WE COLLECT ABOUT YOU?

We may disclose personal information we collect about you to other Morgan Stanley companies and to non-affiliated third parties.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Privacy Notice (unaudited) (cont'd)

3. HOW DO WE PROTECT THE SECURITY AND CONFIDENTIALITY OF PERSONAL INFORMATION WE COLLECT ABOUT YOU?

4. HOW CAN YOU LIMIT THE SHARING OF CERTAIN TYPES OF PERSONAL INFORMATION WITH OTHER MORGAN STANLEY COMPANIES?

5. HOW CAN YOU LIMIT THE USE OF CERTAIN TYPES OF PERSONAL INFORMATION BY OTHER MORGAN STANLEY COMPANIES FOR MARKETING?

6. HOW CAN YOU SEND US AN OPT-OUT INSTRUCTION?

• Calling us at (800) 548-7786
Monday-Friday between 8a.m. and 6p.m.(EST)

• Writing to us at the following address:

Boston Financial Data Services, Inc.
c/o Privacy Coordinator
P.O. Box 219804
Kansas City, Missouri 64121

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Privacy Notice (unaudited) (cont'd)

7. WHAT IF AN AFFILIATED COMPANY BECOMES A NON-AFFILIATED THIRD PARTY?

SPECIAL NOTICE TO RESIDENTS OF VERMONT

If you wish to receive offers for investment products and services offered by or through other Morgan Stanley companies, please notify us in writing at the following address:

Boston Financial Data Services, Inc.
c/o Privacy Coordinator
P.O. Box 219804
Kansas City, Missouri 64121

SPECIAL NOTICE TO RESIDENTS OF CALIFORNIA

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited)

Independent Trustees:

Name, Age and Address of
Independent Trustee

Position(s)
Held with
Registrant

Length of Time
Served*

Principal Occupation(s)
During Past 5 Years
and Other Relevant
Professional Experience

Number of
Portfolios in
Fund Complex
Overseen by
Independent
Trustee**

Other Directorships
Held by Independent
Trustee***

Frank L. Bowman (71)
c/o Perkins Coie LLP
Counsel to the Independent Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
August
2006

Kathleen A. Dennis (63)
c/o Perkins Coie LLP
Counsel to the Independent Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
August
2006

Director of various non-profit organizations.

Nancy C. Everett (61)
c/o Perkins Coie LLP
Counsel to the Independent Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
January
2015

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Age and Address of
Independent Trustee

Position(s)
Held with
Registrant

Length of Time
Served*

Principal Occupation(s)
During Past 5 Years
and Other Relevant
Professional Experience

Number of
Portfolios in
Fund Complex
Overseen by
Independent
Trustee**

Other Directorships
Held by Independent
Trustee***

Jakki L. Haussler (59)
c/o Perkins Coie LLP
Counsel to the Independent Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
January
2015

Dr. Manuel H. Johnson (67)
c/o Johnson Smick International, Inc.
220 I Street, N.E. — Suite 200
Washington, D.C. 20002

Trustee

Since
July
1991

100

Director of NVR, Inc. (home construction).

Joseph J. Kearns (74)
c/o Kearns & Associates LLC
23823 Malibu Road
S-50-440
Malibu, CA 90265

Trustee

Since
August
1994

101

Director of Electro Rent Corporation (equipment leasing). Prior to December 31, 2013, Director of The Ford Family Foundation.

Michael F. Klein (57)
c/o Perkins Coie LLP
Counsel to the Independent Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
August
2006

Director of certain investment funds managed or sponsored by Aetos Capital, LLC; Director of Sanitized AG and Sanitized Marketing AG (specialty chemicals).

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Age and Address of
Independent Trustee

Position(s)
Held with
Registrant

Length of Time
Served*

Principal Occupation(s)
During Past 5 Years
and Other Relevant
Professional Experience

Number of
Portfolios in
Fund Complex
Overseen by
Independent
Trustee**

Other Directorships
Held by Independent
Trustee***

Michael E. Nugent (80)
522 Fifth Avenue
New York, NY 10036

Chair of the Board and Trustee

Chair of the Boards since July 2006 and Trustee since July 1991

100

None.

W. Allen Reed (69)
c/o Perkins Coie LLP
Counsel to the Independent Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
August
2006

Director of Legg Mason, Inc.; formerly, Director of the Auburn University Foundation (2010-2015).

Fergus Reid (84)
c/o Joe Pietryka, Inc.
85 Charles Colman Blvd.
Pawling, NY 12564

Trustee

Since
June
1992

Chairman, Joe Pietryka, Inc.; Chairperson of the Governance Committee and Director or Trustee of various Morgan Stanley Funds (since June 1992).

100

Formerly, Trustee and Director of certain investment companies in the JP Morgan Fund Complex managed by JP Morgan Investment Management Inc. (1987-2012).

* This is the earliest date the Trustee began serving the Morgan Stanley Funds. Each Trustee serves an indefinite term, until his or her successor is elected.

*** This includes any directorships at public companies and registered investment companies held by the Trustee at any time during the past five years.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited) (cont'd)

Executive Officers:

Name, Age and Address of Executive Officer

Position(s) Held
with
Registrant

Length of Time
Served*

Principal Occupation(s) During Past 5 Years

John H. Gernon (53)
522 Fifth Avenue
New York, NY 10036

President and Principal Executive Officer

Since
September
2013

Stefanie V. Chang Yu (49)
522 Fifth Avenue
New York, NY 10036

Chief Compliance Officer

Since
December
1997

Joseph C. Benedetti (51)
522 Fifth Avenue
New York, NY 10036

Vice President

Since
January
2014

Francis J. Smith (51)
522 Fifth Avenue
New York, NY 10036

Treasurer and Principal Financial Officer

Treasurer since July 2003 and Principal Financial Officer since September 2002

Executive Director of the Adviser and various entities affiliated with the Adviser; Treasurer (since July 2003) and Principal Financial Officer of various Morgan Stanley Funds (since September 2002).

Mary E. Mullin (49)
522 Fifth Avenue
New York, NY 10036

Secretary

Since
June
1999

Executive Director of the Adviser; Secretary of various Morgan Stanley Funds (since June 1999).

* This is the earliest date the officer began serving the Morgan Stanley Funds. Each officer serves a one-year term, until his or her successor is elected and has qualified.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Adviser and Administrator

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

Distributor

Morgan Stanley Distribution, Inc.
522 Fifth Avenue
New York, New York 10036

Dividend Disbursing and Transfer Agent

Boston Financial Data Services, Inc.
2000 Crown Colony Drive
Quincy, Massachusetts 02169

Co-Transfer Agent

Morgan Stanley Services Company, Inc.
522 Fifth Avenue
New York, New York 10036

Custodian

State Street Bank and Trust Company
One Lincoln Street
Boston, Massachusetts 02111

Legal Counsel

Dechert LLP
1095 Avenue of the Americas
New York, New York 10036

Counsel to the Independent Trustees

Perkins Coie LLP
30 Rockefeller Plaza
New York, New York 10112

Independent Registered Public Accounting Firm

Ernst & Young LLP
200 Clarendon Street
Boston, Massachusetts 02116

Reporting to Shareholders

Proxy Voting Policies and Procedures and Proxy Voting Record

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable Portfolio of Morgan Stanley Institutional Funds Trust, which describes in detail the Portfolio's investment policies, risks, fees and expenses. Please read the prospectus carefully before you invest or send money. For additional information, including information regarding the investments comprising the Portfolio, please visit our website at www.morganstanley.com/im or call toll free 1 (800) 548-7786.

Printed in U.S.A.
This Report has been prepared for shareholders and may be distributed to others only if preceded or accompanied by a current prospectus.

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

IFTLDANN
1627666 EXP. 11.30.17

INVESTMENT MANAGEMENT

Morgan Stanley Institutional Fund Trust

Strategic Income Portfolio

Annual Report

September 30, 2016

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Table of Contents

Shareholders' Letter					2
Expense Example					3
Investment Overview					4
Portfolio of Investments					7
Statement of Assets and Liabilities					13
Statement of Operations					15
Statements of Changes in Net Assets					16
Financial Highlights					17
Notes to Financial Statements					21
Report of Independent Registered Public Accounting Firm					31
Investment Advisory Agreement Approval					32
Privacy Notice					34
Trustee and Officer Information					37

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Shareholders' Letter (unaudited)

Dear Shareholders,

We are pleased to provide this Annual report, in which you will learn how your investment in Strategic Income Portfolio (the "Portfolio") performed during the latest twelve-month period.

As always, we thank you for selecting Morgan Stanley Investment Management, and look forward to working with you in the months and years ahead.

Sincerely,

John H. Gernon
President and Principal Executive Officer

October 2016

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Expense Example (unaudited)

Strategic Income Portfolio

This example is based on an investment of $1,000 invested at the beginning of the six-month period ended September 30, 2016 and held for the entire six-month period (unless otherwise noted).

Actual Expenses

Hypothetical Example for Comparison Purposes

	Beginning Account Value 4/1/16		Actual Ending Account Value 9/30/16		Hypothetical Ending Account Value		Actual Expenses Paid During Period*		Hypothetical Expenses Paid During Period*		Net Expense Ratio During Period**
Strategic Income Portfolio Class I	$	1,000.00	$	1,032.80	$	1,020.10	$	4.98	$	4.95		0.98	%***
Strategic Income Portfolio Class A		1,000.00		1,031.70		1,018.30		6.81		6.76		1.34	***
Strategic Income Portfolio Class C		1,000.00		1,027.20		1,012.21		10.54		10.46		2.08	***
Strategic Income Portfolio Class IS		1,000.00		1,033.00		1,020.35		4.73		4.70		0.93	***

** Annualized.

*** Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Overview (unaudited)

Strategic Income Portfolio

The Portfolio seeks total return comprised of income and capital appreciation.

Performance

For the fiscal year ended September 30, 2016, the Portfolio's Class I shares had a total return based on net asset value and reinvestment of distributions per share of 2.91%, net of fees. The Portfolio's Class I shares outperformed against the Portfolio's benchmark, the Bank of America/Merrill Lynch 3-Month U.S. Treasury Bill Index (the "Index"), which returned 0.27%.

Factors Affecting Performance

• Global government bond yields fell over the period, boosting prices (as bond yields and prices move in opposite directions). Yields on the 10-year U.S. Treasury fell to as low as 1.36% and returned 5.6% over the period.⁽¹⁾ Ten-year Japanese government bonds returned 4.9%, German 10-year bunds returned 8.5%, and U.K. 10-year gilts returned 12.4%.⁽¹⁾

• The largest contributor to positive performance was the Fund's allocation to non-agency residential mortgage-backed securities (RMBS). While non-agency RMBS yield spreads did widen in early 2016, the sector was relatively resilient and the relatively small amount of spread widening was largely a result of a rise in global risk premium rather than increased credit risks in the U.S. housing and mortgage markets. Non-agency RMBS spreads are now at their tightest levels since 2014 for most securities. U.S. housing market and mortgage market fundamentals have remained positive. National home prices are up 5.1% over the past year.⁽²⁾ Home prices are up 37% nationally from the lows in 2012 and are now less than 1% below the peak from July 2006.⁽²⁾ Mortgage performance also remains strong. We remain overweight the sector.

• The Portfolio's exposures to investment grade credit and to high yield were large drivers of positive performance. In the beginning of 2016, weaker expectations for oil demand combined with fears of new supply coming on line, particularly from Iran where sanctions were loosened during the month, pushed oil prices down to levels not seen in a decade. The broader commodity market suffered from similar fears of high supply and weaker demand, and iron ore and copper both reached cycle low levels. In addition, concerns regarding the rising potential for weakness in the U.S. economy arising from contagion from the emerging world put further pressure on markets. While all parts of the global credit market were weaker, the industrials sector meaningfully underperformed the financial sector, in large part reflecting the negative performance of sectors exposed to commodity prices. The market has since experienced a rally in risk assets and recovery in credit markets. Global credit has also benefited from the technical support afforded by accommodative central bank policy and depressed global yields.

• The Portfolio's exposure to emerging market debt was also a contributor to positive performance. Emerging market debt experienced broad-based weakness in the fourth quarter of 2015 and the start of 2016 as the potential for rising U.S. interest rates, the direction of commodity prices, and the

⁽¹⁾ Source: Bloomberg L.P. Data as of September 30, 2016.

⁽²⁾ Source: S&P Case-Shiller U.S. National Home Price Index. Data as of September 30, 2016.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Overview (unaudited) (cont'd)

Strategic Income Portfolio

uncertain path of Chinese economic growth, currency and monetary policy were risk factors weighing on emerging market asset prices. Emerging market assets have since recovered along with other risk assets, as fundamentals, technical factors, and the macro environment have been supportive.

• The Portfolio's exposure to commercial mortgage-backed securities (CMBS) detracted from performance as CMBS has underperformed most credit sectors year-to-date in 2016. Commercial real estate fundamental conditions have been strong as unemployment has remained low and the U.S. economy has continued its moderate growth. However, the technicals have been challenged given concerns over supply/demand dynamics and concerns over late-2015 and 2016 vintage origination CMBS due to the substantial increase in property values over the last few years. We have favored more seasoned CMBS issues, which have benefited from recent property price appreciation, over newly originated deals, which may have somewhat inflated property valuations as part of their underwriting.

Management Strategies

• Throughout the period, the Portfolio was positioned with exposure to the investment grade credit sector, primarily focused on financials, and to the high yield credit sector, as we believe valuations relative to fundamentals have been attractive for these segments. These positions have aided performance as the market has stabilized.

• The Portfolio also had allocations non-agency mortgage securities and CMBS. Non-agency mortgage positions added to performance during the period as the sector remained mostly immune to global volatility; however, CMBS positioning detracted from performance.

• We continue being overweight spread product (non-government bonds) as we believe the yield advantage could provide attractive returns over the near term.

* Minimum Investment

** Commenced operations on December 30, 2014.

In accordance with SEC regulations, the Portfolio's performance shown assumes that all recurring fees (including management fees) were deducted and all dividends and distributions were reinvested. The performance of Class A, Class C and Class IS shares will vary from the performance of Class I shares based upon their different inception dates and will be negatively impacted by additional fees assessed to those classes (where applicable).

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Overview (unaudited) (cont'd)

Strategic Income Portfolio

Performance Compared to the Bank of America/Merrill Lynch 3-Month U.S. Treasury Bill Index⁽¹⁾, and the Lipper Alternative Credit Focus Funds Index⁽²⁾

	Period Ended September 30, 2016 Total Returns⁽³⁾
				Average Annual
	One Year			Five Years		Ten Years		Since Inception⁽⁶⁾
Portfolio — Class I Shares w/o sales charges⁽⁴⁾		2.91	%		—		—		0.84	%
Portfolio — Class A Shares w/o sales charges⁽⁴⁾		2.51			—		—		0.52
Portfolio — Class A Shares with maximum 4.25% sales charges⁽⁴⁾		–1.80			—		—		–1.92
Portfolio — Class C Shares w/o sales charges⁽⁵⁾		1.77			—		—		–0.69
Portfolio — Class C Shares with maximum 1.00% deferred sales charges⁽⁵⁾		0.78			—		—		–0.69
Portfolio — Class IS Shares w/o sales charges⁽⁴⁾		2.96			—		—		0.88
Bank of America/Merrill Lynch 3-Month U.S. Treasury Bill Index		0.27			—		—		0.17
Lipper Alternative Credit Focus Funds Index		2.62			—		—		0.69

⁽¹⁾ Bank of America/Merrill Lynch 3-Month U.S. Treasury Bill Index tracks the performance of U.S. Treasury bills with a remaining maturity of three months. Index is unmanaged and its returns do not include any sales charges or fees. Such costs would lower performance. It is not possible to invest directly in an index.

⁽²⁾ The Lipper Alternative Credit Focus Funds Index is an equally weighted performance index of the largest qualifying funds (based on net assets) in the Lipper Alternative Credit Focus Funds classification. The Index, which is adjusted for capital gains distributions and income dividends, is unmanaged and should not be considered an investment. There are currently 30 funds represented in this Index. As of the date of this report, the Portfolio was in the Lipper Alternative Credit Focus Funds classification.

⁽³⁾ Total returns for the Portfolio reflect expenses waived and/or reimbursed, if applicable, by the Adviser. Without such waivers and/or reimbursements, total returns would have been lower.

⁽⁴⁾ Commenced operations on December 30, 2014.

⁽⁵⁾ Commenced operations on April 30, 2015.

⁽⁶⁾ For comparative purposes, average annual since inception returns listed for the Indexes refer to the inception date of Class I of the Portfolio, not the inception of the Indexes.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments

Strategic Income Portfolio

	Face Amount (000)		Value (000)
Fixed Income Securities (81.3%)
Asset-Backed Securities (13.0%)
AMRESCO Residential Securities Corp. Mortgage Loan Trust,
1.08%, 9/25/27 (a)	$	6	$	6
Bear Stearns Asset-Backed Securities I Trust,
0.85%, 3/25/37 (a)		86		50
0.88%, 5/25/37 (a)		97		61
BNC Mortgage Loan Trust,
0.69%, 3/25/37 (a)		100		77
Carrington Mortgage Loan Trust,
0.75%, 1/25/37 (a)		100		63
Countrywide Asset-Backed Certificates,
0.89%, 4/25/36 (a)		100		88
4.87%, 7/25/36		127		105
Credit Suisse First Boston Mortgage Securities Corp.,
1.15%, 1/25/32 (a)		57		51
CWABS Asset-Backed Certificates Trust,
4.76%, 10/25/46 (a)		94		67
Ellington Loan Acquisition Trust,
1.63%, 5/25/37 (a)(b)		100		93
GSAA Home Equity Trust,
6.00%, 11/25/36		32		20
GSAMP Trust,
0.85%, 3/25/46 (a)		100		80
Lehman ABS Manufactured Housing Contract Trust,
3.70%, 4/15/40		21		21
Nationstar Home Equity Loan Trust,
0.78%, 4/25/37 (a)		100		94
Ownit Mortgage Loan Trust,
0.80%, 3/25/37 (a)		61		50
RAMP Trust,
0.85%, 11/25/35 (a)		63		53
RMAT LLC,
4.83%, 6/25/35 (b)		62		61
Truman Capital Mortgage Loan Trust,
2.23%, 1/25/34 (a)(b)		70		69
3.30%, 11/25/31 (a)(b)		63		62
VOLT XXXIII LLC,
4.25%, 3/25/55 (b)		99		96
				1,267
Collateralized Mortgage Obligation — Agency Collateral Series (0.2%)
Government National Mortgage Association, IO
0.80%, 8/20/58 (a)		555		18
Commercial Mortgage-Backed Securities (4.0%)
COMM Mortgage Trust,
2.87%, 2/10/48 (b)		100		78
GS Mortgage Securities Trust,
4.47%, 2/10/48 (a)(b)		100		79
HILT Mortgage Trust,
4.27%, 7/15/29 (a)(b)		100		95

	Face Amount (000)		Value (000)
JPMBB Commercial Mortgage Securities Trust,
3.98%, 2/15/48 (a)(b)	$	100	$	76
Wells Fargo Commercial Mortgage Trust,
4.24%, 5/15/48 (a)		75		62
				390
Corporate Bonds (37.1%)
Finance (16.1%)
ABN Amro Bank N.V,
6.38%, 4/27/21	EUR	100		138
Ally Financial, Inc.,
4.13%, 3/30/20	$	25		26
Assicurazioni Generali SpA,
7.75%, 12/12/42 (a)	EUR	100		132
Bank of America Corp.,
MTN
4.25%, 10/22/26	$	50		53
BNP Paribas SA,
4.38%, 5/12/26 (b)		200		207
BPCE SA,
5.15%, 7/21/24 (b)		200		211
Citigroup, Inc.,
5.50%, 9/13/25		75		86
Cooperatieve Rabobank UA,
2.50%, 5/26/26 (a)	EUR	100		118
Discover Financial Services,
3.95%, 11/6/24	$	25		26
Goldman Sachs Group, Inc. (The),
0.45%, 10/29/19 (a)	EUR	100		113
Kennedy-Wilson, Inc.,
5.88%, 4/1/24	$	25		25
Lloyds Bank PLC,
6.50%, 3/24/20	EUR	50		66
Muenchener Rueckversicherungs-Gesellschaft AG in Muenchen,
6.00%, 5/26/41 (a)		100		134
Nationwide Building Society,
4.13%, 3/20/23 (a)		100		117
Vonovia Finance BV,
4.00%, 12/17/21 (a)(c)		100		119
				1,571
Industrials (19.4%)
Air Canada,
6.75%, 10/1/19 (b)	$	45		47
Akamai Technologies, Inc.,
0.00%, 2/15/19		50		49
Aramark Services, Inc.,
4.75%, 6/1/26 (b)		25		25
AT&T, Inc.,
4.50%, 3/9/48 (b)		31		31
Ball Corp.,
4.00%, 11/15/23		25		25
Bharti Airtel International Netherlands BV,
3.38%, 5/20/21	EUR	100		123

The accompanying notes are an integral part of the financial statements.
7

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Strategic Income Portfolio

	Face Amount (000)		Value (000)
Industrials (cont'd)
Carrizo Oil & Gas, Inc.,
6.25%, 4/15/23	$	15	$	15
Charter Communications Operating LLC/ Charter Communications Operating Capital,
4.91%, 7/23/25 (b)		50		55
Citrix Systems, Inc.,
0.50%, 4/15/19		50		57
Continental Airlines Pass-Through Certificates,
6.13%, 4/29/18		25		26
Crown Castle International Corp.,
5.25%, 1/15/23		25		28
CSC Holdings LLC,
5.25%, 6/1/24		25		24
Ctrip.com International Ltd.,
1.25%, 10/15/18		25		32
DISH DBS Corp.,
5.00%, 3/15/23		25		24
Dollar Tree, Inc.,
5.75%, 3/1/23		25		27
First Data Corp.,
5.38%, 8/15/23 (b)		25		26
General Motors Financial Co., Inc.,
4.30%, 7/13/25		50		52
Global Partners LP/GLP Finance Corp.,
7.00%, 6/15/23		25		23
Hanesbrands, Inc.,
4.63%, 5/15/24 (b)		9		9
4.88%, 5/15/26 (b)		16		16
Harland Clarke Holdings Corp.,
9.75%, 8/1/18 (b)		25		26
HCA, Inc.,
4.75%, 5/1/23		25		26
Hilcorp Energy I LP/Hilcorp Finance Co.,
5.75%, 10/1/25 (b)		15		15
KFC Holding Co/Pizza Hut Holdings LLC/Taco Bell of America LLC,
5.25%, 6/1/26 (b)		25		27
Lamar Media Corp.,
5.00%, 5/1/23		25		27
Lear Corp.,
5.25%, 1/15/25		50		54
Lundin Mining Corp.,
7.50%, 11/1/20 (b)		25		27
Mallinckrodt International Finance SA/Mallinckrodt CB LLC,
5.50%, 4/15/25 (b)		25		24
MasTec, Inc.,
4.88%, 3/15/23		25		25
MGM Resorts International,
6.00%, 3/15/23		25		27
Midcontinent Communications & Midcontinent Finance Corp.,
6.25%, 8/1/21 (b)		25		26

	Face Amount (000)		Value (000)
MPLX LP,
4.00%, 2/15/25	$	25	$	25
Netflix, Inc.,
5.50%, 2/15/22		25		27
ON Semiconductor Corp.,
Series B
2.63%, 12/15/26		50		60
OPE KAG Finance Sub, Inc.,
7.88%, 7/31/23 (b)		25		24
Outfront Media Capital LLC/Outfront Media Capital Corp.,
5.25%, 2/15/22		25		26
PetSmart, Inc.,
7.13%, 3/15/23 (b)		25		26
RR Donnelley & Sons Co.,
7.88%, 3/15/21		10		11
RSI Home Products, Inc.,
6.50%, 3/15/23 (b)		25		27
Sally Holdings LLC/Sally Capital, Inc.,
5.63%, 12/1/25		25		27
Shell International Finance BV,
1.38%, 9/12/19		50		50
Shire Acquisitions Investments Ireland DAC,
2.40%, 9/23/21		50		50
Standard Industries, Inc.,
5.38%, 11/15/24 (b)		50		52
Starwood Property Trust, Inc.,
4.55%, 3/1/18		50		55
Suburban Propane Partners LP/Suburban Energy Finance Corp.,
5.75%, 3/1/25		25		25
Tallgrass Energy Partners LP/Tallgrass Energy Finance Corp.,
5.50%, 9/15/24 (b)		25		25
Telefonica Europe BV,
5.88%, 3/31/24 (a)(c)	EUR	100		122
Tesla Motors, Inc.,
0.25%, 3/1/19	$	50		46
Teva Pharmaceutical Finance Netherlands III BV,
2.20%, 7/21/21		25		25
Toll Brothers Finance Corp.,
0.50%, 9/15/32		50		49
Tops Holding LLC/Tops Markets II Corp.,
8.00%, 6/15/22 (b)		25		23
Transurban Finance Co., Pty Ltd.,
3.38%, 3/22/27 (b)		25		25
Whole Foods Market, Inc.,
5.20%, 12/3/25 (b)		25		27
Wynn Las Vegas LLC/Wynn Las Vegas Capital Corp.,
5.50%, 3/1/25 (b)		25		25
Zachry Holdings, Inc.,
7.50%, 2/1/20 (b)		25		25
				1,895

The accompanying notes are an integral part of the financial statements.
8

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Strategic Income Portfolio

	Face Amount (000)		Value (000)
Utilities (1.6%)
AES Corp.,
4.88%, 5/15/23	$	75	$	76
Energy Transfer Partners LP,
2.50%, 6/15/18		75		76
				152
				3,618
Mortgages — Other (10.2%)
Alternative Loan Trust,
2.89%, 3/25/35 (a)		89		81
PAC
0.98%, 10/25/36 (a)		67		42
Banc of America Alternative Loan Trust,
0.98%, 11/25/36 (a)		57		35
5.71%, 10/25/36 (a)		103		65
Bear Stearns Structured Products, Inc. Trust,
2.97%, 1/26/36 (a)		36		29
Bear Stearns Trust,
2.69%, 2/25/36 (a)		54		46
2.95%, 4/25/35 (a)		53		39
3.38%, 3/25/36 (a)		109		83
Citigroup Mortgage Loan Trust,
2.91%, 6/25/36 (a)		42		34
First Horizon Mortgage Pass-Through Trust,
6.25%, 11/25/36		23		22
Grifonas Finance PLC,
0.09%, 8/28/39 (a)	EUR	49		42
GSR Mortgage Loan Trust,
3.37%, 12/25/34 (a)	$	93		90
HarborView Mortgage Loan Trust,
0.72%, 1/19/38 (a)		33		28
IndyMac INDX Mortgage Loan Trust,
2.86%, 12/25/34 (a)		50		47
JP Morgan Mortgage Trust,
2.96%, 6/25/37 (a)		43		38
Lehman Mortgage Trust,
6.00%, 7/25/36 - 6/25/37		144		106
Luminent Mortgage Trust,
0.76%, 5/25/37 (a)		111		86
Lusitano Mortgages No. 5 PLC,
0.00%, 7/15/59 (a)	EUR	51		46
MASTR Alternative Loan Trust,
6.25%, 7/25/36	$	46		40
				999
Sovereign (14.0%)
Brazil Notas do Tesouro Nacional, Series F,
10.00%, 1/1/21	BRL	960		282
Bundesrepublik Deutschland,
1.00%, 8/15/25	EUR	45		56
Cyprus Government International Bond,
3.88%, 5/6/22		40		47

	Face Amount (000)		Value (000)
Hungary Government Bond,
5.50%, 6/24/25	HUF	18,000	$	80
7.50%, 11/12/20		23,000		104
Hungary Government International Bond,
5.38%, 3/25/24	$	100		116
Indonesia Government International Bond,
5.88%, 1/15/24 (b)		200		236
New Zealand Government Bond,
4.50%, 4/15/27	NZD	70		62
Poland Government Bond,
2.50%, 7/25/26	PLN	670		169
Portugal Government International Bond,
5.13%, 10/15/24 (b)	$	50		50
Portugal Obrigacoes do Tesouro OT,
5.65%, 2/15/24 (b)	EUR	40		53
Select Medical Corp.,
6.38%, 6/1/21	$	50		50
South Africa Government Bond,
8.00%, 1/31/30	ZAR	50		3
United Kingdom Gilt,
2.00%, 9/7/25	GBP	40		58
				1,366
U.S. Treasury Securities (2.8%)
U.S. Treasury Bonds,
2.50%, 2/15/45	$	35		36
3.88%, 8/15/40		50		65
U.S. Treasury Inflation Indexed Bond,
0.25%, 1/15/25		173		176
				277
Total Fixed Income Securities (Cost $7,863)				7,935
	Shares
Short-Term Investments (17.9%)
Investment Company (17.7%)
Morgan Stanley Institutional Liquidity Funds — Government Portfolio — Institutional Class (See Note G) (Cost $1,725)		1,725,403		1,725
	Face Amount (000)
U.S. Treasury Security (0.2%)
U.S. Treasury Bill
0.41%, 3/23/17 (d) (Cost $15)	$	15		15
Total Short-Term Investments (Cost $1,740)				1,740
Total Investments (99.2%) (Cost $9,603) (e)(f)				9,675
Other Assets in Excess of Liabilities (0.8%)				79
Net Assets (100.0%)			$	9,754

The accompanying notes are an integral part of the financial statements.
9

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Strategic Income Portfolio

(a) Variable/Floating Rate Security — Interest rate changes on these instruments are based on changes in a designated base rate. The rates shown are those in effect on September 30, 2016.

(b) 144A security — Certain conditions for public sale may exist. Unless otherwise noted, these securities are deemed to be liquid.

(c) Perpetual — One or more securities do not have a predetermined maturity date. Rates for these securities are fixed for a period of time, after which they revert to a floating rate. Interest rates in effect are as of September 30, 2016.

(d) Rate shown is the yield to maturity at September 30, 2016.

(e) Securities are available for collateral in connection with open foreign currency forward exchange contracts, futures contracts and swap agreements.

(f) At September 30, 2016, the aggregate cost for federal income tax purposes is approximately $9,603,000. The aggregate gross unrealized appreciation is approximately $206,000 and the aggregate gross unrealized depreciation is approximately $134,000 resulting in net unrealized appreciation of approximately $72,000.

IO Interest Only.

MTN Medium Term Note.

PAC Planned Amortization Class.

Foreign Currency Forward Exchange Contracts:

The Portfolio had the following foreign currency forward exchange contracts open at September 30, 2016:

Counterparty	Contracts to Deliver (000)			In Exchange For (000)			Delivery Date	Unrealized Appreciation (Depreciation) (000)
Australia and New Zealand Banking Group	CAD	67		$	52		10/5/16	$	1
Australia and New Zealand Banking Group	EUR	88		NZD	135		10/5/16		(—	@)
Australia and New Zealand Banking Group	JPY	2,448		$	24		10/5/16		—	@
Australia and New Zealand Banking Group	NZD	135		EUR	87		10/5/16		(1	)
Australia and New Zealand Banking Group	NZD	54		$	39		10/5/16		—	@
Australia and New Zealand Banking Group	PLN	333		$	87		10/5/16		—	@
Australia and New Zealand Banking Group	$	—	@	AUD	—	@	10/5/16		—	@
Australia and New Zealand Banking Group	$	29		BRL	97		10/5/16		—	@
Australia and New Zealand Banking Group	$	72		BRL	235		10/5/16		(—	@)
Australia and New Zealand Banking Group	$	235		BRL	767		10/5/16		1
Australia and New Zealand Banking Group	$	69		EUR	62		10/5/16		—	@
Australia and New Zealand Banking Group	$	39		NZD	54		10/5/16		—	@
Australia and New Zealand Banking Group	ZAR	1,644		$	115		10/5/16		(5	)
Barclays Bank PLC	$	116		PLN	449		10/5/16		1
Citibank NA	NOK	405		EUR	45		10/5/16		(—	@)
Citibank NA	NOK	413		$	52		10/5/16		—	@
Citibank NA	$	51		CAD	66		10/5/16		(—	@)
Citibank NA	$	1,308		EUR	1,164		10/5/16		(—	@)
HSBC Bank PLC	GBP	83		$	109		10/5/16		2
HSBC Bank PLC	JPY	32		$	—	@	10/5/16		(—	@)
HSBC Bank PLC	$	—	@	CAD	1		10/5/16		(—	@)
HSBC Bank PLC	$	108		GBP	83		10/5/16		(—	@)
HSBC Bank PLC	$	56		ZAR	817		10/5/16		3
JPMorgan Chase Bank NA	EUR	44		NOK	405		10/5/16		2
JPMorgan Chase Bank NA	HUF	54,756		$	199		10/5/16		(1	)
JPMorgan Chase Bank NA	$	65		EUR	58		10/5/16		—	@
JPMorgan Chase Bank NA	$	54		MXN	1,039		10/5/16		(1	)
JPMorgan Chase Bank NA	$	50		NOK	413		10/5/16		2
JPMorgan Chase Bank NA	$	150		PLN	575		10/5/16		—	@
JPMorgan Chase Bank NA	$	62		ZAR	890		10/5/16		3
JPMorgan Chase Bank NA	ZAR	64		$	5		10/5/16		(—	@)
UBS AG	AUD	—	@	$	—	@	10/5/16		(—	@)
UBS AG	BRL	1,099		$	337		10/5/16		(1	)
UBS AG	CAD	59		MXN	850		10/5/16		(1	)
UBS AG	EUR	1,284		$	1,445		10/5/16		2
UBS AG	HUF	17,164		$	63		10/5/16		1
UBS AG	JPY	2,358		MXN	450		10/5/16		(—	@)
UBS AG	MXN	850		CAD	58		10/5/16		—	@
UBS AG	MXN	450		JPY	2,454		10/5/16		1
UBS AG	MXN	1,621		$	87		10/5/16		4
UBS AG	PLN	108		$	28		10/5/16		(—	@)
UBS AG	PLN	582		$	151		10/5/16		(1	)
UBS AG	$	79		HUF	21,707		10/5/16		1
UBS AG	$	183		HUF	50,212		10/5/16		—	@
UBS AG	$	25		JPY	2,480		10/5/16		(—	@)

The accompanying notes are an integral part of the financial statements.
10

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Strategic Income Portfolio

Foreign Currency Forward Exchange Contracts (cont'd):

Counterparty	Contracts to Deliver (000)			In Exchange For (000)			Delivery Date	Unrealized Appreciation (Depreciation) (000)
UBS AG	$	30		MXN	582		10/5/16	$	(—	@)
Australia and New Zealand Banking Group	AUD	—	@	$	—	@	11/4/16		—	@
Australia and New Zealand Banking Group	BRL	767		$	233		11/4/16		(1	)
Australia and New Zealand Banking Group	NZD	135		EUR	87		11/4/16		—	@
Australia and New Zealand Banking Group	$	39		NZD	54		11/4/16		(—	@)
Citibank NA	CAD	57		$	43		11/4/16		—	@
Citibank NA	CAD	66		$	51		11/4/16		—	@
Citibank NA	EUR	45		NOK	405		11/4/16		—	@
Citibank NA	EUR	321		$	361		11/4/16		(—	@)
Citibank NA	EUR	1,164		$	1,310		11/4/16		—	@
Citibank NA	JPY	2,349		MXN	450		11/4/16		(—	@)
Citibank NA	MXN	850		CAD	57		11/4/16		—	@
Citibank NA	$	23		JPY	2,357		11/4/16		(—	@)
Citibank NA	$	30		MXN	582		11/4/16		(—	@)
Citibank NA	$	52		NOK	413		11/4/16		(—	@)
HSBC Bank PLC	GBP	83		$	108		11/4/16		—	@
JPMorgan Chase Bank NA	PLN	575		$	150		11/4/16		(—	@)
JPMorgan Chase Bank NA	$	5		ZAR	64		11/4/16		—	@
UBS AG	CAD	57		MXN	850		11/4/16		(—	@)
UBS AG	HUF	50,212		$	183		11/4/16		(—	@)
UBS AG	JPY	2,480		$	25		11/4/16		—	@
UBS AG	MXN	450		JPY	2,346		11/4/16		—	@
UBS AG	MXN	582		$	30		11/4/16		—	@
								$	12

Futures Contracts:

The Portfolio had the following futures contracts open at September 30, 2016:

	Number of Contracts		Value (000)			Expiration Date	Unrealized Appreciation (Depreciation) (000)
Short:
German Euro BOBL (Germany)		4	$	(593	)	Dec-16	$	(1	)
German Euro Bund (Germany)		5		(931	)	Dec-16		(5	)
U.S. Treasury 10 yr. Note (United States)		8		(1,049	)	Dec-16		1
U.S. Treasury 10 yr. Ultra Long Bond (United States)		8		(1,153	)	Dec-16		3
U.S. Treasury 2 yr. Note (United States)		1		(218	)	Dec-16		(—	@)
U.S. Treasury 5 yr. Note (United States)		5		(608	)	Dec-16		(—	@)
U.S. Treasury Ultra Bond (United States)		1		(184	)	Dec-16		3
							$	1

Credit Default Swap Agreements:

The Portfolio had the following credit default swap agreements open at September 30, 2016:

Swap Counterparty and Reference Obligation	Buy/Sell Protection	Notional Amount (000)		Pay/Receive Fixed Rate			Termination Date	Upfront Payment Paid (Received) (000)			Unrealized Depreciation (000)			Value (000)			Credit Rating of Reference Obligation† (Unaudited)
Deutsche Bank AG CMBX.NA.BB.60	Sell	$	28		5.00	%	5/11/63	$	(—	@)	$	(5	)	$	(5	)	NR
Goldman Sachs International CMBX.NA.BB.60	Sell		20		5.00		5/11/63		(—	@)		(4	)		(4	)	NR
Goldman Sachs International CMBX.NA.BBB.60	Sell		200		3.00		5/11/63		(13	)		(5	)		(18	)	NR
Goldman Sachs International CMBX.NA.BBB.60	Sell		109		3.00		5/11/63		(5	)		(5	)		(10	)	NR

The accompanying notes are an integral part of the financial statements.
11

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Strategic Income Portfolio

Credit Default Swap Agreements (cont'd):

Swap Counterparty and Reference Obligation	Buy/Sell Protection	Notional Amount (000)		Pay/Receive Fixed Rate			Termination Date	Upfront Payment Paid (Received) (000)			Unrealized Depreciation (000)			Value (000)			Credit Rating of Reference Obligation† (Unaudited)
Goldman Sachs International CMBX.NA.BBB.60	Sell	$	27		3.00	%	5/11/63	$	(1	)	$	(1	)	$	(2	)	NR
Goldman Sachs International CMBX.NA.BBB.60	Sell		64		3.00		5/11/63		(2	)		(3	)		(5	)	NR
Morgan Stanley & Co., LLC* CDX.NA.HY.26	Buy		200		5.00		6/20/21		(9	)		(1	)		(10	)	NR
		$	648					$	(30	)	$	(24	)	$	(54	)

@ Value is less than $500.

† Credit rating as issued by Standard & Poor's.

* Cleared swap agreement, the broker is Morgan Stanley & Co., LLC.

NR Not Rated.

AUD — Australian Dollar

BRL — Brazilian Real

CAD — Canadian Dollar

EUR — Euro

GBP — British Pound

HUF — Hungarian Forint

JPY — Japanese Yen

MXN — Mexican Peso

NOK — Norwegian Krone

NZD — New Zealand Dollar

PLN — Polish Zloty

USD — United States Dollar

ZAR — South African Rand

Portfolio Composition

Classification	Percentage of Total Investments
Industrials		19.6	%
Short-Term Investments		18.0
Finance		16.2
Sovereign		14.1
Asset-Backed Securities		13.1
Mortgages — Other		10.3
Other**		8.7
Total Investments		100.0	%***

** Industries and/or investment types representing less than 5% of total investments.

*** Does not include open short futures contracts with an underlying face amount of approximately $4,736,000 with net unrealized appreciation of approximately $1,000. Does not include open foreign currency forward exchange contracts with net unrealized appreciation of approximately $12,000 and does not include open swap agreements with total unrealized depreciation of approximately $24,000.

The accompanying notes are an integral part of the financial statements.
12

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Strategic Income Portfolio

Statement of Assets and Liabilities	September 30, 2016 (000)
Assets:
Investments in Securities of Unaffiliated Issuers, at Value (Cost $7,878)	$	7,950
Investment in Security of Affiliated Issuer, at Value (Cost $1,725)		1,725
Total Investments in Securities, at Value (Cost $9,603)		9,675
Foreign Currency, at Value (Cost $1)		—	@
Receivable for Investments Sold		222
Interest Receivable		83
Receivable for Variation Margin on Futures Contracts		69
Due from Adviser		28
Unrealized Appreciation on Foreign Currency Forward Exchange Contracts		24
Tax Reclaim Receivable		1
Receivable from Affiliate		—	@
Other Assets		22
Total Assets		10,124
Liabilities:
Payable for Investments Purchased		268
Unrealized Depreciation on Swap Agreements		23
Premium Received on Open Swap Agreements		21
Payable for Professional Fees		17
Unrealized Depreciation on Foreign Currency Forward Exchange Contracts		12
Payable for Custodian Fees		9
Payable for Transfer Agency Fees — Class I		1
Payable for Transfer Agency Fees — Class A		1
Payable for Transfer Agency Fees — Class C		1
Payable for Transfer Agency Fees — Class IS		1
Payable for Administration Fees		1
Payable for Variation Margin on Swap Agreements		1
Payable for Sub Transfer Agency Fees — Class A		—	@
Other Liabilities		14
Total Liabilities		370
Net Assets	$	9,754
Net Assets Consist Of:
Paid-in-Capital	$	10,056
Accumulated Net Investment Loss		(29	)
Accumulated Net Realized Loss		(332	)
Unrealized Appreciation (Depreciation) on:
Investments		72
Futures Contracts		1
Swap Agreements		(24	)
Foreign Currency Forward Exchange Contracts		12
Foreign Currency Translations		(2	)
Net Assets	$	9,754

The accompanying notes are an integral part of the financial statements.
13

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Strategic Income Portfolio

Statement of Assets and Liabilities (cont'd)	September 30, 2016 (000)
CLASS I:
Net Assets	$	10
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		1,000
Net Asset Value, Offering and Redemption Price Per Share	$	9.69
CLASS A:
Net Assets	$	40
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		4,102
Net Asset Value, Redemption Price Per Share	$	9.69
Maximum Sales Load		4.25	%
Maximum Sales Charge	$	0.43
Maximum Offering Price Per Share	$	10.12
CLASS C:
Net Assets	$	35
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		3,622
Net Asset Value, Offering and Redemption Price Per Share	$	9.66
CLASS IS:
Net Assets	$	9,669
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		998,000
Net Asset Value, Offering and Redemption Price Per Share	$	9.69

@ Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
14

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Strategic Income Portfolio

Statement of Operations	Year Ended September 30, 2016 (000)
Investment Income:
Interest from Securities of Unaffiliated Issuers	$	309
Dividends from Security of Affiliated Issuer (Note G)		3
Total Investment Income		312
Expenses:
Professional Fees		113
Registration Fees		47
Offering Costs		42
Advisory Fees (Note B)		38
Custodian Fees (Note F)		30
Pricing Fees		23
Shareholder Reporting Fees		8
Administration Fees (Note C)		8
Transfer Agency Fees — Class I (Note E)		—	@
Transfer Agency Fees — Class A (Note E)		—	@
Transfer Agency Fees — Class C (Note E)		2
Transfer Agency Fees — Class IS (Note E)		—	@
Trustees' Fees and Expenses		2
Shareholder Services Fees — Class A (Note D)		—	@
Distribution and Shareholder Services Fees — Class C (Note D)		—	@
Other Expenses		22
Total Expenses		335
Expenses Reimbursed by Adviser (Note B)		(180	)
Waiver of Advisory Fees (Note B)		(38	)
Reimbursement of Class Specific Expenses — Class I (Note B)		(—	@)
Reimbursement of Class Specific Expenses — Class A (Note B)		(—	@)
Reimbursement of Class Specific Expenses — Class C (Note B)		(2	)
Reimbursement of Class Specific Expenses — Class IS (Note B)		(—	@)
Rebate from Morgan Stanley Affiliate (Note G)		(1	)
Reimbursement of Custodian Fees (Note F)		(22	)
Net Expenses		92
Net Investment Income		220
Realized Gain (Loss):
Investments Sold		44
Foreign Currency Forward Exchange Contracts		(55	)
Foreign Currency Transactions		1
Futures Contracts		(279	)
Swap Agreements		2
Net Realized Loss		(287	)
Change in Unrealized Appreciation (Depreciation):
Investments		304
Foreign Currency Forward Exchange Contracts		(10	)
Foreign Currency Translations		(1	)
Futures Contracts		69
Swap Agreements		(22	)
Net Change in Unrealized Appreciation (Depreciation)		340
Net Realized Loss and Change in Unrealized Appreciation (Depreciation)		53
Net Increase in Net Assets Resulting from Operations	$	273

@ Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
15

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Strategic Income Portfolio

Statements of Changes in Net Assets	Year Ended September 30, 2016 (000)			Period from December 30, 2014^ to September 30, 2015 (000)
Increase (Decrease) in Net Assets:
Operations:
Net Investment Income	$	220		$	140
Net Realized Gain (Loss)		(287	)		11
Net Change in Unrealized Appreciation (Depreciation)		340			(281	)
Net Increase (Decrease) in Net Assets Resulting from Operations		273			(130	)
Distributions from and/or in Excess of:
Class I:
Net Investment Income		(—	@)		(—	@)
Class A:
Net Investment Income		(—	@)		(—	@)
Class C:
Net Investment Income		(—	@)		(—	@)*
Class IS:
Net Investment Income		(379	)		(75	)
Total Distributions		(379	)		(75	)
Capital Share Transactions:⁽¹⁾
Class I:
Subscribed		—			10
Class A:
Subscribed		37			10
Redeemed		(7	)		—
Class C:
Subscribed		25			10	*
Class IS:
Subscribed		—			9,980
Net Increase in Net Assets Resulting from Capital Share Transactions		55			10,010
Total Increase (Decrease) in Net Assets		(51	)		9,805
Net Assets:
Beginning of Period		9,805			—
End of Period (Including Accumulated Net Investment Loss and Accumulated Undistributed Net Investment Income of $(29) and $167, respectively)	$	9,754		$	9,805
(1) Capital Share Transactions:
Class I:
Shares Subscribed		—			1
Class A:
Shares Subscribed		4			1
Shares Redeemed		(1	)		—
Net Increase in Class A Shares Outstanding		3			1
Class C:
Shares Subscribed		3			1	*
Class IS:
Shares Subscribed		—			998

^ Commencement of Operations.

* For the period April 30, 2015 through September 30, 2015.

@ Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
16

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Strategic Income Portfolio

	Class I
Selected Per Share Data and Ratios	Year Ended September 30, 2016††			Period from December 30, 2014^ to September 30, 2015
Net Asset Value, Beginning of Period	$	9.79		$	10.00
Income (Loss) from Investment Operations:
Net Investment Income†		0.22			0.14
Net Realized and Unrealized Gain (Loss)		0.06			(0.28	)
Total from Investment Operations		0.28			(0.14	)
Distributions from and/or in Excess of:
Net Investment Income		(0.38	)		(0.07	)
Net Asset Value, End of Period	$	9.69		$	9.79
Total Return++		2.91	%		(1.39	)%#
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	10		$	10
Ratio of Expenses to Average Net Assets ⁽¹⁾		0.99	%+		0.98	%+*
Ratio of Net Investment Income to Average Net Assets ⁽¹⁾		2.25	%+		1.81	%+*
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.01	%		0.02	%*
Portfolio Turnover Rate		47	%		39	%#
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		7.28	%		17.80	%*
Net Investment Loss to Average Net Assets		(4.04	)%		(15.01	)%*

^ Commencement of Operations.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value as of the last business day of the period.

# Not Annualized.

* Annualized.

The accompanying notes are an integral part of the financial statements.
17

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Strategic Income Portfolio

	Class A
Selected Per Share Data and Ratios	Year Ended September 30, 2016††			Period from December 30, 2014^ to September 30, 2015
Net Asset Value, Beginning of Period	$	9.79		$	10.00
Income (Loss) from Investment Operations:
Net Investment Income†		0.18			0.11
Net Realized and Unrealized Gain (Loss)		0.06			(0.27	)
Total from Investment Operations		0.24			(0.16	)
Distributions from and/or in Excess of:
Net Investment Income		(0.34	)		(0.05	)
Net Asset Value, End of Period	$	9.69		$	9.79
Total Return++		2.51	%		(1.56	)%#
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	40		$	10
Ratio of Expenses to Average Net Assets ⁽¹⁾		1.34	%+		1.33	%+*
Ratio of Net Investment Income to Average Net Assets ⁽¹⁾		1.86	%+		1.46	%+*
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.01	%		0.02	%
Portfolio Turnover Rate		47	%		39	%#
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		6.73	%		18.06	%*
Net Investment Loss to Average Net Assets		(3.53	)%		(15.27	)%*

†† Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class A shares. The Ratio of Expenses to Average Net Assets and the Ratio of Net Investment Income to Average Net Assets would be unchanged as the change to current period custodian fees was offset against current period expense waivers/reimbursements with no impact to net expenses or net investment income.

^ Commencement of Operations.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

# Not Annualized.

* Annualized.

The accompanying notes are an integral part of the financial statements.
18

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Strategic Income Portfolio

	Class C
Selected Per Share Data and Ratios	Year Ended September 30, 2016††			Period from April 30, 2015^ to September 30, 2015
Net Asset Value, Beginning of Period	$	9.76		$	10.06
Income (Loss) from Investment Operations:
Net Investment Income†		0.11			0.05
Net Realized and Unrealized Gain (Loss)		0.06			(0.32	)
Total from Investment Operations		0.17			(0.27	)
Distributions from and/or in Excess of:
Net Investment Income		(0.27	)		(0.03	)
Net Asset Value, End of Period	$	9.66		$	9.76
Total Return++		1.77	%		(2.71	)%#
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	35		$	10
Ratio of Expenses to Average Net Assets ⁽¹⁾		2.09	%+		2.10	%+*
Ratio of Net Investment Income to Average Net Assets ⁽¹⁾		1.14	%+		1.13	%+*
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.01	%		0.00	%§*
Portfolio Turnover Rate		47	%		39	%#
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		28.93	%		19.28	%*
Net Investment Loss to Average Net Assets		(25.70	)%		(16.05	)%*

†† Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class C shares. The Ratio of Expenses to Average Net Assets and the Ratio of Net Investment Income to Average Net Assets would be unchanged as the change to current period custodian fees was offset against current period expense waivers/reimbursements with no impact to net expenses or net investment income.

^ Commencement of Offering.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value which does not reflect sales charges, if applicable, as of the last business day of the period.

§ Amount is less than 0.005%.

# Not Annualized.

* Annualized.

The accompanying notes are an integral part of the financial statements.
19

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Strategic Income Portfolio

	Class IS
Selected Per Share Data and Ratios	Year Ended September 30, 2016††			Period from December 30, 2014^ to September 30, 2015
Net Asset Value, Beginning of Period	$	9.79		$	10.00
Income (Loss) from Investment Operations:
Net Investment Income†		0.23			0.14
Net Realized and Unrealized Gain (Loss)		0.05			(0.27	)
Total from Investment Operations		0.28			(0.13	)
Distributions from and/or in Excess of:
Net Investment Income		(0.38	)		(0.08	)
Net Asset Value, End of Period	$	9.69		$	9.79
Total Return++		2.96	%		(1.37	)%#
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	9,669		$	9,775
Ratio of Expenses to Average Net Assets ⁽¹⁾		0.94	%+		0.93	%+*
Ratio of Net Investment Income to Average Net Assets ⁽¹⁾		2.35	%+		1.88	%+*
Ratio of Rebate from Morgan Stanley Affiliates to Average Net Assets		0.01	%		0.02	%*
Portfolio Turnover Rate		47	%		39	%#
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		3.45	%		4.04	%*
Net Investment Loss to Average Net Assets		(0.16	)%		(1.23	)%*

†† Refer to Note F in the Notes to Financial Statements for discussion of prior period custodian out-of-pocket expenses that were reimbursed in the current period. The amount of the reimbursement was immaterial on a per share basis and did not impact the total return of Class IS shares. The Ratio of Expenses to Average Net Assets and the Ratio of Net Investment Income to Average Net Assets would be unchanged as the change to current period custodian fees was offset against current period expense waivers/reimbursements with no impact to net expenses or net investment income.

^ Commencement of Operations.

† Per share amount is based on average shares outstanding.

++ Calculated based on the net asset value as of the last business day of the period.

# Not Annualized.

* Annualized.

The accompanying notes are an integral part of the financial statements.
20

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements

The accompanying financial statements relate to the Strategic Income Portfolio. The Portfolio seeks a total return comprised of income and capital appreciation. The Portfolio offers four classes of shares — Class I, Class A, Class C and Class IS.

reported bid and asked prices are not reflective of a security's market value, portfolio securities are valued at their fair value as determined in good faith under procedures established by and under the general supervision of the Trustees. Occasionally, developments affecting the closing prices of securities and other assets may occur between the times at which valuations of such securities are determined (that is, close of the foreign market on which the securities trade) and the close of business of the New York Stock Exchange ("NYSE"). If developments occur during such periods that are expected to materially affect the value of such securities, such valuations may be adjusted to reflect the estimated fair value of such securities as of the close of the NYSE, as determined in good faith by the Trustees or by the Adviser using a pricing service and/or procedures approved by the Trustees; (5) quotations of foreign portfolio securities, other assets and liabilities and forward contracts stated in foreign currency are translated into U.S. dollar equivalents at the prevailing market rates prior to the close of the NYSE; and (6) investments in mutual funds, including the Morgan Stanley Institutional Liquidity Funds, are valued at the net asset value ("NAV") as of the close of each business day.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

• Level 1 – unadjusted quoted prices in active markets for identical investments

• Level 2 – other significant observable inputs (including quoted prices for similar investments,

interest rates, prepayment speeds, credit risk, etc.)

The following is a summary of the inputs used to value the Portfolio's investments as of September 30, 2016.

Investment Type	Level 1 Unadjusted quoted prices (000)		Level 2 Other significant observable inputs (000)		Level 3 Significant unobservable inputs (000)		Total (000)
Assets:
Fixed Income Securities
Asset-Backed Securities	$	—	$	1,267	$	—	$	1,267
Collateralized Mortgage Obligation — Agency Collateral Series		—		18		—		18
Commercial Mortgage-Backed Securities		—		390		—		390
Corporate Bonds		—		3,618		—		3,618
Mortgages — Other		—		999		—		999
Sovereign		—		1,366		—		1,366
U.S. Treasury Securities		—		277		—		277
Total Fixed Income Securities		—		7,935		—		7,935
Short-Term Investments
Investment Company		1,725		—		—		1,725
U.S. Treasury Security		—		15		—		15
Total Short-Term Investments		1,725		15		—		1,740
Foreign Currency Forward Exchange Contracts		—		24		—		24
Futures Contracts		7		—		—		7
Total Assets		1,732		7,974		—		9,706

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

Investment Type	Level 1 Unadjusted quoted prices (000)			Level 2 Other significant observable inputs (000)			Level 3 Significant unobservable inputs (000)		Total (000)
Liabilities:
Foreign Currency Forward Exchange Contracts	$	—		$	(12	)	$	—	$	(12	)
Futures Contracts		(6	)		—			—		(6	)
Credit Default Swap Agreements		—			(24	)		—		(24	)
Total Liabilities		(6	)		(36	)		—		(42	)
Total	$	1,726		$	7,938		$	—	$	9,664

– investments, other assets and liabilities at the prevailing rate of exchange on the valuation date;

– investment transactions and investment income at the prevailing rates of exchange on the dates of such transactions.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

A derivative instrument often has risks similar to its underlying asset and may have additional risks, including imperfect correlation between the value of the derivative and the underlying asset, risks of default by the counterparty to certain transactions, magnification of losses incurred due to changes in the market value of the securities, instruments, indices or interest rates to which the derivative instrument relates, risks that the transactions may not be liquid and risks arising from margin requirements. The use of derivatives involves risks that are different from, and possibly greater than, the risks associated with other portfolio investments. Derivatives may involve the use of highly specialized instruments that require investment techniques and risk analyses different from those associated with other portfolio investments. All of the Portfolio's holdings, including derivative instruments, are marked-to-market each day with the change in value reflected in unrealized appreciation (depreciation). Upon disposition, a realized gain or loss is recognized.

Certain derivative transactions may give rise to a form of leverage. Leverage magnifies the potential for gain and the risk of loss. Leverage associated with derivative transactions may cause the Portfolio to liquidate portfolio positions when it may not be advantageous to do so to satisfy its obligations or to meet earmarking or segregation requirements, pursuant to applicable Securities and Exchange Commission rules and regulations, or may cause the Portfolio to be more volatile than if the Portfolio had not been leveraged. Although the Adviser and/or Sub-Adviser seek to use derivatives to further the Portfolio's investment objectives, there is no assurance that the use of derivatives will achieve this result.

Following is a description of the derivative instruments and techniques that the Portfolio used during the period and their associated risks:

received from or made to the broker based upon changes in the value of the contract (the variation margin). A decision as to whether, when and how to use futures contracts involves the exercise of skill and judgment and even a well-conceived futures transaction may be unsuccessful because of market behavior or unexpected events. In addition to the derivatives risks discussed above, the prices of futures contracts can be highly volatile, using futures contracts can lower total return, and the potential loss from futures contracts can exceed the Portfolio's initial investment in such contracts. No assurance can be given that a liquid market will exist for any particular futures contract at any particular time. There is also the risk of loss by the Portfolio of margin deposits in the event of bankruptcy of a broker with which the Portfolio has open positions in the futures contract.

Swaps: The Portfolio may enter into over-the-counter ("OTC") swap contracts or cleared swap transactions. A swap contract is an agreement between two parties pursuant to which the parties exchange payments at specified dates on the basis of a specified notional amount, with the payments calculated by reference to specified securities, indices, reference rates, currencies or other instruments. Typically swap agreements provide that when the period payment dates for both parties are the same, the payments are made on a net basis (i.e., the two payment streams are netted out, with only the net amount paid by one party to the other). The Portfolio's obligations or rights under a swap contract entered into on a net basis will generally be equal only to the net amount to be paid or received under the agreement, based on the relative values of the positions held by each party. Cleared swap transactions may help reduce counterparty credit risk. In a cleared swap, the Portfolio's ultimate counterparty is a clearinghouse rather than a swap dealer, bank or other financial institution. OTC swap agreements are not entered into or traded on exchanges and often there is no central clearing or guaranty function for OTC swaps. These OTC swaps are often subject to credit risk or the risk of default or non-performance by the counterparty. Both OTC and cleared swaps could result in losses if interest rates, foreign currency exchange rates or other factors are not correctly anticipated by the Portfolio or if the reference index, security or investments do not perform as expected. During the period swap agreements are open,

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

payments are received from or made to the clearinghouse or counterparty based upon changes in the value of the contract (variation margin). The Dodd-Frank Wall Street Reform and Consumer Protection Act and related regulatory developments require the clearing and exchange-trading of certain standardized swap transactions. Mandatory exchange-trading and clearing is occurring on a phased-in basis.

Upfront payments paid or received by the Portfolio will be reflected as an asset or liability, respectively, in the Statement of Assets and Liabilities.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

agreement between the contracting parties to exchange a specified amount of currency at a specified future time at a specified rate. The rate can be higher or lower than the spot rate between the currencies that are the subject of the contract. Currency contracts may be used to protect against uncertainty in the level of future foreign currency exchange rates or to gain or modify exposure to a particular currency. In addition, the Portfolio may use cross currency hedging or proxy hedging with respect to currencies in which the Portfolio has or expects to have portfolio or currency exposure. Cross currency hedges involve the sale of one currency against the positive exposure to a different currency and may be used for hedging purposes or to establish an active exposure to the exchange rate between any two currencies. To the extent hedged by the use of currency contracts, the precise matching of the currency contract amounts and the value of the securities involved will not generally be possible because the future value of such securities in foreign currencies will change as a consequence of market movements in the value of those securities between the date on which the contract is entered into and the date it matures. Furthermore, such transactions may reduce or preclude the opportunity for gain if the value of the currency should move in the direction opposite to the position taken. There is additional risk to the extent that currency contracts create exposure to currencies in which the Portfolio's securities are not denominated. Unanticipated changes in currency prices may result in poorer overall performance for the Portfolio than if it had not entered into such contracts. The use of currency contracts involves the risk of loss from the insolvency or bankruptcy of the counterparty to the contract or the failure of the counterparty to make payments or otherwise comply with the terms of the contract. A currency contract is marked-to-market daily and the change in market value is recorded by the Portfolio as unrealized gain or loss. The Portfolio records realized gains (losses) when the currency contract is closed equal to the difference between the value of the currency contract at the time it was opened and the value at the time it was closed.

Portfolio uses derivative instruments, how these derivative instruments are accounted for and their effects on the Portfolio's financial position and results of operations.

The following tables set forth the fair value of the Portfolio's derivative contracts by primary risk exposure as of September 30, 2016.

Asset Derivatives
Statement of Assets and
Liabilities Location

Primary Risk
Exposure

Value
(000)

Foreign Currency
Forward Exchange
Contracts

Unrealized Appreciation on
Foreign Currency Forward
Exchange Contracts

Currency Risk

Futures Contracts

Variation Margin on
Futures Contracts

Interest Rate Risk

(a)

Total

Liability Derivatives
Statement of Assets and
Liabilities Location

Primary Risk
Exposure

Value
(000)

Foreign Currency
Forward Exchange
Contracts

Unrealized Depreciation on
Foreign Currency Forward
Exchange Contracts

Currency Risk

$(12)

Futures Contracts

Variation Margin on
Futures Contracts

Interest Rate Risk

(6)(a)

Swap Agreements

Unrealized Depreciation on
Swap Agreements

Credit Risk

(23)

Swap Agreement

Variation Margin on
Swap Agreement

Credit Risk

(1)(a)

Total

(42

)

Realized Gain (Loss)
Primary Risk Exposure	Derivative Type	Value (000)
Currency Risk	Foreign Currency Forward Exchange Contracts	$	(55	)
Interest Rate Risk	Futures Contracts		(279	)
Credit Risk	Swap Agreements		2
	Total	$	(332	)
Change in Unrealized Appreciation (Depreciation)
Primary Risk Exposure	Derivative Type	Value (000)
Currency Risk	Foreign Currency Forward Exchange Contracts	$	(10	)
Interest Rate Risk	Futures Contracts		69
Credit Risk	Swap Agreements		(22	)
	Total	$	37

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

At September 30, 2016, the Portfolio's derivative assets and liabilities are as follows:

Gross Amounts of Assets and Liabilities Presented in the Statement of Assets and Liabilities
Derivatives(b)	Assets(c) (000)		Liabilities(c) (000)
Foreign Currency Forward Exchange Contracts	$	24	$	(12	)
Swap Agreements		—		(23	)
Total	$	24	$	(35	)

(b) Excludes exchange traded derivatives.

(c) Absent an event of default or early termination, OTC derivative assets and liabilities are presented gross and not offset in the Statement of Assets and Liabilities.

The following tables present derivative financial instruments that are subject to enforceable netting arrangements as of September 30, 2016.

Gross Amounts Not Offset in the Statement of Assets and Liabilities
Counterparty	Gross Asset Derivatives Presented in Statement of Assets and Liabilities (000)			Financial Instrument (000)			Collateral Received(d) (000)		Net Amount (not less than $0) (000)
Australia and New Zealand Banking Group	$	2		$	(2	)	$	—	$	0
Barclays Bank PLC		1			—			—		1
Citibank NA		—	@		(—	@)		—		0
HSBC Bank PLC		5			(—	@)		—		5
JPMorgan Chase Bank NA		7			(2	)		—		5
UBS AG		9			(3	)		—		6
Total	$	24		$	(7	)	$	—	$	17

@ Amount is less than $500.

Gross Amounts Not Offset in the Statement of Assets and Liabilities
Counterparty	Gross Liability Derivatives Presented in Statement of Assets and Liabilities (000)			Financial Instrument (000)			Collateral Pledged (000)		Net Amount (not less than $0) (000)
Australia and New Zealand Banking Group	$	7		$	(2	)	$	—	$	5
Citibank NA		—	@		(—	@)		—		0
Deutsche Bank AG		5			—			—		5
Goldman Sachs International		18			—			—		18
HSBC Bank PLC		—	@		(—	@)		—		0
JPMorgan Chase Bank NA		2			(2	)		—		0
UBS AG		3			(3	)		—		0
Total	$	35		$	(7	)	$	—	$	28

@ Amount is less than $500.

For the year ended September 30, 2016, the approximate average monthly amount outstanding for each derivative type is as follows:

Foreign Currency Forward Exchange Contracts:
Average monthly principal amount	$	5,768,000
Futures Contracts:
Average monthly original value	$	5,108,000
Swap Agreements:
Average monthly notional amount	$	215,000

5. Indemnifications: The Fund enters into contracts that contain a variety of indemnifications. The Fund's maximum exposure under these arrangements is unknown. However, the Fund has not had prior claims or losses pursuant to these contracts and expects the risk of loss to be remote.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

6. Dividends and Distributions to Shareholders: Dividend income and distributions to shareholders are recorded on the ex-dividend date. Dividends from net investment income, if any, are declared and paid quarterly. Net realized capital gains, if any, are distributed at least annually.

7. Security Transactions, Income and Expenses: Security transactions are accounted for on the trade date (date the order to buy or sell is executed). Realized gains and losses on the sale of investment securities are determined on the specific identified cost method. Dividend income and other distributions are recorded on the ex-dividend date (except for certain foreign dividends which may be recorded as soon as the Portfolio is informed of such dividends) net of applicable withholding taxes. Interest income is recognized on the accrual basis except where collection is in doubt. Discounts are accreted and premiums are amortized over the life of the respective securities. Most expenses of the Fund can be directly attributed to a particular Portfolio. Expenses which cannot be directly attributed are apportioned among the Portfolios based upon relative net assets or other appropriate methods. Income, expenses (other than class specific expenses — distribution and shareholder services, transfer agency and sub transfer agency fees) and realized and unrealized gains or losses are allocated to each class of shares based upon their relative net assets.

B. Advisory/Sub-Advisory Fees: The Adviser, a wholly-owned subsidiary of Morgan Stanley, provides the Portfolio with advisory services under the terms of an Investment Advisory Agreement, paid quarterly, at the annual rate based on the daily net assets as follows:

First $500 million				Over $500 million
	0.40	%			0.35	%

For the year ended September 30, 2016, the advisory fee rate (net of waivers/rebate) was equivalent to an annual effective rate of 0.00% of the Portfolio's average daily net assets.

prospectus or until such time as the Trustees act to discontinue all or a portion of such waivers and/or reimbursements when they deem such action is appropriate. For the year ended September 30, 2016, approximately $38,000 of advisory fees were waived and approximately $182,000 of other expenses were reimbursed by the Adviser pursuant to this arrangement.

The Adviser has entered into a Sub-Advisory Agreement with the Sub-Adviser, a wholly-owned subsidiary of Morgan Stanley. The Sub-Adviser provides the Portfolio with advisory services subject to the overall supervision of the Adviser and the Fund's Officers and Trustees. The Adviser pays the Sub-Adviser on a monthly basis a portion of the net advisory fees the Adviser receives from the Portfolio.

C. Administration Fees: The Adviser also serves as Administrator to the Fund and provides administrative services pursuant to an Administration Agreement for an annual fee, accrued daily and paid monthly, of 0.08% of the Portfolio's average daily net assets. Under a Sub-Administration Agreement between the Administrator and State Street Bank and Trust Company ("State Street"), State Street provides certain administrative services to the Fund. For such services, the Administrator pays State Street a portion of the fee the Administrator receives from the Portfolio.

D. Distribution and Shareholder Services Fees: Morgan Stanley Distribution, Inc. ("MSDI" or the "Distributor"), a wholly-owned subsidiary of the Adviser and Sub-Adviser, and an indirect subsidiary of Morgan Stanley, serves as the Fund's Distributor of Portfolio shares pursuant to a Distribution Agreement. The Fund has adopted a Shareholder Services Plan with respect to Class A shares pursuant to Rule 12b-1 under the Act. Under the Shareholder Services Plan, the Portfolio pays the Distributor a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.25% of the Portfolio's average daily net assets attributable to Class A shares.

The distribution and shareholder services fees are used to support the expenses associated with servicing and maintaining accounts. The Distributor may compensate other parties for

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

providing shareholder support services to investors who purchase Class A and Class C shares.

In December 2015, the Fund's Custodian announced that it had identified inconsistencies in the way in which clients were invoiced for out-of-pocket expenses from 1998 until November 2015. The dollar amount difference between what was charged and what should have been charged, plus interest, was paid back to the Portfolio in September 2016 as a reimbursement. State Street reimbursed the Portfolio directly, which was recognized as a change in accounting estimate and was reflected as "Reimbursement of Custodian Fees" in the Statement of Operations. Pursuant to the expense limitations described in Note B, the Portfolio has experienced expenses reimbursed by the Adviser during the current period. Accordingly, the reimbursement of out-of-pocket expenses in the current period resulted in the reduction in the current period Expenses reimbursed by the Adviser.

G. Security Transactions and Transactions with Affiliates: For the year ended September 30, 2016, purchases and sales of investment securities for the Portfolio, other than long-term U.S. Government securities and short-term investments, were approximately $3,775,000 and $5,172,000, respectively. For the year ended September 30, 2016, purchases and sales of long-term U.S. Government securities were approximately $161,000 and $567,000, respectively.

The Portfolio invests in the Institutional Class of the Morgan Stanley Institutional Liquidity Funds (the "Liquidity Funds"), an open-end management investment company managed by the Adviser. Advisory fees paid by the Portfolio are reduced by an amount equal to its pro-rata share of the advisory and administration fees paid by the Portfolio due to its investment in the Liquidity Funds. For the year ended September 30, 2016,

advisory fees paid were reduced by approximately $1,000 relating to the Portfolio's investment in the Liquidity Funds.

A summary of the Portfolio's transactions in shares of the Liquidity Funds during the year ended September 30, 2016 is as follows:

Value September 30, 2015 (000)				Purchases at Cost (000)				Sales (000)				Dividend Income (000)				Value September 30, 2016 (000)
$	65			$	6,249			$	4,589			$	3			$	1,725

FASB ASC 740-10, "Income Taxes — Overall", sets forth a minimum threshold for financial statement recognition of the benefit of a tax position taken or expected to be taken in a tax

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

return. Management has concluded there are no significant uncertain tax positions that would require recognition in the financial statements. If applicable, the Portfolio recognizes interest accrued related to unrecognized tax benefits in "Interest Expense" and penalties in "Other Expenses" in the Statement of Operations. The Portfolio files tax returns with the U.S. Internal Revenue Service, New York and various states. Each of the tax years in the two-year period ended September 30, 2016, remains subject to examination by taxing authorities.

2016 Distributions Paid From: Ordinary Income (000)				2015 Distributions Paid From: Ordinary Income (000)
$	379			$	75

Permanent differences, primarily due to differing treatments of gains (losses) related to foreign currency transactions, basis adjustments for swap transactions, paydown adjustments and nondeductible expenses, resulted in the following reclassifications among the components of net assets at September 30, 2016:

Accumulated Net Investment Loss (000)				Accumulated Net Realized Loss (000)				Paid-in- Capital (000)
$	(37	)		$	41			$	(4	)

At September 30, 2016, the components of distributable earnings for the Portfolio on a tax basis were as follows:

Undistributed Ordinary Income (000)				Undistributed Long-Term Capital Gain (000)
$	85			$	—

At September 30, 2016, the Portfolio had available for federal income tax purposes unused short term and long term capital losses of approximately $178,000 and $153,000, respectively, that do not have an expiration date.

J. Other: At September 30, 2016, the Portfolio did not have record owners of 10% or greater.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Report of Independent Registered Public Accounting Firm

To the Shareholders and Board of Trustees of
Morgan Stanley Institutional Fund Trust —
Strategic Income Portfolio

We have audited the accompanying statement of assets and liabilities, including the portfolio of investments, of Strategic Income Portfolio (one of the portfolios constituting Morgan Stanley Institutional Fund Trust) (the "Portfolio") as of September 30, 2016, the related statement of operations for the year then ended and the statements of changes in net assets and the financial highlights for each of the periods indicated therein. These financial statements and financial highlights are the responsibility of the Portfolio's management. Our responsibility is to express an opinion on these financial statements and financial highlights based on our audits.

In our opinion, the financial statements and financial highlights referred to above present fairly, in all material respects, the financial position of Strategic Income Portfolio (one of the portfolios constituting Morgan Stanley Institutional Fund Trust) at September 30, 2016, the results of its operations for the year then ended and the changes in its net assets and the financial highlights for each of the periods indicated therein, in conformity with U.S. generally accepted accounting principles.

Boston, Massachusetts
November 22, 2016

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Advisory Agreement Approval (unaudited)

Nature, Extent and Quality of Services

The Board reviewed and considered the nature and extent of the investment advisory services provided by the Adviser (as defined herein) under the advisory agreement, including portfolio management, investment research and equity and fixed income securities trading. The Board reviewed similar information and factors regarding the Sub-Adviser (as defined herein), to the extent applicable. The Board also reviewed and considered the nature and extent of the non-advisory, administrative services provided by the Adviser under the administration agreement, including accounting, operations, clerical, bookkeeping, compliance, business management and planning, legal services and the provision of supplies, office space and utilities at the Investment Adviser's expense. The Board also considered the Adviser's investment in personnel and infrastructure that benefits the Portfolio. (The Adviser and Sub-Adviser together are referred to as the "Adviser" and the advisory, sub-advisory and administration agreements together are referred to as the "Management Agreement.") The Board also considered that the Adviser serves a variety of other investment advisory clients and has experience overseeing service providers. The Board also compared the nature of the services provided by the Adviser with similar services provided by non-affiliated advisers as reported to the Board by Broadridge Financial Solutions, Inc. ("Broadridge").

Performance, Fees and Expenses of the Portfolio

The Board reviewed the performance, fees and expenses of the Portfolio compared to its peers, as determined by Broadridge, and to appropriate benchmarks where applicable. The Board discussed with the Adviser the performance goals and the actual results achieved in managing the Portfolio. When considering a fund's performance, the Board and the Adviser place emphasis on trends and longer-term returns (focusing on one-year, three-year and five-year performance, as of December 31, 2015, or since inception, as applicable). When a fund underperforms its benchmark and/or its peer group average, the Board and the Adviser discuss the causes of such underperformance and, where necessary, they discuss specific changes to investment strategy or investment personnel. The Board noted that the Portfolio's performance was better than its peer group average for the one-year period and the period since the end of December 2014, the month of the Portfolio's inception. The Board discussed with the Adviser the level of the advisory and administration fees (together, the "management fee") for this Portfolio relative to comparable funds and/or other accounts advised by the Adviser and/or compared to its peers as determined by Broadridge. In addition to the management fee, the Board also reviewed the Portfolio's total expense ratio. The Board noted that the Portfolio's management fee was lower than its peer group average and total expense ratio was higher than but close to its peer group average. After discussion, the Board concluded that the Portfolio's (i) performance was competitive with its peer group average; and (ii) management fee and total expense ratio were competitive with its peer group averages.

Economies of Scale

Profitability of the Adviser and Affiliates

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Advisory Agreement Approval (unaudited) (cont'd)

Other Benefits of the Relationship

Resources of the Adviser and Historical Relationship Between the Portfolio and the Adviser

Other Factors and Current Trends

General Conclusion

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Privacy Notice (unaudited)

MORGAN STANLEY INVESTMENT MANAGEMENT INC.
AN IMPORTANT NOTICE CONCERNING OUR U.S. PRIVACY POLICY

WE RESPECT YOUR PRIVACY

1. WHAT PERSONAL INFORMATION DO WE COLLECT ABOUT YOU?

For example:

• We may obtain information about your creditworthiness and credit history from consumer reporting agencies.

• We may collect background information from and through third-party vendors to verify representations you have made and to comply with various regulatory requirements.

2. WHEN DO WE DISCLOSE PERSONAL INFORMATION WE COLLECT ABOUT YOU?

We may disclose personal information we collect about you to other Morgan Stanley companies and to non-affiliated third parties.

a. Information We Disclose to Other Morgan Stanley Companies.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Privacy Notice (unaudited) (cont'd)

b. Information We Disclose to Non-affiliated Third Parties.

3. HOW DO WE PROTECT THE SECURITY AND CONFIDENTIALITY OF PERSONAL INFORMATION WE COLLECT ABOUT YOU?

4. HOW CAN YOU LIMIT THE SHARING OF CERTAIN TYPES OF PERSONAL INFORMATION WITH OTHER MORGAN STANLEY COMPANIES?

5. HOW CAN YOU LIMIT THE USE OF CERTAIN TYPES OF PERSONAL INFORMATION BY OTHER MORGAN STANLEY COMPANIES FOR MARKETING?

6. HOW CAN YOU SEND US AN OPT-OUT INSTRUCTION?

• Calling us at (800) 548-7786
Monday–Friday between 8a.m. and 6p.m.(EST)

• Writing to us at the following address:

Boston Financial Data Services, Inc.
c/o Privacy Coordinator
P.O. Box 219804
Kansas City, Missouri 64121

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Privacy Notice (unaudited) (cont'd)

7. WHAT IF AN AFFILIATED COMPANY BECOMES A NON-AFFILIATED THIRD PARTY?

SPECIAL NOTICE TO RESIDENTS OF VERMONT

If you wish to receive offers for investment products and services offered by or through other Morgan Stanley companies, please notify us in writing at the following address:

Boston Financial Data Services, Inc.
c/o Privacy Coordinator
P.O. Box 219804
Kansas City, Missouri 64121

SPECIAL NOTICE TO RESIDENTS OF CALIFORNIA

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited)

Independent Trustees:

Name, Age and Address of
Independent Trustee

Position(s)
Held with
Registrant

Length of Time
Served*

Principal Occupation(s) During Past 5 Years
and Other Relevant Professional Experience

Number of
Portfolios in
Fund Complex
Overseen by
Independent
Trustee**

Other Directorships
Held by Independent
Trustee***

Frank L. Bowman (71)
c/o Perkins Coie LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
August
2006

Kathleen A. Dennis (63)
c/o Perkins Coie LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
August
2006

Director of various non-profit organizations.

Nancy C. Everett (61)
c/o Perkins Coie LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
January
2015

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Age and Address of
Independent Trustee

Position(s)
Held with
Registrant

Length of Time
Served*

Principal Occupation(s) During Past 5 Years
and Other Relevant Professional Experience

Number of
Portfolios in
Fund Complex
Overseen by
Independent
Trustee**

Other Directorships
Held by Independent
Trustee***

Jakki L. Haussler (59)
c/o Perkins Coie LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
January
2015

Dr. Manuel H. Johnson (67)
c/o Johnson Smick
International, Inc.
220 I Street, N.E. —
Suite 200
Washington, D.C. 20002

Trustee

Since
July
1991

100

Director of NVR, Inc. (home construction).

Joseph J. Kearns (74)
c/o Kearns & Associates LLC
23823 Malibu Road
S-50-440
Malibu, CA 90265

Trustee

Since
August
1994

101

Director of Electro Rent Corporation (equipment leasing). Prior to December 31, 2013, Director of The Ford Family Foundation.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Age and Address of
Independent Trustee

Position(s)
Held with
Registrant

Length of Time
Served*

Principal Occupation(s) During Past 5 Years
and Other Relevant Professional Experience

Number of
Portfolios in
Fund Complex
Overseen by
Independent
Trustee**

Other Directorships
Held by Independent
Trustee***

Michael F. Klein (57)
c/o Perkins Coie LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
August
2006

Director of certain investment funds managed or sponsored by Aetos Capital, LLC; Director of Sanitized AG and Sanitized Marketing AG (specialty chemicals).

Michael E. Nugent (80)
522 Fifth Avenue
New York, NY 10036

Chair of the
Board and
Trustee

Chair of the
Boards since
July 2006 and
Trustee since
July 1991

100

None.

W. Allen Reed (69)
c/o Perkins Coie LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
August
2006

Director of Legg Mason, Inc.; formerly, Director of the Auburn University Foundation (2010-2015).

Fergus Reid (84)
c/o Joe Pietryka, Inc.
85 Charles Colman Blvd.
Pawling, NY 12564

Trustee

Since
June
1992

Chairman, Joe Pietryka, Inc.; Chairperson of the Governance Committee and Director or Trustee of various Morgan Stanley Funds (since June 1992).

100

Formerly, Trustee and Director of certain investment companies in the JP Morgan Fund Complex managed by JP Morgan Investment Management Inc. (1987-2012).

* This is the earliest date the Trustee began serving the Morgan Stanley Funds. Each Trustee serves an indefinite term, until his or her successor is elected.

*** This includes any directorships at public companies and registered investment companies held by the Trustee at any time during the past five years.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited) (cont'd)

Executive Officers:

Name, Age and Address of Executive Officer

Position(s) Held
with
Registrant

Length of
Time Served*

Principal Occupation(s) During Past 5 Years

John H. Gernon (53)
522 Fifth Avenue
New York, NY 10036

President and
Principal
Executive
Officer

Since
September
2013

Stefanie V. Chang Yu (49)
522 Fifth Avenue
New York, NY 10036

Chief
Compliance
Officer

Since
December
1997

Joseph C. Benedetti (51)
522 Fifth Avenue
New York, NY 10036

Vice President

Since
January
2014

Francis J. Smith (51)
522 Fifth Avenue
New York, NY 10036

Treasurer and
Principal
Financial
Officer

Treasurer
since July
2003 and
Principal
Financial
Officer since
September
2002

Executive Director of the Adviser and various entities affiliated with the Adviser; Treasurer (since July 2003) and Principal Financial Officer of various Morgan Stanley Funds (since September 2002).

Mary E. Mullin (49)
522 Fifth Avenue
New York, NY 10036

Secretary

Since
June
1999

Executive Director of the Adviser; Secretary of various Morgan Stanley Funds (since June 1999).

* This is the earliest date the officer began serving the Morgan Stanley Funds. Each officer serves a one-year term, until his or her successor is elected and has qualified.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Adviser and Administrator

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

Sub-Adviser

Morgan Stanley Investment Management Limited
25 Cabot Square, Canary Wharf
London, E14 4QA, England

Distributor

Morgan Stanley Distribution, Inc.
522 Fifth Avenue
New York, New York 10036

Dividend Disbursing and Transfer Agent

Boston Financial Data Services, Inc.
2000 Crown Colony Drive
Quincy, Massachusetts 02169

Custodian

State Street Bank and Trust Company
One Lincoln Street
Boston, Massachusetts 02111

Legal Counsel

Dechert LLP
1095 Avenue of the Americas
New York, New York 10036

Counsel to the Independent Trustees

Perkins Coie LLP
30 Rockefeller Plaza
New York, New York 10112

Independent Registered Public Accounting Firm

Ernst & Young LLP
200 Clarendon Street
Boston, Massachusetts 02116

Reporting to Shareholders

Proxy Voting Policies and Procedures and Proxy Voting Record

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospect of the applicable Portfolio of Morgan Stanley Institutional Funds Trust, which describes in detail the Portfolio's investment policies, risks, fees and expenses. Please read the prospectus carefully before you invest or send money. For additional information, including information regarding the investments comprising the Portfolio, please visit our website at www.morganstanley.com/im or call toll free 1 (800) 548-7786.

Printed in U.S.A.
This Report has been prepared for shareholders and may be distributed to others only if preceded or accompanied by a current prospectus.

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

IFTSIPANN
1627780 EXP. 11.30.17

INVESTMENT MANAGEMENT

Morgan Stanley Institutional Fund Trust

Ultra-Short Income Portfolio

Annual Report

September 30, 2016

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Table of Contents

Shareholders' Letter					2
Expense Example					3
Investment Overview					4
Portfolio of Investments					7
Statement of Assets and Liabilities					10
Statement of Operations					11
Statement of Changes in Net Assets					12
Financial Highlights					13
Notes to Financial Statements					16
Report of Independent Registered Public Accounting Firm					21
Investment Advisory Agreement Approval					22
Privacy Notice					24
Trustee and Officer Information					27

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Shareholders' Letter (unaudited)

Dear Shareholders,

We are pleased to provide this Annual report, in which you will learn how your investment in Ultra-Short Income Portfolio (the "Portfolio") performed during the period ended September 30, 2016.

As always, we thank you for selecting Morgan Stanley Investment Management, and look forward to working with you in the months and years ahead.

Sincerely,

John H. Gernon
President and Principal Executive Officer

October 2016

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Expense Example (unaudited)

Ultra-Short Income Portfolio

As a shareholder of the Portfolio, you may incur ongoing costs, which may include advisory fees, administration fees, distribution and shareholder services fees; and other Portfolio expenses. This example is intended to help you understand your ongoing costs (in dollars) of investing in the Portfolio and to compare these costs with the ongoing costs of investing in other mutual funds.

This example is based on an investment of $1,000 invested at the beginning of the period and held for the entire period 4/28/16 – 9/30/16 (unless otherwise noted).

Actual Expenses

Hypothetical Example for Comparison Purposes

	Beginning Account Value 4/28/16		Actual Ending Account Value 9/30/16		Hypothetical Ending Account Value		Actual Expenses Paid During Period*		Hypothetical Expenses Paid During Period*		Net Expense Ratio During Period**
Ultra-Short Income Portfolio Class IR	$	1,000.00	$	1,002.60	$	1,020.54	$	0.77	$	0.78		0.18	%
Ultra-Short Income Portfolio Institutional Class		1,000.00		1,002.40		1,020.33		0.98		0.99		0.23
Ultra-Short Income Portfolio Class A		1,000.00		1,001.40		1,019.44		1.88		1.89		0.44

* Expenses are calculated using each Portfolio Class' annualized net expense ratio (as disclosed), multiplied by the average account value over the period, and multiplied by 156/366 (to reflect the actual days in the period).

** Annualized.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Overview (unaudited)

Ultra-Short Income Portfolio

The Portfolio seeks current income with capital preservation while maintaining liquidity.

Performance

For the period from inception on April 28, 2016 through the fiscal year end on September 30, 2016, the Portfolio's Institutional Share Class had a total return of 0.24%. The Portfolio's Institutional Share Class outperformed against the Portfolio's benchmark, the Bank of America/Merrill Lynch 3-Month U.S. Treasury Bill Index (the "Index"), which returned 0.15%. For the seven-day period ended September 30, 2016, the Portfolio's Institutional Share Class provided an annualized current yield of 0.74% (subsidized) and 0.58% (non-subsidized), while its 30-day moving average annualized yield was 0.70% (subsidized) and 0.52% (non-subsidized). The 30-day SEC yield was 0.70% (subsidized) and 0.52% (non-subsidized). The non-subsidized yield reflects what the yield would have been had a fee and/or expense waiver not been in place during the period shown. Past performance is no guarantee of future results.

Factors Affecting Performance

• Economic conditions and expectations for U.S. central bank policy, along with changes in the regulatory framework for money market funds, were the primary drivers of market dynamics in the short-term fixed income space for the reporting period.

• Specific to the regulatory landscape, October 14, 2016 was the implementation date for the Securities and Exchange Commission's (SEC) revised 2a-7 rule, which regulates money market funds (MMFs). Sweeping changes to the regulatory framework for MMFs included the required adoption of trigger-based redemption fees and liquidity gates for both prime and tax-exempt MMFs and, for institutional prime and tax-exempt MMFs, the mandatory conversion to float the funds' net asset values (NAV) per share. MMFs investing primarily in U.S. government securities were not subject to these elements of the rule changes.

• Money market participants widely expected a shifting of assets away from prime and tax-exempt MMFs in favor of government MMFs due to the

new requirements. Anticipating the outflows, MMF managers tended to adopt a defensive approach, bolstering portfolio liquidity and limiting term investments leading up to the October implementation date. This led to a shift in the supply/demand equilibrium for non-government money market instruments, creating a technical imbalance that forced Libor rates higher through the third quarter of 2016 with 3-month Libor rates increasing 20 basis points, or bps, (from 0.65% to 0.85%) and 6-month Libor rates increasing 32 bps (from 0.92% to 1.24%).ⁱ

• From an economic perspective, second-quarter 2016 gross domestic product (GDP) rose at 1.1% annualized, below median forecasts of 2.5%.ⁱⁱ Household purchases were the lone bright spot in the quarter, as businesses trimmed inventories and reduced outlays on equipment and construction projects.

• Non-farm payrolls rose an average of 146,000 in the second quarter of 2016, indicating a general slowdown in the hiring market.ⁱⁱⁱ Industries that showed strong first-quarter growth pulled back, highlighted by the retail sector's largest payroll cut in two years. The biggest surprise of the quarter came with the May non-farm payrolls. Employers added the fewest number of workers in almost six years, originally reported at 38,000 but revised down to 24,000, reflecting broad cutbacks that raised concern about the health of the U.S. economy. Payroll growth in June 2016 rebounded and came in at 271,000, which far exceeded consensus expectations of 180,000, due to strong performance across multiple sectors. These June numbers tempered fears of a slowing labor market caused by the poor May results. The unemployment rate ended the quarter at 4.9%.

• Third-quarter 2016 employment continued its positive momentum, with non-farm payrolls averaging 190,000 for July and August. The unemployment rate remained constant at 4.9% as people reentering the workforce were able to find jobs. September payrolls increased 156,000, slightly lower than expectations, and the unemployment rate ticked up to 5.0%. However, positive revisions

ⁱ Source: Intercontinental Exchange and Bloomberg L.P.

ⁱⁱ Source: Bureau of Economic Analysis

ⁱⁱⁱ Source for all labor market data: Bureau of Labor Statistics

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Overview (unaudited) (cont'd)

Ultra-Short Income Portfolio

for the prior period and an increase in the labor force participation rate largely offset the slightly negative headline numbers.

• At the April 2016 Federal Open Market Committee (FOMC) meeting, rates were left unchanged and the Committee signaled its openness to raising rates in June 2016 if upcoming data warranted. The Federal Reserve (Fed) acknowledged that financial conditions eased somewhat since the March meeting and removed the assessment that "financial conditions continue to pose risks to the outlook" of the economy.

• In May 2016, the April FOMC minutes were released and surprised the market with a hawkish tone. The minutes stated that "most" participants judged that it "likely would be appropriate for the Committee to increase the target range for the federal funds rate in June" if economic data were supportive. Referring to the June 2016 meeting, officials judged it appropriate to leave their options open, making a decision based on upcoming economic data points.

• June 2016 was full of market-moving events across the globe. The month started with the May 2016 non-farm payroll report, which came in at 38,000, significantly below the 160,000 consensus. This was later revised to 24,000. The addition was the fewest new jobs since September 2010, and immediately the market priced out any rate hike at the FOMC meeting later in the month. With the poor non-farm payroll result still fresh and the upcoming Brexit vote on the horizon, as expected the Fed held rates steady at its mid-month meeting and maintained a target federal funds range of 0.25% to 0.50%. The Fed did express confidence in a jobs rebound and reiterated that interest rates would be likely to rise at a gradual level. In addition, the "dot plot," which charts the Fed's interest rate forecasts, took on a dovish tone, decreasing the members voting for a 2016 hike, as well as lowering the 2017 and 2018 interest rate path.

• In a referendum on June 23, 2016, the United Kingdom voted to leave the European Union (EU), with 52% in favor. The vote to leave was supported by resentment over Britain's high annual

contributions to the EU as well as concerns about the uptick in immigration due to the recent refugee crisis. The process of leaving the EU is a lengthy one, as it will take two years from the time the UK files the official notification through Article 50 of the Lisbon Treaty. This is unchartered territory, and the global markets reacted accordingly. Risk assets were down and investors piled into perceived safe-haven assets, sending yields to near-record lows. The 30-year U.S. Treasury declined to 2.19% and the 10-year slid to 1.39% in days following the referendum.^iv

• In July 2016, markets managed to stabilize from the turbulence following the Brexit vote the prior month. The July FOMC meeting went fairly in line with market expectations, with no changes to policy and rates. The tone of the meeting was hawkish, with the Fed saying that "near-term risks to the economic outlook have diminished." The Committee repeated that it expects conditions will evolve in a manner that warrants a gradual increase in the federal funds rate.

• With no FOMC meeting taking place in August 2016, market participants were focused on the annual Jackson Hole, Wyoming summit, which was highlighted by comments from Fed Chair Janet Yellen. "In light of the continued solid performance of the labor market and our outlook for economic activity and inflation, I believe the case for an increase in the federal funds rate has strengthened in recent months," she said in a speech to central bankers and economists. These remarks appeared to leave open the possibility of an interest-rate hike in September 2016, and bonds fell while the dollar rose.

• At the September FOMC meeting, however, the Committee left the target range for the federal funds rate unchanged, citing that the risks to the economic outlook remained balanced and, although the case for an increase in policy rates had strengthened, the Committee decided to wait for further progress toward its objectives. The non-hike appeared to be a very close call, as three Committee members dissented against the decision. However, there was a material split in the Committee, as three

^iv Source: Bloomberg L.P., July 1, 2016

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Overview (unaudited) (cont'd)

Ultra-Short Income Portfolio

other members called for no further rate increases for the remainder of the year, blurring the expectations of an additional rate hike before year-end.

Management Strategies

• Our investment philosophy continues to revolve around prudent credit, duration, and risk management, and we are very comfortable with our approach.

* Minimum Investment

** Commenced operations on April 28, 2016.

In accordance with SEC regulations, the Portfolio's performance shown assumes that all recurring fees (including management fees) were deducted and all dividends and distributions were reinvested. The performance of Class A, and Class IR shares will vary from the performance of Class Institutional shares and will be negatively impacted by additional fees assessed to those classes (where applicable).

Performance Compared to the Bank of America/Merrill Lynch 3-Month U.S. Treasury Bill Index⁽¹⁾, and the Lipper Ultra Short Obligations Funds Index⁽²⁾

	Period Ended September 30, 2016 Total Returns⁽³⁾
	One Year		Five Years		Ten Years		Since Inception⁽⁵⁾
Portfolio — Class IR Shares w/o sales charges⁽⁴⁾		—		—		—		0.26	%
Portfolio — Class Institutional Shares w/o sales charges⁽⁴⁾		—		—		—		0.24
Portfolio — Class A Shares w/o sales charges⁽⁴⁾		—		—		—		0.14
Bank of America/Merrill Lynch 3-Month U.S. Treasury Bill Index		—		—		—		0.15
Lipper Ultra Short Obligations Funds Index		—		—		—		0.76

Performance data quoted represents past performance, which is no guarantee of future results, and current performance may be lower or higher than the figures shown. Performance assumes that all dividends and distributions, if any, were reinvested. Returns for period less than one year are not annualized. For the most recent month-end performance figures, please visit www.morganstanley.com/im. Investment returns and principal value will fluctuate so that Portfolio shares, when redeemed, may be worth more or less than their original cost. Total returns do not reflect the deduction of taxes that a shareholder would pay on Portfolio distributions or the redemption of Portfolio shares. Performance of share classes will vary due to differences in expenses.

⁽²⁾ The Lipper Ultra Short Obligations Funds Index is an equally weighted performance index of the largest qualifying funds (based on net assets) in the Lipper Ultra Short Obligations Funds classification. The Index, which is adjusted for capital gains distributions and income dividends, is unmanaged and should not be considered an investment. There are currently 30 funds represented in this Index. As of the date of this report, the Portfolio was in the Lipper Ultra Short Obligations' Funds classification.

⁽³⁾ Total returns for the Portfolio reflect expenses waived and/or reimbursed, if applicable, by the Adviser. Without such waivers and/or reimbursements, total returns would have been lower.

⁽⁴⁾ Commenced operations on April 28, 2016.

⁽⁵⁾ For comparative purposes, average annual since inception returns listed for the Indexes refer to the inception date of the Portfolio, not the inception of the Indexes.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments

Ultra-Short Income Portfolio

	Face Amount (000)		Value (000)
Certificates of Deposit (4.1%)
International Banks (4.1%)
Bank of Montreal
0.93%, 12/14/16	$	5,000	$	5,002
Credit Suisse AG
0.90%, 11/7/16		4,000		4,001
DZ Bank AG
0.95%, 12/22/16		10,000		9,999
Oversea-Chinese Banking Corp. Ltd.
0.90%, 11/16/16		5,000		5,002
Toronto-Dominion Bank
0.90%, 1/5/17		2,000		2,000
Total Certificates of Deposit (Cost $26,000)				26,004
Commercial Paper (a) (10.8%)
Automobiles (0.8%)
Harley-Davidson Financial Services, Inc.
0.64%, 10/6/16		5,000		4,999
Health Care Services (0.7%)
UnitedHealth Group, Inc.
0.75%, 11/4/16		5,000		4,996
International Banks (7.7%)
BPCE
1.05%, 1/5/17		5,000		4,987
Cooperatieve Rabobank UA
0.87%, 11/2/16		10,000		9,996
DNB Bank ASA
0.86%, 11/14/16		4,920		4,917
Macquarie Bank Ltd.
1.00%, 12/21/16		10,000		9,985
National Australia Bank Ltd.
0.87%, 11/16/16		1,855		1,854
Nordea Bank AB
0.92%, 11/23/16		10,000		9,991
Sumitomo Mitsui Banking Corp.,
0.90%, 10/24/16		2,500		2,499
1.00%, 1/3/17		5,000		4,987
				49,216
Publishing & Broadcasting (0.8%)
NBCUniversal Enterprise, Inc.
0.65%, 10/12/16		5,000		4,999
Transportation (0.8%)
Ryder System, Inc.
0.75%, 10/17/16		5,000		4,998
Total Commercial Paper (Cost $69,192)				69,208
Corporate Bond (1.1%)
International Bank (1.1%)
ABN AMRO Bank
4.25%, 2/2/17 (b)(c) (Cost $6,851)		6,784		6,854

	Face Amount (000)		Value (000)
Floating Rate Notes (55.2%)
Automobiles (3.9%)
Toyota Motor Credit
1.23%, 6/19/17	$	25,000	$	24,998
Domestic Banks (2.4%)
Bank of America NA
1.29%, 11/14/16		5,000		5,004
HSBC Bank USA NA
1.07%, 5/12/17		6,100		6,089
Wells Fargo Bank NA
1.04%, 2/15/17		4,000		4,001
				15,094
International Banks (48.9%)
ANZ New Zealand International Ltd.,
1.11%, 1/31/17 (b)		10,000		10,007
1.13%, 3/13/17		4,000		4,001
ASB Finance Ltd. London
1.11%, 3/6/17 (b)		5,000		5,002
Australia & New Zealand Banking Group Ltd.
0.87%, 12/15/16 (b)		5,000		5,002
Bank of Montreal
1.00%, 1/23/17		7,000		7,002
Bank of Nova Scotia,
1.07%, 12/5/16		3,000		3,002
1.11%, 3/28/17 (b)		7,000		6,999
1.14%, 3/6/17		5,000		5,002
1.14%, 3/3/17		5,100		5,103
1.15%, 2/23/17		3,000		3,002
1.24%, 5/12/17		3,500		3,502
BNZ International Funding Ltd.
1.07%, 3/31/17 (b)		14,000		13,995
Canadian Imperial Bank of Commerce,
1.12%, 2/15/17		10,000		10,006
1.15%, 2/21/17		5,000		5,003
1.19%, 5/23/17 (c)		6,411		6,412
Commonwealth Bank of Australia
0.98%, 2/6/17 (b)		10,000		10,002
Credit Suisse AG,
1.01%, 12/14/16		5,000		5,003
1.65%, 9/12/17		7,000		7,008
DNB Bank ASA
1.11%, 3/27/17 (b)		10,000		9,999
HSBC Bank PLC,
0.99%, 11/29/16 (b)		5,000		5,003
1.19%, 3/20/17 (b)		5,000		5,002
Mizuho Bank Ltd.
1.27%, 3/7/17		4,000		4,000
National Australia Bank Ltd.
1.11%, 4/27/17		4,850		4,848
Nordea Bank Finland PLC
1.01%, 11/14/16		3,000		3,002

The accompanying notes are an integral part of the financial statements.
7

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Ultra-Short Income Portfolio

	Face Amount (000)		Value (000)
International Banks (cont'd)
Oversea-Chinese Banking Corp. Ltd.
1.16%, 2/22/17	$	5,000	$	5,003
Rabobank Nederland
0.86%, 11/9/16		2,000		2,001
Royal Bank of Canada,
0.92%, 1/6/17		15,000		15,005
1.10%, 1/23/17		13,000		13,008
Skandinaviska Enskilda Banken AB,
0.87%, 12/2/16		1,400		1,400
0.94%, 1/9/17		7,476		7,479
Sumitomo Mitsui Banking Corp.
1.20%, 2/8/17		7,000		7,003
Sumitomo Mitsui Trust Bank Ltd.
1.26%, 3/7/17		10,000		10,003
Suncorp-Metway Ltd.
1.55%, 3/28/17 (b)		28,750		28,794
Svenska Handelsbanken AB,
0.90%, 1/10/17		5,000		5,001
0.90%, 12/16/16		5,000		5,002
1.05%, 12/19/16		4,100		4,103
1.07%, 11/28/16		2,823		2,825
1.10%, 2/28/17		7,000		7,003
Toronto-Dominion Bank,
0.86%, 11/7/16		7,000		7,002
1.09%, 2/3/17		5,000		5,003
1.18%, 5/1/17		3,000		3,001
UBS AG Stamford
0.94%, 12/13/16		5,000		5,003
Westpac Banking Corp.,
0.97%, 3/8/17 (b)		7,000		6,998
1.04%, 1/19/17		1,000		1,001
1.15%, 2/6/17		2,008		2,010
1.21%, 3/3/17 (b)		11,000		11,009
1.28%, 9/28/17		10,000		9,996
				311,560
Total Floating Rate Notes (Cost $351,526)				351,652
Repurchase Agreements (29.5%)
ABN Amro Securities LLC, (0.50%, dated 9/30/16, due 10/3/16; proceeds $22,001; fully collateralized by various Corporate Bonds, 1.90% - 7.90% due 3/15/17 - 7/15/46, U.S. Government agency securities, 3.00% - 5.00% due 11/15/40 - 10/1/46 and a U.S. Government obligation, 2.13% due 8/31/20; valued at $23,037)		22,000		22,000
Bank of Montreal, (0.50%, dated 9/30/16, due 10/3/16; proceeds $1,000; fully collateralized by various Corporate Bonds; 1.07% - 5.65% due 2/21/17 - 11/23/43; valued at $1,051)		1,000		1,000

	Face Amount (000)		Value (000)
Citigroup Global Markets, Inc., (0.55%, dated 9/30/16, due 10/3/16; proceeds $23,001; fully collateralized by various Common Stocks; valued at $24,150)	$	23,000	$	23,000
HSBC Securities USA, Inc., (0.60%, dated 9/30/16, due 10/3/16; proceeds $15,001; fully collateralized by various Corporate Bonds; 6.63% - 11.00% due 5/1/19 - 5/15/22; valued at $15,900)		15,000		15,000
ING Financial Markets LLC, (0.63%, dated 9/30/16, due 10/3/16; proceeds $24,001; fully collateralized by various Corporate Bonds; 3.50% - 10.13% due 4/15/18 - 6/15/24; valued at $25,441)		24,000		24,000
JP Morgan Securities LLC, (1.09%, dated 9/19/16, due 3/3/17; proceeds $5,025; fully collateralized by various Corporate Bonds; 7.25% - 8.88% due 2/1/18 - 4/1/19; valued at $5,301) (Demand 10/6/16)		5,000		5,000
JP Morgan Securities LLC, (1.08%, dated 6/6/16 - 8/8/16, due 3/3/17; proceeds $15,111; fully collateralized by various Corporate Bonds; 5.50% - 10.63% due 2/1/18 - 8/1/23; valued at $15,903) (Demand 10/6/16)		15,000		15,000
Merrill Lynch Pierce Fenner & Smith, (1.02%, dated 8/12/16, due 2/13/17; proceeds $10,052; fully collateralized by various Common Stocks, Convertible Bonds, 0.50% - 4.50% due 11/15/16 - 9/15/32, and a Convertible Preferred Stock; valued at $11,015) (Demand 10/12/16)		10,000		10,000
Mizuho Securities USA, Inc., (0.50%, dated 9/30/16, due 10/3/16; proceeds $23,001; fully collateralized by various Common Stocks; valued at $24,150)		23,000		23,000
Pershing LLC, (0.61%, dated 9/30/16, due 10/3/16; proceeds $26,001; fully collateralized by various Corporate Bonds; 0.77% - 11.50% due 10/6/16 - 12/31/99; valued at $27,553) (d)		26,000		26,000
Scotia Capital USA, Inc., (0.60%, dated 9/30/16, due 10/3/16; proceeds $4,000; fully collateralized by a Corporate Bond; 6.80% due 12/15/16; valued at $4,241)		4,000		4,000
Wells Fargo Securities LLC, (1.07%, dated 8/11/16, due 11/9/16; proceeds $15,040; fully collateralized by various Corporate Bonds; 7.00% - 11.25% due 4/1/19 - 4/1/45; valued at $15,900)		15,000		15,000

The accompanying notes are an integral part of the financial statements.
8

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Portfolio of Investments (cont'd)

Ultra-Short Income Portfolio

	Face Amount (000)		Value (000)
Repurchase Agreements (cont'd)
Wells Fargo Securities LLC, (1.07%, dated 8/19/16, due 11/9/16; proceeds $5,012; fully collateralized by various Corporate Bonds; 5.50% - 9.00% due 4/15/19 - 4/1/45; valued at $5,300)	$	5,000	$	5,000
Total Repurchase Agreements (Cost $188,000)				188,000
Total Investments (100.7%) (Cost $641,569) (e)(f)				641,718
Liabilities in Excess of Other Assets (–0.7%)				(4,750	)
Net Assets (100.0%)			$	636,968

(a) The rates shown are the effective yields at the date of purchase.

(b) 144A security — Certain conditions for public sale may exist. Unless otherwise noted, these securities are deemed to be liquid.

(d) Perpetual — One or more securities do not have a predetermined maturity date. Rates for these securities are fixed for a period of time, after which they revert to a floating rate. Interest rates in effect are as of September 30, 2016.

(e) Securities are available for collateral in connection with securities purchased on a forward commitment basis.

(f) At September 30, 2016, the aggregate cost for federal income tax purposes is approximately $641,569,000. The aggregate gross unrealized appreciation is approximately $177,000 and the aggregate gross unrealized depreciation is approximately $28,000 resulting in net unrealized appreciation of approximately $149,000.

Portfolio Composition

Classification	Percentage of Total Investments
Floating Rate Notes		54.8	%
Repurchase Agreements		29.3
Commercial Paper		10.8
Other*		5.1
Total Investments		100.0	%

* Industries and/or investment types representing less than 5% of total investments.

The accompanying notes are an integral part of the financial statements.
9

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Ultra-Short Income Portfolio

Statement of Assets and Liabilities	September 30, 2016 (000)
Assets:
Investments in Securities of Unaffiliated Issuers, at Value (Cost $641,569, including value of repurchase agreements of $188,000)	$	641,718
Cash		70
Receivable for Portfolio Shares Sold		6,170
Interest Receivable		324
Prepaid Offering Costs		86
Due from Adviser		23
Other Assets		52
Total Assets		648,443
Liabilities:
Payable for Investments Purchased		9,764
Payable for Portfolio Shares Redeemed		1,353
Dividends Payable		172
Payable for Professional Fees		59
Payable for Administration Fees		37
Payable for Shareholder Services Fees — Institutional Class		7
Payable for Shareholder Services Fees — Class A		23
Payable for Custodian Fees		18
Payable for Offering Costs		13
Payable for Transfer Agency Fees — Class IR		1
Payable for Transfer Agency Fees — Institutional Class		—	@
Payable for Transfer Agency Fees — Class A		—	@
Other Liabilities		28
Total Liabilities		11,475
Net Assets	$	636,968
Net Assets Consist of:
Paid-in-Capital	$	636,808
Distributions in Excess of Net Investment Income		(25	)
Accumulated Undistributed Net Realized Gain		36
Unrealized Appreciation (Depreciation) on:
Investments		149
Net Assets	$	636,968
CLASS IR:
Net Assets	$	276,348
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		27,623,387
Net Asset Value, Offering and Redemption Price Per Share	$	10.00
Institutional Class:
Net Assets	$	196,092
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		19,605,875
Net Asset Value, Offering and Redemption Price Per Share	$	10.00
CLASS A:
Net Assets	$	164,528
Shares Outstanding (unlimited number of shares authorized, no par value) (not in 000's)		16,451,557
Net Asset Value, Offering and Redemption Price Per Share	$	10.00

@ Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
10

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Ultra-Short Income Portfolio

Statement of Operations	Period from April 28, 2016^ to September 30, 2016 (000)
Investment Income:
Interest from Securities of Unaffiliated Issuers	$	1,219
Expenses:
Advisory Fees (Note B)		299
Administration Fees (Note C)		119
Professional Fees		94
Offering Costs		64
Shareholder Services Fees — Institutional Class (Note D)		14
Shareholder Services Fees — Class A (Note D)		33
Shareholder Reporting Fees		25
Custodian Fees (Note F)		21
Pricing Fees		5
Transfer Agency Fees — Class IR (Note E)		1
Transfer Agency Fees — Institutional Class (Note E)		1
Transfer Agency Fees — Class A (Note E)		1
Trustees' Fees and Expenses		2
Registration Fees		—	@
Other Expenses		2
Total Expenses		681
Waiver of Advisory Fees (Note B)		(299	)
Expenses Reimbursed by Adviser (Note B)		(64	)
Reimbursement of Class Specific Expenses — Class IR (Note B)		(1	)
Reimbursement of Class Specific Expenses — Institutional Class (Note B)		(1	)
Net Expenses		316
Net Investment Income		903
Realized Gain:
Investments Sold		36
Change in Unrealized Appreciation (Depreciation):
Investments		149
Net Realized Gain and Change in Unrealized Appreciation (Depreciation)		185
Net Increase in Net Assets Resulting from Operations	$	1,088

^ Commencement of Operations.

@ Amount is less than $500.

The accompanying notes are an integral part of the financial statements.
11

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Ultra-Short Income Portfolio

Statement of Changes in Net Assets	Period from April 28, 2016^ to September 30, 2016 (000)
Increase in Net Assets:
Operations:
Net Investment Income	$	903
Net Realized Gain		36
Net Change in Unrealized Appreciation		149
Net Increase in Net Assets Resulting from Operations		1,088
Distributions from and/or in Excess of:
Class IR:
Net Investment Income		(676	)
Institutional Class:
Net Investment Income		(185	)
Class A:
Net Investment Income		(67	)
Total Distributions		(928	)
Capital Share Transactions:⁽¹⁾
Class IR:
Subscribed		302,012
Distributions Reinvested		55
Redeemed		(25,833	)
Institutional Class:
Subscribed		229,457
Distributions Reinvested		154
Redeemed		(33,552	)
Class A:
Subscribed		180,915
Distributions Reinvested		61
Redeemed		(16,461	)
Net Increase in Net Assets Resulting from Capital Share Transactions		636,808
Total Increase in Net Assets		636,968
Net Assets:
Beginning of Period		—
End of Period (Including Distributions in Excess of Net Investment Income $(25))	$	636,968
(1) Capital Share Transactions:
Class IR:
Shares Subscribed		30,201
Shares Issued on Distributions Reinvested		5
Shares Redeemed		(2,583	)
Net Increase in Class IR Shares Outstanding		27,623
Institutional Class:
Shares Subscribed		22,946
Shares Issued on Distributions Reinvested		15
Shares Redeemed		(3,355	)
Net Increase in Institutional Class Shares Outstanding		19,606
Class A:
Shares Subscribed		18,092
Shares Issued on Distributions Reinvested		6
Shares Redeemed		(1,646	)
Net Increase in Class A Shares Outstanding		16,452

^ Commencement of Operations.

The accompanying notes are an integral part of the financial statements.
12

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Ultra-Short Income Portfolio

	Class IR
Selected Per Share Data and Ratios	Period from April 28, 2016^ to September 30, 2016
Net Asset Value, Beginning of Period	$	10.00
Income from Investment Operations:
Net Investment Income†		0.03
Net Realized and Unrealized Gain		0.00	‡
Total from Investment Operations		0.03
Distributions from and/or in Excess of:
Net Investment Income		(0.03	)
Net Asset Value, End of Period	$	10.00
Total Return++		0.26	%#
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	276,348
Ratio of Expenses to Average Net Assets⁽¹⁾		0.18	%*
Ratio of Net Investment Income to Average Net Assets⁽¹⁾		0.61	%*
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		0.42	%*
Net Investment Income to Average Net Assets		0.37	%*

^ Commencement of Operations.

† Per share amount is based on average shares outstanding.

‡ Amount is less than $0.005 per share.

++ Calculated based on the net asset value as of the last business day of the period.

# Not Annualized.

* Annualized.

The accompanying notes are an integral part of the financial statements.
13

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Ultra-Short Income Portfolio

	Institutional Class
Selected Per Share Data and Ratios	Period from April 28, 2016^ to September 30, 2016
Net Asset Value, Beginning of Period	$	10.00
Income (Loss) from Investment Operations:
Net Investment Income†		0.02
Net Realized and Unrealized Gain		0.00	‡
Total from Investment Operations		0.02
Distributions from and/or in Excess of:
Net Investment Income		(0.02	)
Net Asset Value, End of Period	$	10.00
Total Return++		0.24	%#
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	196,092
Ratio of Expenses to Average Net Assets⁽¹⁾		0.23	%*
Ratio of Net Investment Income to Average Net Assets⁽¹⁾		0.65	%*
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		0.48	%*
Net Investment Income to Average Net Assets		0.40	%*

^ Commencement of Operations.

† Per share amount is based on average shares outstanding.

‡ Amount is less than $0.005 per share.

++ Calculated based on the net asset value as of the last business day of the period.

# Not Annualized.

* Annualized.

The accompanying notes are an integral part of the financial statements.
14

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Financial Highlights

Ultra-Short Income Portfolio

	Class A
Selected Per Share Data and Ratios	Period from April 28, 2016^ to September 30, 2016
Net Asset Value, Beginning of Period	$	10.00
Income (Loss) from Investment Operations:
Net Investment Income†		0.01
Net Realized and Unrealized Gain		0.00	‡
Total from Investment Operations		0.01
Distributions from and/or in Excess of:
Net Investment Income		(0.01	)
Net Asset Value, End of Period	$	10.00
Total Return++		0.14	%#
Ratios and Supplemental Data:
Net Assets, End of Period (Thousands)	$	164,528
Ratio of Expenses to Average Net Assets⁽¹⁾		0.44	%*
Ratio of Net Investment Income to Average Net Assets⁽¹⁾		0.48	%*
⁽¹⁾ Supplemental Information on the Ratios to Average Net Assets:
Ratios Before Expense Limitation:
Expenses to Average Net Assets		0.68	%*
Net Investment Income to Average Net Assets		0.24	%*

^ Commencement of Operations.

† Per share amount is based on average shares outstanding.

‡ Amount is less than $0.005 per share.

++ Calculated based on the net asset value as of the last business day of the period.

# Not Annualized.

* Annualized.

The accompanying notes are an integral part of the financial statements.
15

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements

The accompanying financial statements relate to the Ultra-Short Income Portfolio. The Portfolio seeks current income with capital preservation while maintaining liquidity.

The Portfolio commenced operations on April 28, 2016 and offers three classes of shares — Class IR, Institutional Class and Class A.

general supervision of the Trustees. Occasionally, developments affecting the closing prices of securities and other assets may occur between the times at which valuations of such securities are determined (that is, close of the foreign market on which the securities trade) and the close of business of the New York Stock Exchange ("NYSE"). If developments occur during such periods that are expected to materially affect the value of such securities, such valuations may be adjusted to reflect the estimated fair value of such securities as of the close of the NYSE, as determined in good faith by the Trustees or by the Adviser using a pricing service and/or procedures approved by the Trustees; and (3) investments in mutual funds, including the Morgan Stanley Institutional Liquidity Funds, are valued at the net asset value as of the close of each business day.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

on the disposition of the investments. Due to the inherent uncertainty of valuations of such investments, the fair values may differ significantly from the values that would have been used had an active market existed. The Valuation Committee employs various methods for calibrating these valuation approaches including a regular review of valuation methodologies, key inputs and assumptions, transactional back-testing or disposition analysis, and reviews of any related market activity.

• Level 1 – unadjusted quoted prices in active markets for identical investments

• Level 2 – other significant observable inputs (including quoted prices for similar investments, interest rates, prepayment speeds, credit risk, etc.)

documents and, if necessary, available information concerning other securities in similar circumstances

The following is a summary of the inputs used to value the Portfolio's investments as of September 30, 2016.

Investment Type	Level 1 Unadjusted quoted prices (000)		Level 2 Other significant observable inputs (000)		Level 3 Significant unobservable inputs (000)		Total (000)
Assets:
Short-Term Investments
Certificates of Deposit	$	—	$	26,004	$	—	$	26,004
Commercial Paper		—		69,208		—		69,208
Corporate Bond		—		6,854		—		6,854
Floating Rate Notes		—		351,652		—		351,652
Repurchase Agreements		—		188,000		—		188,000
Total Short-Term Investments		—		641,718		—		641,718
Total Assets	$	—	$	641,718	$	—	$	641,718

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

In the event of default on the obligation to repurchase, the Portfolio has the right to liquidate the collateral and apply the proceeds in satisfaction of the obligation. In the event of default or bankruptcy by the counterparty to the agreement, realization and/or retention of the collateral or proceeds may be subject to legal proceedings. The Portfolio, along with other affiliated investment companies, may utilize a joint trading account for the purpose of entering into repurchase agreements.

The Portfolio may enter into repurchase agreements in which eligible securities are transferred into joint trading accounts maintained by the custodian for investment companies advised by the Fund's Adviser. The Portfolio will participate on a pro rata basis with the other investment companies in its share of the securities transferred under such repurchase agreements and in its share of proceeds from any repurchase or other disposition of such securities.

Repurchase agreements are subject to Master Repurchase Agreements which are agreements between the Portfolios' and its counterparties that typically include provisions which provide for the net settlement of all transactions and collateral with the Fund, through a single payment, in the event of default or termination. Amounts presented on the Portfolio of Investments and Statement of Assets and Liabilities are not net settlement amounts but gross. As indicated on the Portfolio of Investments, the cash or securities to be repurchased exceeds the repurchase price to be paid under the repurchase agreement reducing the net settlement amount to zero.

4. When-Issued/Delayed Delivery Securities: The Portfolio purchases and sells when-issued and delayed delivery securities. Securities purchased on a when-issued or delayed delivery basis are purchased for delivery beyond the normal settlement date at a stated price and yield, and no income accrues to the Portfolio on such securities prior to delivery date. Payment and delivery for when-issued and delayed delivery securities can take place a month or more after the date of the transaction. When the Portfolio enters into a purchase transaction on a when-issued or delayed delivery basis, securities are available for collateral in an amount at least equal in value to the Portfolio's commitments to purchase such securities. Purchasing securities on a when-issued or delayed delivery basis may involve a risk that the market price at the time of delivery may be lower than the agreed upon purchase price, in which case

there could be an unrealized loss at the time of delivery. Purchasing investments on a when-issued or delayed delivery basis may be considered a form of leverage which may increase the impact that gains (losses) may have on the Portfolio.

6. Dividends and Distributions to Shareholders: Dividends and distributions to shareholders are recorded on the close of each business day. Dividends from net investment income, if any, are declared daily and paid monthly. Net realized capital gains, if any, are distributed at least annually.

7. Security Transactions, Income and Expenses: Security transactions are accounted for on the trade date (date the order to buy or sell is executed). Realized gains and losses on the sale of investment securities are determined on the specific identified cost method. Dividend income and other distributions are recorded on the ex-dividend date (except for certain foreign dividends which may be recorded as soon as the Portfolio is informed of such dividends) net of applicable withholding taxes. Interest income is recognized on the accrual basis except where collection is in doubt. Discounts are accreted and premiums are amortized over the life of the respective securities. Most expenses of the Fund can be directly attributed to a particular Portfolio. Expenses which cannot be directly attributed are apportioned among the Portfolios based upon relative net assets or other appropriate methods. Income, expenses (other than class specific expenses — distribution and shareholder services and transfer agency fees) and realized and unrealized gains or losses are allocated to each class of shares based upon their relative net assets.

The Adviser has agreed to reduce its advisory fee and/or reimburse the Portfolio so that total annual portfolio operating

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

expenses, excluding certain investment related expenses, taxes, interest and other extraordinary expenses (including litigation), will not exceed 0.25% for Class IR shares, 0.30% for Institutional Class shares and 0.55% for Class A shares. The fee waivers and/or expense reimbursements will continue for at least one year from the date of the Portfolio's prospectus or until such time as the Trustees act to discontinue all or a portion of such waivers and/or reimbursements when they deem such action is appropriate. In addition, the Adviser may make additional voluntary fee waivers and/or expense reimbursements. The ratios of expenses to average net assets disclosed in the Portfolio's Financial Highlights may be lower than the maximum expense ratios due to these additional fee waivers and/or expense reimbursements. The Adviser may also waive additional advisory fees and/or reimburse expenses to enable the Portfolio to maintain a minimum level of daily net investment income. For the period ended September 30, 2016, approximately $299,000 of advisory fees were waived and approximately $66,000 of other expenses were reimbursed by the Adviser pursuant to this arrangement.

C. Administration Fees: The Adviser also serves as Administrator to the Fund and provides administrative services pursuant to an Administration Agreement for an annual fee, accrued daily and paid monthly, of 0.08% of the Portfolio's average daily net assets. Under a Sub-Administration Agreement between the Administrator and State Street Bank and Trust Company ("State Street"), State Street provides certain administrative services to the Fund. For such services, the Administrator pays State Street a portion of the fee the Administrator receives from the Portfolio.

D. Shareholder Services Fees: Morgan Stanley Distribution, Inc. ("MSDI" or the "Distributor"), a wholly-owned subsidiary of the Adviser, and an indirect subsidiary of Morgan Stanley, serves as the Fund's Distributor of Portfolio shares pursuant to a Distribution Agreement. The Fund has adopted a Shareholder Services Plan with respect to the Institutional Class shares pursuant to Rule 12b-1 under the Act. Under the Shareholder Services Plan, the Portfolio pays the Distributor a shareholder services fee, accrued daily and paid monthly, at an annual rate of 0.05% of the Portfolio's average daily net assets attributable to the Institutional Class shares.

The Fund has adopted a Shareholder Services Plan with respect to Class A shares pursuant to Rule 12b-1 under the Act. Under the Shareholder Services Plan, the Portfolio pays the Distributor a shareholder services fee, accrued daily and paid monthly,

at an annual rate of 0.25% of the Portfolio's average daily net assets attributable to Class A shares.

The shareholder services fees are used to support the expenses associated with servicing and maintaining accounts. The Distributor may compensate other parties for providing shareholder support services to investors who purchase Institutional Class and Class A shares.

The Distributor has agreed to reduce its distribution fees to enable the Portfolio to maintain a minimum level of daily net investment income.

Morgan Stanley Services Company Inc. serves as Co-Transfer Agent and provides certain transfer agency services to the Portfolio with respect to certain direct transactions with the Portfolio.

G. Federal Income Taxes: It is the Portfolio's intention to continue to qualify as a regulated investment company and distribute all of its taxable and tax-exempt income. Accordingly, no provision for federal income taxes is required in the financial statements.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Notes to Financial Statements (cont'd)

financial statements. If applicable, the Portfolio recognizes interest accrued related to unrecognized tax benefits in "Interest Expense" and penalties in "Other Expenses" in the Statement of Operations. The Portfolio files tax returns with the U.S. Internal Revenue Service, New York and various states. The tax period ended September 30, 2016, remains subject to examination by taxing authorities.

The tax character of distributions paid may differ from the character of distributions shown in the Statement of Changes in Net Assets due to short-term capital gains being treated as ordinary income for tax purposes. The tax character of distributions paid during fiscal year 2016 was as follows:

2016 Distributions Paid From: Ordinary Income (000)
$	928

At September 30, 2016, the components of distributable earnings for the Portfolio on a tax basis were as follows:

Undistributed Ordinary Income (000)				Undistributed Long-Term Capital Gain (000)
$	245			$	—

H. Credit Facility: As of April 4, 2016, the Fund and other Morgan Stanley funds participate in a $150,000,000 committed, unsecured revolving line of credit facility (the "facility") with State Street. This facility is to be used for temporary emergency purposes or funding of shareholder redemption requests. The interest rate on borrowings is based on the federal funds rate or one month libor rate plus a spread. The facility also has a commitment fee of 0.25% per annum based on the unused portion of the facility. During the period ended September 30, 2016, the Portfolio did not have any borrowings under the facility.

I. Other: At September 30, 2016, the Portfolio had record owners of 10% or greater. Investment activities of these shareholders could have a material impact on the Portfolio. The aggregate percentage of such owners was 56.1%.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Report of Independent Registered Public Accounting Firm

To the Shareholders and Board of Trustees of
Morgan Stanley Institutional Fund Trust —
Ultra-Short Income Portfolio

We have audited the accompanying statement of assets and liabilities, including the portfolio of investments, of Ultra-Short Income Portfolio (one of the portfolios constituting Morgan Stanley Institutional Fund Trust) (the "Portfolio") as of September 30, 2016 and the related statements of operations and changes in net assets and the financial highlights for the period from April 28, 2016 (commencement of operations) to September 30, 2016. These financial statements and financial highlights are the responsibility of the Portfolio's management. Our responsibility is to express an opinion on these financial statements and financial highlights based on our audit.

We conducted our audit in accordance with the standards of the Public Company Accounting Oversight Board (United States). Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements and financial highlights are free of material misstatement. We were not engaged to perform an audit of the Portfolio's internal control over financial reporting. Our audit included consideration of internal control over financial reporting as a basis for designing audit procedures that are appropriate in the circumstances, but not for the purpose of expressing an opinion on the effectiveness of the Portfolio's internal control over financial reporting. Accordingly, we express no such opinion. An audit also includes examining, on a test basis, evidence supporting the amounts and disclosures in the financial statements and financial highlights, assessing the accounting principles used and significant estimates made by management, and evaluating the overall financial statement presentation. Our procedures included confirmation of securities owned as of September 30, 2016, by correspondence with the custodian and others or by other appropriate auditing procedures where replies from others were not received. We believe that our audit provides a reasonable basis for our opinion.

In our opinion, the financial statements and financial highlights referred to above present fairly, in all material respects, the financial position of Ultra-Short Income Portfolio (one of the portfolios constituting Morgan Stanley Institutional Fund Trust) at September 30, 2016, the results of its operations, changes in its net assets and the financial highlights for the period from April 28, 2016 (commencement of operations) to September 30, 2016, in conformity with U.S. generally accepted accounting principles.

Boston, Massachusetts
November 22, 2016

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Advisory Agreement Approval (unaudited)

The Board considered the following factors at the time of approval of the contracts which occurred prior to commencement of operations.

Nature, Extent and Quality of Services

The Board reviewed and considered the nature and extent of the investment advisory services to be provided by the Adviser (as defined herein) under the advisory agreement, including portfolio management, investment research and equity and fixed income securities trading. The Board also reviewed and considered the nature and extent of the non-advisory, administrative services to be provided by the Adviser under the administration agreement, including accounting, operations, clerical, bookkeeping, compliance, business management and planning, legal services and the provision of supplies, office space and utilities at the Adviser's expense. The Board also considered the Adviser's investment in personnel and infrastructure that benefits the Portfolio. (The advisory and administration agreements together are referred to as the "Management Agreement.") The Board also considered that the Adviser serves a variety of other investment advisory clients and has experience overseeing service providers.

The Board reviewed and considered the qualifications of the portfolio managers, the senior administrative managers and other key personnel of the Adviser who will provide the administrative and advisory services to the Portfolio. The Board determined that the Adviser's portfolio managers and key personnel are well qualified by education and/or training and experience to perform the services in an efficient and professional manner. The Board concluded that the nature and extent of the advisory and administrative services to be provided were necessary and appropriate for the conduct of the business and investment activities of the Portfolio and supported its decision to approve the Management Agreement.

Performance, Fees and Expenses of the Portfolio

The Board considered that the Adviser plans to arrange for a public offering of shares of the Portfolio to raise assets for investment and that the offering had not yet begun and concluded that, since the Portfolio currently had no assets to invest (other than seed capital required under the Investment Company Act) and had no track record of performance, this was not a factor it needed to address at the present time.

The Board reviewed the advisory and administrative fee rates (the "management fee rates") proposed to be paid by the Portfolio under the Management Agreement relative to comparable funds advised by the Adviser, when applicable, and compared to their peers as determined by the Adviser, and reviewed the anticipated total expense ratio of the Portfolio. The Board considered that the Portfolio requires the Adviser to develop processes, invest in additional resources and incur additional risks to successfully manage the Portfolio and concluded that the proposed management fee rate and anticipated total expense ratio would be competitive with its peer group averages.

Economies of Scale

The Board considered the growth prospects of the Portfolio and the structure of the proposed management fee schedule, which does not include breakpoints. The Board considered that the Portfolio's potential growth was uncertain and concluded that it would be premature to consider economies of scale as a factor in approving the Management Agreement at the present time.

Profitability of the Adviser and Affiliates

Since the Portfolio had not begun operations and had not paid any fees to the Adviser, the Board concluded that this was not a factor that needed to be considered at the present time.

Other Benefits of the Relationship

The Board considered other direct and indirect benefits to the Adviser and/or its affiliates to be derived from their relationship with the Portfolio and other funds advised by the Adviser. These benefits may include, among other things, fees for trading, distribution and/or shareholder servicing and for transaction processing and reporting platforms used by securities lending agents, and research received by the Adviser generated from commission dollars spent on funds' portfolio trading. Since the Portfolio had not begun operations and had not paid any fees to the Adviser, the Board concluded that these benefits were not a factor that needed to be considered at the present time.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Investment Advisory Agreement Approval (unaudited) (cont'd)

Resources of the Adviser and Historical Relationship Between the Portfolio and the Adviser

The Board considered whether the Adviser is financially sound and has the resources necessary to perform its obligations under the Management Agreement. The Board also reviewed and considered the organizational structure of the Adviser, the policies and procedures formulated and adopted by the Adviser for managing the Portfolio's operations and the Board's confidence in the competence and integrity of the senior managers and key personnel of the Adviser. The Board concluded that the Adviser has the financial resources necessary to fulfill its obligations under the Management Agreement and that it is beneficial for the Portfolio to enter into this relationship with the Adviser.

Other Factors and Current Trends

General Conclusion

After considering and weighing all of the above factors, with various written materials and verbal information presented by the Adviser, the Board concluded that it would be in the best interest of the Portfolio and its future shareholders to approve the Management Agreement, which will remain in effect for two years and thereafter must be approved annually by the Board of the Portfolio if it is to continue in effect. In reaching this conclusion the Board did not give particular weight to any single piece of information or factor referenced above. It is possible that individual Board members may have weighed these factors, and the information presented, differently in reaching their individual decisions to approve the Management Agreement.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Privacy Notice (unaudited)

MORGAN STANLEY INVESTMENT MANAGEMENT INC.
AN IMPORTANT NOTICE CONCERNING OUR U.S. PRIVACY POLICY

WE RESPECT YOUR PRIVACY

1. WHAT PERSONAL INFORMATION DO WE COLLECT ABOUT YOU?

For example:

• We may obtain information about your creditworthiness and credit history from consumer reporting agencies.

• We may collect background information from and through third-party vendors to verify representations you have made and to comply with various regulatory requirements.

2. WHEN DO WE DISCLOSE PERSONAL INFORMATION WE COLLECT ABOUT YOU?

We may disclose personal information we collect about you to other Morgan Stanley companies and to non-affiliated third parties.

a. Information We Disclose to Other Morgan Stanley Companies.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Privacy Notice (unaudited) (cont'd)

b. Information We Disclose to Non-affiliated Third Parties.

3. HOW DO WE PROTECT THE SECURITY AND CONFIDENTIALITY OF PERSONAL INFORMATION WE COLLECT ABOUT YOU?

4. HOW CAN YOU LIMIT THE SHARING OF CERTAIN TYPES OF PERSONAL INFORMATION WITH OTHER MORGAN STANLEY COMPANIES?

5. HOW CAN YOU LIMIT THE USE OF CERTAIN TYPES OF PERSONAL INFORMATION BY OTHER MORGAN STANLEY COMPANIES FOR MARKETING?

6. HOW CAN YOU SEND US AN OPT-OUT INSTRUCTION?

• Calling us at (800) 548-7786
Monday–Friday between 8a.m. and 6p.m.(EST)

• Writing to us at the following address:

Boston Financial Data Services, Inc.
c/o Privacy Coordinator
P.O. Box 219804
Kansas City, Missouri 64121

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Privacy Notice (unaudited) (cont'd)

7. WHAT IF AN AFFILIATED COMPANY BECOMES A NON-AFFILIATED THIRD PARTY?

SPECIAL NOTICE TO RESIDENTS OF VERMONT

If you wish to receive offers for investment products and services offered by or through other Morgan Stanley companies, please notify us in writing at the following address:

Boston Financial Data Services, Inc.
c/o Privacy Coordinator
P.O. Box 219804
Kansas City, Missouri 64121

SPECIAL NOTICE TO RESIDENTS OF CALIFORNIA

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited)

Independent Trustees:

Name, Age and Address of
Independent Trustee

Position(s)
Held with
Registrant

Length of
Time Served*

Principal Occupation(s) During Past 5 Years
and Other Relevant Professional Experience

Number of
Portfolios in
Fund Complex
Overseen by
Trustee**

Other Directorships
Held by Independent
Trustee***

Frank L. Bowman (71)
c/o Perkins Coie LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
August
2006

Director of BP p.l.c.; Director of Naval and Nuclear Technologies LLP; Director Emeritus of the Armed Services YMCA; Director of the U.S. Naval Submarine League; Member of the National Security Advisory Council of the Center for U.S. Global Engagement and a member of the CNA Military Advisory Board; Chairman of the charity J Street Cup Golf ; Trustee of Fairhaven United Methodist Church; and Director of other various non-profit organizations.

Kathleen A. Dennis (63)
c/o Perkins Coie LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
August
2006

Director of various nonprofit organizations.

Nancy C. Everett (61)
c/o Perkins Coie LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
January
2015

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Age and Address of
Independent Trustee

Position(s)
Held with
Registrant

Length of
Time Served*

Principal Occupation(s) During Past 5 Years
and Other Relevant Professional Experience

Number of
Portfolios in
Fund Complex
Overseen by
Trustee**

Other Directorships
Held by Independent
Trustee***

Jakki L. Haussler (59)
c/o Perkins Coie LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
January
2015

Dr. Manuel H. Johnson (67)
c/o Perkins Coli LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
July
1991

100

Director of NVR, Inc. (home construction).

Joseph J. Kearns (74)
c/o Perkins Coli LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
August
1994

101

Director of Electro Rent Corporation (equipment leasing). Prior to December 31, 2013, Director of The Ford Family Foundation.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited) (cont'd)

Independent Trustees: (cont'd)

Name, Age and Address of
Independent Trustee

Position(s)
Held with
Registrant

Length of
Time Served*

Principal Occupation(s) During Past 5 Years
and Other Relevant Professional Experience

Number of
Portfolios in
Fund Complex
Overseen by
Trustee**

Other Directorships
Held by Independent
Trustee***

Michael F. Klein (57)
c/o Perkins Coie LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
August
2006

Director of certain investment funds managed or sponsored by Aetos Capital, LLC; Director of Sanitized AG and Sanitized Marketing AG (specialty chemicals).

Michael E. Nugent (80)
522 Fifth Avenue
New York, NY 10036

Chair of the Board and Trustee

Chair of the Boards since July 2006 and Trustee since July 1991

100

None.

W. Allen Reed (69)
c/o Perkins Coie LLP
Counsel to the Independent
Trustees
30 Rockefeller Plaza
New York, NY 10112

Trustee

Since
August
2006

Director of Legg Mason, Inc.; formerly, Director of the Auburn University Foundation (2010-2015).

Fergus Reid (84)
c/o Joe Pietryka, Inc.
85 Charles Colman Blvd.
Pawling, NY 12564

Trustee

Since
June
1992

Chairman, Joe Pietryka, Inc.; Chairperson of the Governance Committee and Director or Trustee of various Morgan Stanley Funds (since June 1992).

100

Formerly, Trustee and Director of certain investment companies in the JP Morgan Fund Complex managed by JP Morgan Investment Management Inc. (1987-2012).

* This is the earliest date the Trustee began serving the Morgan Stanley Funds. Each Trustee serves an indefinite term, until his or her successor is elected.

*** This includes any directorships at public companies and registered investment companies held by the Trustee at any time during the past five years.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Trustee and Officer Information (unaudited) (cont'd)

Executive Officers:

Name, Age and Address of
Executive Officer

Position(s)
Held with
Registrant

Length of
Time Served*

Principal Occupation(s) During Past 5 Years

John H. Gernon (53)
522 Fifth Avenue
New York, NY 10036

President and Principal Executive Officer

Since
September
2013

Stefanie V. Chang Yu (49)
522 Fifth Avenue
New York, NY 10036

Chief Compliance Officer

Since
December
1997

Joseph C. Benedetti (51)
522 Fifth Avenue
New York, NY 10036

Vice President

Since
January
2014

Francis J. Smith (51)
522 Fifth Avenue
New York, NY 10036

Treasurer and Principal Financial Officer

Treasurer since July 2003 and Principal Financial Officer since September 2002

Executive Director of the Adviser and various entities affiliated with the Adviser; Treasurer (since July 2003) and Principal Financial Officer of various Morgan Stanley Funds (since September 2002).

Mary E. Mullin (49)
522 Fifth Avenue
New York, NY 10036

Secretary

Since
June
1999

Executive Director of the Adviser; Secretary of various Morgan Stanley Funds (since June 1999).

* This is the earliest date the officer began serving the Morgan Stanley Funds. Each officer serves a one-year term, until his or her successor is elected and has qualified.

Morgan Stanley Institutional Fund Trust

Annual Report — September 30, 2016

Adviser and Administrator

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

Distributor

Morgan Stanley Distribution, Inc.
522 Fifth Avenue
New York, New York 10036

Dividend Disbursing and Transfer Agent

Boston Financial Data Services, Inc.
2000 Crown Colony Drive
Quincy, Massachusetts 02169

Co-Transfer Agent

Morgan Stanley Services Company, Inc.
522 Fifth Avenue
New York, New York 10036

Custodian

State Street Bank and Trust Company
One Lincoln Street
Boston, Massachusetts 02111

Legal Counsel

Dechert LLP
1095 Avenue of the Americas
New York, New York 10036

Counsel to the Independent Trustees

Perkins Coie LLP
30 Rockefeller Plaza
New York, New York 10112

Independent Registered Public Accounting Firm

Ernst & Young LLP
200 Clarendon Street
Boston, Massachusetts 02116

Reporting to Shareholders

Proxy Voting Policies and Procedures and Proxy Voting Record

This report is authorized for distribution only when preceded or accompanied by a prospectus or summary prospectus of the applicable Portfolio of Morgan Stanley Institutional Fund Trust, which describes in detail the Portfolio's investment policies, risks, fees and expenses. Please read the prospectus carefully before you invest or send money. For additional information, including information regarding the investments comprising the Portfolio, please visit our website at www.morganstanley.com/im or call toll free 1 (800) 548-7786.

(This Page has been left blank intentionally.)

Printed in U.S.A.
This Report has been prepared for shareholders and may be distributed to others only if preceded or accompanied by a current prospectus.

Morgan Stanley Investment Management Inc.
522 Fifth Avenue
New York, New York 10036

IFTUSIANN
1629560 EXP. 11.30.17

Item 2. Code of Ethics.

(a) The Fund has adopted a code of ethics (the “Code of Ethics”) that applies to its principal executive officer, principal financial officer, principal accounting officer or controller, or persons performing similar functions, regardless of whether these individuals are employed by the Fund or a third party.

(b) No information need be disclosed pursuant to this paragraph.

(d) Not applicable.

(e) Not applicable.

(f)

(1) The Fund’s Code of Ethics is attached hereto as Exhibit 12 A.

(2) Not applicable.

(3) Not applicable.

Item 3. Audit Committee Financial Expert.

The Fund’s Board of Trustees has determined that Joseph J. Kearns, an “independent” Trustee, is an “audit committee financial expert” serving on its audit committee. Under applicable securities laws, a person who is determined to be an audit committee financial expert will not be deemed an “expert” for any purpose, including without limitation for the purposes of Section 11 of the Securities Act of 1933, as a result of being designated or identified as an audit committee financial expert. The designation or identification of a person as an audit committee financial expert does not impose on such person any duties, obligations, or liabilities that are greater than the duties, obligations, and liabilities imposed on such person as a member of the audit committee and Board of Trustees in the absence of such designation or identification.

Item 4. Principal Accountant Fees and Services.

(a)(b)(c)(d) and (g). Based on fees billed for the periods shown:

2016

	Registrant			Covered Entities(1)
Audit Fees	$	501,002		N/A

Non-Audit Fees
Audit-Related Fees	$	—	(2)	$	—	(2)
Tax Fees	$	40,500	(3)	$	9,000,199	(4)
All Other Fees	$	—		$	288,825	(5)
Total Non-Audit Fees	$	40,500		$	9,289,024

Total	$	541,502		$	9,289,024

2015

	Registrant			Covered Entities(1)
Audit Fees	$	517,677		N/A

Non-Audit Fees
Audit-Related Fees	$	—	(2)	$	—	(2)
Tax Fees	$	40,000	(3)	$	7,968,463	(4)
All Other Fees	$	—		$	212,000	(5)
Total Non-Audit Fees	$	40,000		$	8,180,463

Total	$	557,677		$	8,180,463

N/A- Not applicable, as not required by Item 4.

(1) Covered Entities include the Adviser (excluding sub-advisors) and any entity controlling, controlled by or under common control with the Adviser that provides ongoing services to the Registrant.

(2) Audit-Related Fees represent assurance and related services provided that are reasonably related to the performance of the audit of the financial statements of the Covered Entities’ and funds advised by the Adviser or its affiliates, specifically data verification and agreed-upon procedures related to asset securitizations and agreed-upon procedures engagements.

(3) Tax Fees represent tax compliance, tax planning and tax advice services provided in connection with the preparation and review of the Registrant’s tax returns.

(4) Tax Fees represent tax compliance, tax planning and tax advice services provided in connection with the review of Covered Entities’ tax returns.

(5) All other fees represent project management for future business applications and improving business and operational processes.

(e)(1) The audit committee’s pre-approval policies and procedures are as follows:

APPENDIX A

AUDIT COMMITTEE

AUDIT AND NON-AUDIT SERVICES

PRE-APPROVAL POLICY AND PROCEDURES

OF THE

MORGAN STANLEY RETAIL AND INSTITUTIONAL FUNDS

AS ADOPTED AND AMENDED JULY 23, 2004,(1)

1. Statement of Principles

The Audit Committee of the Board is required to review and, in its sole discretion, pre-approve all Covered Services to be provided by the Independent Auditors to the Fund and Covered Entities in order to assure that services performed by the Independent Auditors do not impair the auditor’s independence from the Fund.

The SEC has issued rules specifying the types of services that an independent auditor may not provide to its audit client, as well as the audit committee’s administration of the engagement of the independent auditor. The SEC’s rules establish two different approaches to pre-approving services, which the SEC considers to be equally valid. Proposed services either: may be pre-approved without consideration of specific case-by-case services by the Audit Committee (“general pre-approval”); or require the specific pre-approval of the Audit Committee or its delegate (“specific pre-approval”). The Audit Committee believes that the combination of these two approaches in this Policy will result in an effective and efficient procedure to pre-approve services performed by the Independent Auditors. As set forth in this Policy, unless a type of service has received general pre-approval, it will require specific pre-approval by the Audit Committee (or by any member of the Audit Committee to which pre-approval authority has been delegated) if it is to be provided by the Independent Auditors. Any proposed services exceeding pre-approved cost levels or budgeted amounts will also require specific pre-approval by the Audit Committee.

The appendices to this Policy describe the Audit, Audit-related, Tax and All Other services that have the general pre-approval of the Audit Committee. The term of any general pre-approval is 12 months from the date of pre-approval, unless the Audit Committee considers and provides a different period and states otherwise. The Audit Committee will annually review and pre-approve the services that may be provided by the Independent Auditors without obtaining specific pre-approval from the Audit Committee. The Audit Committee will add to or subtract from the list of general pre-approved services from time to time, based on subsequent determinations.

(1) This Audit Committee Audit and Non-Audit Services Pre-Approval Policy and Procedures (the “Policy”), adopted as of the date above, supersedes and replaces all prior versions that may have been adopted from time to time.

The purpose of this Policy is to set forth the policy and procedures by which the Audit Committee intends to fulfill its responsibilities. It does not delegate the Audit Committee’s responsibilities to pre-approve services performed by the Independent Auditors to management.

The Fund’s Independent Auditors have reviewed this Policy and believes that implementation of the Policy will not adversely affect the Independent Auditors’ independence.

2. Delegation

As provided in the Act and the SEC’s rules, the Audit Committee may delegate either type of pre-approval authority to one or more of its members. The member to whom such authority is delegated must report, for informational purposes only, any pre-approval decisions to the Audit Committee at its next scheduled meeting.

3. Audit Services

The annual Audit services engagement terms and fees are subject to the specific pre-approval of the Audit Committee. Audit services include the annual financial statement audit and other procedures required to be performed by the Independent Auditors to be able to form an opinion on the Fund’s financial statements. These other procedures include information systems and procedural reviews and testing performed in order to understand and place reliance on the systems of internal control, and consultations relating to the audit. The Audit Committee will approve, if necessary, any changes in terms, conditions and fees resulting from changes in audit scope, Fund structure or other items.

In addition to the annual Audit services engagement approved by the Audit Committee, the Audit Committee may grant general pre-approval to other Audit services, which are those services that only the Independent Auditors reasonably can provide. Other Audit services may include statutory audits and services associated with SEC registration statements (on Forms N-1A, N-2, N-3, N-4, etc.), periodic reports and other documents filed with the SEC or other documents issued in connection with securities offerings.

The Audit Committee has pre-approved the Audit services in Appendix B.1. All other Audit services not listed in Appendix B.1 must be specifically pre-approved by the Audit Committee (or by any member of the Audit Committee to which pre-approval has been delegated).

4. Audit-related Services

Audit-related services are assurance and related services that are reasonably related to the performance of the audit or review of the Fund’s financial statements and, to the extent they are Covered Services, the Covered Entities or that are traditionally performed by the Independent Auditors. Because the Audit Committee believes that the provision of Audit-related services does not impair the independence of the auditor and is consistent with the SEC’s rules on auditor independence, the Audit Committee may grant general pre-approval to Audit-related services. Audit-related services include, among others, accounting consultations related to accounting, financial reporting or disclosure matters not classified as “Audit services”; assistance with understanding and implementing new accounting and financial reporting guidance from rulemaking authorities; agreed-upon or expanded audit procedures related to accounting and/or billing records required to respond to or comply with financial, accounting or regulatory

reporting matters; and assistance with internal control reporting requirements under Forms N-SAR and/or N-CSR.

The Audit Committee has pre-approved the Audit-related services in Appendix B.2. All other Audit-related services not listed in Appendix B.2 must be specifically pre-approved by the Audit Committee (or by any member of the Audit Committee to which pre-approval has been delegated).

5. Tax Services

The Audit Committee believes that the Independent Auditors can provide Tax services to the Fund and, to the extent they are Covered Services, the Covered Entities, such as tax compliance, tax planning and tax advice without impairing the auditor’s independence, and the SEC has stated that the Independent Auditors may provide such services.

Pursuant to the preceding paragraph, the Audit Committee has pre-approved the Tax Services in Appendix B.3. All Tax services in Appendix B.3 must be specifically pre-approved by the Audit Committee (or by any member of the Audit Committee to which pre-approval has been delegated).

6. All Other Services

The Audit Committee believes, based on the SEC’s rules prohibiting the Independent Auditors from providing specific non-audit services, that other types of non-audit services are permitted. Accordingly, the Audit Committee believes it may grant general pre-approval to those permissible non-audit services classified as All Other services that it believes are routine and recurring services, would not impair the independence of the auditor and are consistent with the SEC’s rules on auditor independence.

The Audit Committee has pre-approved the All Other services in Appendix B.4. Permissible All Other services not listed in Appendix B.4 must be specifically pre-approved by the Audit Committee (or by any member of the Audit Committee to which pre-approval has been delegated).

7. Pre-Approval Fee Levels or Budgeted Amounts

Pre-approval fee levels or budgeted amounts for all services to be provided by the Independent Auditors will be established annually by the Audit Committee. Any proposed services exceeding these levels or amounts will require specific pre-approval by the Audit Committee. The Audit Committee is mindful of the overall relationship of fees for audit and non-audit services in determining whether to pre-approve any such services.

8. Procedures

All requests or applications for services to be provided by the Independent Auditors that do not require specific approval by the Audit Committee will be submitted to the Fund’s Chief Financial Officer and must include a detailed description of the services to be rendered. The Fund’s Chief Financial Officer will determine whether such services are included within the list of services that have received the general pre-approval of the Audit Committee. The Audit Committee will be informed on a timely basis of any such services rendered by the Independent Auditors. Requests or applications to provide services that require specific approval by the

Audit Committee will be submitted to the Audit Committee by both the Independent Auditors and the Fund’s Chief Financial Officer, and must include a joint statement as to whether, in their view, the request or application is consistent with the SEC’s rules on auditor independence.

The Audit Committee has designated the Fund’s Chief Financial Officer to monitor the performance of all services provided by the Independent Auditors and to determine whether such services are in compliance with this Policy. The Fund’s Chief Financial Officer will report to the Audit Committee on a periodic basis on the results of its monitoring. Both the Fund’s Chief Financial Officer and management will immediately report to the chairman of the Audit Committee any breach of this Policy that comes to the attention of the Fund’s Chief Financial Officer or any member of management.

9. Additional Requirements

The Audit Committee has determined to take additional measures on an annual basis to meet its responsibility to oversee the work of the Independent Auditors and to assure the auditor’s independence from the Fund, such as reviewing a formal written statement from the Independent Auditors delineating all relationships between the Independent Auditors and the Fund, consistent with Independence Standards Board No. 1, and discussing with the Independent Auditors its methods and procedures for ensuring independence.

10. Covered Entities

Covered Entities include the Fund’s investment adviser(s) and any entity controlling, controlled by or under common control with the Fund’s investment adviser(s) that provides ongoing services to the Fund(s). Beginning with non-audit service contracts entered into on or after May 6, 2003, the Fund’s audit committee must pre-approve non-audit services provided not only to the Fund but also to the Covered Entities if the engagements relate directly to the operations and financial reporting of the Fund. This list of Covered Entities would include:

Morgan Stanley Retail Funds

Morgan Stanley Investment Advisors Inc.

Morgan Stanley & Co. Incorporated

Morgan Stanley DW Inc.

Morgan Stanley Investment Management Inc.

Morgan Stanley Investment Management Limited

Morgan Stanley Investment Management Private Limited

Morgan Stanley Asset & Investment Trust Management Co., Limited

Morgan Stanley Investment Management Company

Morgan Stanley Services Company, Inc.

Morgan Stanley Distributors Inc.

Morgan Stanley Trust FSB

Morgan Stanley Institutional Funds

Morgan Stanley Investment Management Inc.

Morgan Stanley Investment Advisors Inc.

Morgan Stanley Investment Management Limited

Morgan Stanley Investment Management Private Limited

Morgan Stanley Asset & Investment Trust Management Co., Limited

Morgan Stanley Investment Management Company

Morgan Stanley & Co. Incorporated

Morgan Stanley Distribution, Inc.

Morgan Stanley AIP GP LP

Morgan Stanley Alternative Investment Partners LP

(e)(2) Beginning with non-audit service contracts entered into on or after May 6, 2003, the audit committee also is required to pre-approve services to Covered Entities to the extent that the services are determined to have a direct impact on the operations or financial reporting of the Registrant. 100% of such services were pre-approved by the audit committee pursuant to the Audit Committee’s pre-approval policies and procedures (attached hereto).

(f) Not applicable.

(g) See table above.

(h) The audit committee of the Board of Trustees has considered whether the provision of services other than audit services performed by the auditors to the Registrant and Covered Entities is compatible with maintaining the auditors’ independence in performing audit services.

Item 5. Audit Committee of Listed Registrants.

(a) The Fund has a separately-designated standing audit committee established in accordance with Section 3(a)(58)(A) of the Exchange Act whose members are:

Joseph J. Kearns, Jakki L. Haussler, Michael F. Klein and Allen W. Reed.

(b) Not applicable.

Item 6. Schedule of Investments

(a) Refer to Item 1.

(b) Not applicable.

Item 7. Disclosure of Proxy Voting Policies and Procedures for Closed-End Management Investment Companies.

Applicable only to reports filed by closed-end funds.

Item 8. Portfolio Managers of Closed-End Management Investment Companies

Applicable only to reports filed by closed-end funds.

Item 9. Closed-End Fund Repurchases

Applicable only to reports filed by closed-end funds.

Item 10. Submission of Matters to a Vote of Security Holders

Not applicable.

Item 11. Controls and Procedures

(a) The Fund’s principal executive officer and principal financial officer have concluded that the Fund’s disclosure controls and procedures are sufficient to ensure that information required to be disclosed by the Fund in this Form N-CSR was recorded, processed, summarized and reported within the time periods specified in the Securities and Exchange Commission’s rules and forms, based upon such officers’ evaluation of these controls and procedures as of a date within 90 days of the filing date of the report.

(b) There were no changes in the registrant’s internal control over financial reporting that occurred during the second fiscal quarter of the period covered by this report that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting.

Item 12. Exhibits

(a) The Code of Ethics for Principal Executive and Senior Financial Officers is attached hereto.

(b) A separate certification for each principal executive officer and principal financial officer of the registrant are attached hereto as part of EX-99.CERT.

SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934 and the Investment Company Act of 1940, the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized.

Morgan Stanley Institutional Fund Trust

/s/ John H. Gernon
John H. Gernon
Principal Executive Officer
November 17, 2016

Pursuant to the requirements of the Securities Exchange Act of 1934 and the Investment Company Act of 1940, this report has been signed by the following persons on behalf of the registrant and in the capacities and on the dates indicated.

/s/ John H. Gernon
John H. Gernon
Principal Executive Officer
November 17, 2016

/s/ Francis Smith
Francis Smith
Principal Financial Officer
November 17, 2016

Morgan Stanley Institutional Fund Trust N-CSRCertified annual shareholder report (management investment company)