UNITED STATES SECURITIES AND EXCHANGE ~~COMMISSION~~COMM ISSION

Washington, D.C. 20549

FORM 10-Q

(Mark One)


þ		Quarterly Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934

For the quarterly period ended: ~~December~~March 31, ~~2009~~2010


o		Transition Report Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934

For the transition period from to

Commission File Number 0-25434

BROOKS AUTOMATION, ~~INC.~~INC.

(Exact name of registrant as specified in its charter)


Delaware		04-3040660

(State or other jurisdiction of		(I.R.S. Employer
incorporation or organization)		~~(I.R.S. Employer~~ Identification No.)

15 Elizabeth Drive
Chelmsford, Massachusetts
(Address of principal executive offices)

01824
(Zip Code)

Registrant’s telephone number, including area code: (978) 262-2400

Indicate by check mark whether the registrant: (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yesþ Noo

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files). Yeso Noo

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company. See the definitions of “large accelerated filer,” “accelerated filer” and “smaller reporting company” in Rule 12b-2 of the Exchange Act. (Check one):


Large accelerated filero	Accelerated filerþ	~~Accelerated~~Non-accelerated filerþo	~~Non-accelerated filer~~Smaller reporting companyo
	(Do not check if a smaller reporting company)			~~Smaller reporting company~~o

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). Yeso Noþ

~~APPLICABLE ONLY TO ISSUERS INVOLVED IN BANKRUPTCY PROCEDINGS DURING THE PRECEDING FIVE YEARS~~

Indicate by check mark whether the registrant has filed all documents and reports required to be filed by Section 12, 13 or 15(d) of the Securities Exchange Act of 1934 subsequent to the distribution of securities under a plan confirmed by a court. Yeso Noo

Indicate the number of shares outstanding of each of the registrant’s classes of common stock, as of the latest practical date, ~~January 29,~~April 30, 2010: Common stock, $0.01 par value ~~64,551,247~~64,993,400 shares

PART I. FINANCIAL INFORMATION

Item 1.Consolidated Financial Statements

BROOKS AUTOMATION, INC.

CONSOLIDATED BALANCE SHEETS

(unaudited)

(In thousands, except share and per share data)


	December 31,			September 30,			March 31,			September 30,
	2009			2009			2010			2009
Assets
Current assets
Cash and cash equivalents	$	47,164		$	59,985		$	48,621		$	59,985
Marketable securities		38,038			28,046			35,804			28,046
Accounts receivable, net		53,193			38,428			67,584			38,428
Insurance receivable for litigation		204			120
Inventories, net		89,763			84,738			103,528			84,738
Prepaid expenses and other current assets		10,464			9,872			13,939			9,992

Total current assets		238,826			221,189			269,476			221,189
Property, plant and equipment, net		71,391			74,793			68,420			74,793
Long-term marketable securities		26,157			22,490			41,335			22,490
Goodwill		48,138			48,138			48,138			48,138
Intangible assets, net		13,133			14,081			13,063			14,081
Equity investment in joint ventures		29,362			29,470			28,962			29,470
Other assets		2,684			3,161			2,613			3,161

Total assets	$	429,691		$	413,322		$	472,007		$	413,322

Liabilities and equity
Current liabilities
Accounts payable	$	46,243		$	26,360		$	66,721		$	26,360
Deferred revenue		4,097			2,916			3,917			2,916
Accrued warranty and retrofit costs		5,734			5,698			7,122			5,698
Accrued compensation and benefits		10,370			14,317			11,232			14,317
Accrued restructuring costs		4,786			5,642			4,434			5,642
Accrued income taxes payable		2,925			2,686			2,197			2,686
Accrued expenses and other current liabilities		11,716			12,870			10,753			12,870

Total current liabilities		85,871			70,489			106,376			70,489
Accrued long-term restructuring		2,263			2,019			1,344			2,019
Income taxes payable		11,035			10,755			11,097			10,755
Long-term pension liability		8,070			7,913			8,249			7,913
Other long-term liabilities		2,625			2,523			2,630			2,523

Total liabilities		109,864			93,699			129,696			93,699

Contingencies (Note 14)
Contingencies (Note 15)
Equity
Preferred stock, $0.01 par value, 1,000,000 shares authorized, no shares issued and outstanding		—			—			—			—
Common stock, $0.01 par value, 125,000,000 shares authorized, 78,013,116 shares issued and 64,551,247 shares outstanding at December 31, 2009, 77,883,173 shares issued and 64,421,304 shares outstanding at September 30, 2009		780			779
Common stock, $0.01 par value, 125,000,000 shares authorized, 78,453,069 shares issued and 64,991,200 shares outstanding at March 31, 2010, 77,883,173 shares issued and 64,421,304 shares outstanding at September 30, 2009								785			779
Additional paid-in capital		1,798,235			1,795,619			1,799,781			1,795,619
Accumulated other comprehensive income		16,781			16,318			16,766			16,318
Treasury stock at cost, 13,461,869 shares at December 31, 2009 and September 30, 2009		(200,956	)		(200,956	)
Treasury stock at cost, 13,461,869 shares at March 31, 2010 and September 30, 2009								(200,956	)		(200,956	)
Accumulated deficit		(1,295,426	)		(1,292,631	)		(1,274,397	)		(1,292,631	)

Total Brooks Automation, Inc. stockholders’ equity		319,414			319,129			341,979			319,129
Noncontrolling interest in subsidiaries		413			494			332			494

Total equity		319,827			319,623			342,311			319,623

Total liabilities and equity	$	429,691		$	413,322		$	472,007		$	413,322

BROOKS AUTOMATION, INC.

CONSOLIDATED STATEMENTS OF OPERATIONS

(unaudited)

(In thousands, except per share data)


	Three months ended						Three months ended						Six months ended
	December 31,						March 31,						March 31,
	2009			2008			2010			2009			2010			2009
Revenues
Product	$	91,521		$	59,086		$	133,389		$	25,883		$	224,910		$	84,969
Services		14,676			14,360			14,964			11,416			29,640			25,776

Total revenues		106,197			73,446			148,353			37,299			254,550			110,745

Cost of revenues
Product		67,245			53,869			97,271			31,909			164,516			85,778
Services		12,706			13,189			12,132			12,670			24,838			25,859
Impairment of long-lived assets								—			20,516			—			20,516

Total cost of revenues		79,951			67,058			109,403			65,095			189,354			132,153

Gross profit		26,246			6,388
Gross profit (loss)								38,950			(27,796	)		65,196			(21,408	)

Operating expenses
Research and development		7,541			9,277			7,677			7,666			15,218			16,943
Selling, general and administrative		18,979			27,634			20,842			25,207			39,821			52,841
Impairment of goodwill								—			71,800			—			71,800
Impairment of long-lived assets								—			14,588			—			14,588
Restructuring charges		1,522			4,105			484			5,861			2,006			9,966

Total operating expenses		28,042			41,016			29,003			125,122			57,045			166,138

Operating loss		(1,796	)		(34,628	)
Operating income (loss)								9,947			(152,918	)		8,151			(187,546	)
Interest income		328			897			265			646			593			1,543
Interest expense		16			126			11			72			27			198
Sale of intellectual property rights								7,840			—			7,840			—
Loss on investment		191			1,185			—			—			191			1,185
Other expense, net		197			38			91			111			288			149

Loss before income taxes and equity in earnings (losses) of joint ventures		(1,872	)		(35,080	)
Income tax provision		635			391
Income (loss) before income taxes and equity in earnings (losses) of joint ventures								17,950			(152,455	)		16,078			(187,535	)
Income tax provision (benefit)								(2,819	)		189			(2,184	)		580

Loss before equity in earnings (losses) of joint ventures		(2,507	)		(35,471	)
Income (loss) before equity in earnings (losses) of joint ventures								20,769			(152,644	)		18,262			(188,115	)
Equity in earnings (losses) of joint ventures		(370	)		301			179			11			(191	)		312

Net loss	$	(2,877	)	$	(35,170	)
Net income (loss)							$	20,948		$	(152,633	)	$	18,071		$	(187,803	)
Add: Net loss attributable to noncontrolling interests		82			87			81			90			163			177

Net loss attributable to Brooks Automation, Inc.	$	(2,795	)	$	(35,083	)
Net income (loss) attributable to Brooks Automation, Inc.							$	21,029		$	(152,543	)	$	18,234		$	(187,626	)


Basic net loss per share attributable to Brooks Automation, Inc. common stockholders	$	(0.04	)	$	(0.56	)
Basic net income (loss) per share attributable to Brooks Automation, Inc. common stockholders							$	0.33		$	(2.43	)	$	0.29		$	(2.99	)

Diluted net loss per share attributable to Brooks Automation, Inc. common stockholders	$	(0.04	)	$	(0.56	)
Diluted net income (loss) per share attributable to Brooks Automation, Inc. common stockholders							$	0.33		$	(2.43	)	$	0.28		$	(2.99	)

Shares used in computing loss per share
Shares used in computing earnings (loss) per share
Basic		63,394			62,651			63,679			62,844			63,535			62,747
Diluted		63,394			62,651			64,196			62,844			64,042			62,747

BROOKS AUTOMATION, INC.

CONSOLIDATED STATEMENTS OF CASH FLOWS

(unaudited)

(In thousands)


	Three months ended						Six months ended
	December 31,						March 31,
	2009			2008			2010			2009
Cash flows from operating activities
Net loss	$	(2,877	)	$	(35,170	)
Adjustments to reconcile net loss to net cash provided by (used in) operating activities:
Net income (loss)							$	18,071		$	(187,803	)
Adjustments to reconcile net income (loss) to net cash provided by (used in) operating activities:
Depreciation and amortization		4,794			8,380			9,460			16,324
Impairment of goodwill								—			71,800
Impairment of long-lived assets								—			35,104
Sale of intellectual property rights								(7,840	)		—
Stock-based compensation		1,517			1,524			3,561			3,394
Amortization of premium (discount) on marketable securities		136			(34	)
Amortization of premium on marketable securities								368			19
Undistributed (earnings) losses of joint ventures		370			(301	)		191			(312	)
Gain on disposal of long-lived assets		—			(8	)
(Gain) loss on disposal of long-lived assets								(4	)		70
Loss on investment		191			1,185			191			1,185
Changes in operating assets and liabilities, net of acquisitions and disposals:
Accounts receivable		(14,759	)		26,330			(29,258	)		40,688
Inventories		(5,163	)		(3,252	)		(19,653	)		6,522
Prepaid expenses and other current assets		(834	)		71			(4,132	)		4,254
Accounts payable		19,902			(7,580	)		40,424			(21,109	)
Deferred revenue		1,199			(330	)		1,062			(1,151	)
Accrued warranty and retrofit costs		32			(237	)		1,414			(1,502	)
Accrued compensation and benefits		(2,834	)		(1,201	)		(2,972	)		(3,486	)
Accrued restructuring costs		(605	)		890			(1,857	)		1,898
Accrued expenses and other		413			(3,745	)		235			(2,820	)

Net cash provided by (used in) operating activities		1,482			(13,478	)		9,261			(36,925	)

Cash flows from investing activities
Purchases of property, plant and equipment		(461	)		(5,084	)		(1,163	)		(9.091	)
Purchases of marketable securities		(43,983	)		(35,022	)		(70,872	)		(50,539	)
Sale/maturity of marketable securities		29,853			22,533			43,757			36,735
Proceeds from the sale of investment		240			—
Proceeds from the sale of intellectual property rights								7,840			—
Purchase of intangible assets								(892	)		—
Other								243			—

Net cash used in investing activities		(14,351	)		(17,573	)		(21,087	)		(22,895	)

Cash flows from financing activities
Proceeds from issuance of common stock, net of issuance costs								590			675

Net cash provided by financing activities								590			675

Effects of exchange rate changes on cash and cash equivalents		48			(1,118	)		(128	)		(1,967	)

Net decrease in cash and cash equivalents		(12,821	)		(32,169	)		(11,364	)		(61,112	)
Cash and cash equivalents, beginning of period		59,985			110,269			59,985			110,269

Cash and cash equivalents, end of period	$	47,164		$	78,100		$	48,621		$	49,157

BROOKS AUTOMATION, INC.

NOTES TO CONSOLIDATED FINANCIAL STATEMENTS (unaudited)

1. Basis of Presentation

The unaudited condensed consolidated financial statements of Brooks Automation, Inc. and its subsidiaries (“Brooks” or the “Company”) included herein have been prepared in accordance with generally accepted accounting principles. In the opinion of management, all material adjustments which are of a normal and recurring nature necessary for a fair presentation of the results for the periods presented have been reflected.

Certain information and footnote disclosures normally included in the Company’s annual consolidated financial statements have been condensed or omitted and, accordingly, the accompanying financial information should be read in conjunction with the consolidated financial statements and notes thereto contained in the Company’s Annual Report on Form 10-K, filed with the United States Securities and Exchange Commission (the “SEC”) for the year ended September 30, 2009. Certain reclassifications have been made in the prior period consolidated financial statements to conform to the current presentation.

~~We evaluated subsequent events through February 5, 2010, the date of financial statement issuance.~~

Recently Enacted Accounting Pronouncements

In September 2006, the Financial Accounting Standards Board (“FASB”) issued authoritative guidance for Fair Value Measurements and Disclosures which defines fair value, establishes a framework for measuring fair value and expands disclosures about assets and liabilities measured at fair value in the financial statements. In February 2008, the FASB issued authoritative guidance which ~~allows~~allowed for the delay of the effective date for fair value measurements for one year for all non-financial assets and non-financial liabilities, except for items that are recognized or disclosed at fair value in the financial statements on a recurring basis (at least annually). In April 2009, the FASB issued additional authoritative guidance in determining whether a market is active or inactive, and whether a transaction is distressed, is applicable to all assets and liabilities (i.e., financial and non-financial) and ~~will require~~requires enhanced disclosures. This standard was effective beginning with the Company’s fourth quarter of fiscal 2009. The measurement and disclosure requirements related to financial assets and financial liabilities were effective for the Company beginning on October 1, 2008. See Note ~~13.~~14. On October 1, 2009 the Company adopted the fair value measurement standard for all non-financial assets and non-financial liabilities, which had no impact on its financial position or results of operations.

In December 2007, the FASB revised the authoritative guidance for Business Combinations, which significantly changes the accounting for business combinations in a number of areas including the treatment of contingent consideration, pre-acquisition contingencies, transaction costs, restructuring costs and income taxes. On October 1, 2009 the Company adopted this standard prospectively and will apply the standard to any business combination with an acquisition date after October 1, 2009.

In December 2007, the FASB issued authoritative guidance regarding Consolidation, which establishes accounting and reporting standards for noncontrolling interests in a subsidiary and for the deconsolidation of a subsidiary. This standard clarifies that a noncontrolling interest in a subsidiary is an ownership interest in the consolidated entity that should be reported as equity in the consolidated financial statements. The amount of net income attributable to the noncontrolling interest will be included in consolidated net income on the face of the income statement. Further, it clarifies that changes in a parent’s ownership interest in a subsidiary that do not result in deconsolidation are equity transactions if the parent retains its controlling financial interest. In addition, this standard requires that a parent recognize a gain or loss in net income when a subsidiary is deconsolidated. On October 1, 2009 the Company adopted this standard retrospectively, which did not have a material impact on its financial position or results of operations.

In June 2008, the FASB issued authoritative guidance regarding whether instruments granted in share-based payment transactions are participating securities, which classifies unvested share-based payment awards that contain nonforfeitable rights to dividends or dividend equivalents (whether paid or unpaid) as participating securities and requires them to be included in the computation of earnings per share pursuant to the two-class method. On October 1, 2009 the Company adopted this standard, which had no impact on its financial position or results of operations.

In December 2008, the FASB issued authoritative guidance regarding Compensation — Retirement Benefits, which requires enhanced disclosures about the plan assets of a company’s defined benefit pension and other postretirement plans. The enhanced disclosures are intended to provide users of financial statements with a greater understanding of: (1) how investment allocation decisions are made, including the factors that are pertinent to an understanding of investment policies and strategies; (2) the major categories of plan assets; (3) the inputs and valuation techniques used to measure the fair value of plan assets; (4) the effect of fair value measurements using significant unobservable inputs (Level 3) on changes in plan assets for the period; and (5) significant concentrations of risk within plan assets. This standard will be effective for the Company for the fiscal year ending September 30, 2010. The Company is currently evaluating the potential impact of this guidance on its future disclosures.

In June 2009, the FASB issued an amendment to the accounting and disclosure requirements for the consolidation of variable interest entities (VIEs), which requires a qualitative approach to identifying a controlling financial interest in a VIE, and requires ongoing assessment of whether an entity is a VIE and whether an interest in a VIE makes the holder the primary beneficiary of the VIE. This guidance is effective for fiscal years beginning after November 15, 2009. The Company is currently evaluating the potential impact of this standard on its financial position and results of operations.

In September 2009, the FASB issued authoritative guidance on revenue arrangements with multiple deliverables. This guidance provides another alternative for establishing fair value for a deliverable. When vendor specific objective evidence or third-party evidence for deliverables in an arrangement cannot be determined, companies will be required to develop a best estimate of the selling price for separate deliverables and allocate arrangement consideration using the relative selling price method. This guidance is effective October 1, 2010, and early adoption is permitted. The Company is currently evaluating the potential impact of this guidance on its financial position and results of operations.

2. Stock Based Compensation

The following table reflects compensation expense recorded during the three and six months ended ~~December~~March 31, ~~2009~~2010 and ~~2008~~2009 (in thousands):


	Three months ended				Three months ended				Six months ended
	December 31,				March 31,				March 31,
	2009		2008		2010		2009		2010		2009
Stock options	$	43	$	133	$	42	$	72	$	85	$	205
Restricted stock		1,368		1,251		1,901		1,707		3,269		2,958
Employee stock purchase plan		106		140		101		91		207		231

	$	1,517	$	1,524	$	2,044	$	1,870	$	3,561	$	3,394

goals which will be measured at the end of fiscal year 2012. Total compensation on these awards is a maximum of $1.3 million. Awards only subject to service criteria are being recorded to expense ratably over the three year vesting period. Awards subject to performance criteria are expensed over the related service period when attainment of the performance condition is considered probable. The total amount of compensation recorded will depend on the Company’s achievement of performance targets. Changes to the projected attainment of performance targets during the vesting period may result in an adjustment to the amount of cumulative compensation recorded as of the date the estimate is revised.

Stock Option Activity

The following table summarizes stock option activity for the ~~three~~six months ended ~~December~~March 31, ~~2009:~~2010:

Weighted-
Average Weighted Aggregate
Number of Remaining Average Intrinsic Value
Options Contractual Term Exercise Price (In Thousands)
Outstanding at September 30, 2009 1,189,897 $ 17.54
Forfeited/expired (59,175 ) 14.20

Outstanding at December 31, 2009 1,130,722 1.3 years $ 17.71 $ 28
Vested and unvested expected to vest at December 31, 2009 1,129,477 1.3 years $ 17.72 $ 28
Options exercisable at December 31, 2009 1,105,722 1.3 years $ 17.82 $ 28

Weighted-
Average Weighted Aggregate
Number of Remaining Average Intrinsic Value
Options Contractual Term Exercise Price (In Thousands)
Outstanding at September 30, 2009 1,189,897 $ 17.54
Forfeited/expired (375,262 ) 14.09

Outstanding at March 31, 2010 814,635 1.5 years $ 19.13 $ 35
Vested and unvested expected to vest at March 31, 2010 813,754 1.5 years $ 19.13 $ 35
Options exercisable at March 31, 2010 789,635 1.5 years $ 19.32 $ 35

The aggregate intrinsic value in the table above represents the total intrinsic value, based on the Company’s closing stock price of ~~$8.58~~$8.82 as of ~~December~~March 31, ~~2009,~~2010, which would have been received by the option holders had all option holders exercised their options as of that date.

No stock options were granted during the three and six months ended ~~December~~March 31, ~~2009~~2010 and ~~2008.~~2009. There were no stock option exercises in the three and six months ended ~~December~~March 31, ~~2009~~2010 and 2008. The total intrinsic value of options exercised during the three month period ended December 31, 2009 and 2008 was $0. The total cash received from employees as a result of employee stock option exercises during the three months ended December 31, 2009 and 2008 was $0.2009.

As of ~~December~~March 31, ~~2009~~2010 future compensation cost related to nonvested stock options is approximately $0.1 million and will be recognized over an estimated weighted average period of ~~0.8~~0.6 years.

Restricted Stock Activity

A summary of the status of the Company’s restricted stock as of ~~December~~March 31, ~~2009~~2010 and changes during the ~~three~~six months ended ~~December~~March 31, ~~2009~~2010 is as follows:


	Three months ended					Six months ended
	December 31, 2009					March 31, 2010
				Weighted					Weighted
				Average					Average
				Grant-Date					Grant-Date
	Shares			Fair Value		Shares			Fair Value
Outstanding at September 30, 2009		1,162,086		$	8.96		1,162,086		$	8.96
Awards granted		178,346			7.85		661,846			8.36
Awards vested		(206,458	)		8.49		(696,507	)		8.01
Awards canceled		(9,388	)		6.70		(23,013	)		7.31

Outstanding at December 31, 2009		1,124,586		$	8.89
Outstanding at March 31, 2010							1,104,412		$	9.26

As of ~~December~~March 31, ~~2009,~~2010, the unrecognized compensation cost related to nonvested restricted stock is ~~$4.3~~$5.7 million and will be recognized over an estimated weighted average amortization period of ~~1.1~~1.6 years.

Employee Stock Purchase Plan

There were no116,160 shares purchased under the employee stock purchase plan during the three and six months ended ~~December~~March 31, 2010 for aggregate proceeds of $0.6 million. There were 172,437 shares purchased under the employee stock purchase plan during the three and six months ended March 31, 2009 ~~and 2008.~~for aggregate proceeds of $0.7 million.

3. Goodwill

The components of the Company’s goodwill by business segment at ~~December~~March 31, ~~2009~~2010 are as follows (in thousands):


	Critical			Systems			Global
	Solutions			Solutions			Customer
	Group			Group			Operations			Other			Total
Gross goodwill	$	353,253		$	151,184		$	151,238		$	7,421		$	663,096
Less: aggregate impairment charges recorded		(305,115	)		(151,184	)		(151,238	)		(7,421	)		(614,958	)

	$	48,138		$	—		$	—		$	—		$	48,138

The Company did not have any adjustments to goodwill during the three and six months ended ~~December~~March 31, ~~2009.~~2010.

Components of the Company’s identifiable intangible assets are as follows (in thousands):


	December 31, 2009						September 30, 2009						March 31, 2010						September 30, 2009
			Accumulated		Net Book				Accumulated		Net Book				Accumulated		Net Book				Accumulated		Net Book
	Cost		Amortization		Value		Cost		Amortization		Value		Cost		Amortization		Value		Cost		Amortization		Value
Patents	$	6,915	$	6,815	$	100	$	6,915	$	6,812	$	103	$	7,808	$	6,834	$	974	$	6,915	$	6,812	$	103
Completed technology		43,502		35,737		7,765		43,502		35,280		8,222		43,502		36,194		7,308		43,502		35,280		8,222
Trademarks and trade names		3,779		3,140		639		3,779		3,060		719		3,779		3,220		559		3,779		3,060		719
Customer relationships		18,860		14,231		4,629		18,860		13,823		5,037		18,860		14,638		4,222		18,860		13,823		5,037

	$	73,056	$	59,923	$	13,133	$	73,056	$	58,975	$	14,081	$	73,949	$	60,886	$	13,063	$	73,056	$	58,975	$	14,081

Financial information for the Company’s business segments is as follows (in thousands):


	Critical			Systems			Global						Critical			Systems			Global
	Solutions			Solutions			Customer						Solutions			Solutions			Customer
	Group			Group			Operations			Total			Group			Group			Operations			Total
Three months ended December 31, 2009
Three months ended March 31, 2010
Revenues
Product	$	43,186		$	47,099		$	1,236		$	91,521		$	60,033		$	72,573		$	783		$	133,389
Services		—			—			14,676			14,676			—			—			14,964			14,964

	$	43,186		$	47,099		$	15,912		$	106,197		$	60,033		$	72,573		$	15,747		$	148,353


Gross profit	$	15,777		$	7,556		$	2,913		$	26,246		$	22,554		$	13,065		$	3,331		$	38,950
Segment operating income (loss)	$	1,868		$	318		$	(1,884	)	$	302		$	7,696		$	4,133		$	(538	)	$	11,291

Three months ended December 31, 2008
Three months ended March 31, 2009
Revenues
Product	$	35,883		$	22,636		$	567		$	59,086		$	17,237		$	8,248		$	398		$	25,883
Services		—			—			14,360			14,360			—			—			11,416			11,416

													$	17,237		$	8,248		$	11,814		$	37,299


Gross loss													$	(87	)	$	(5,920	)	$	(1,273	)	$	(7,280	)
Segment operating loss													$	(13,050	)	$	(15,157	)	$	(6,327	)	$	(34,534	)

Six months ended March 31, 2010
Revenues
Product													$	103,219		$	119,672		$	2,019		$	224,910
Services														—			—			29,640			29,640

													$	103,219		$	119,672		$	31,659		$	254,550


Gross profit													$	38,331		$	20,621		$	6,244		$	65,196
Segment operating income (loss)													$	9,564		$	4,451		$	(2,422	)	$	11,593

Six months ended March 31, 2009
Revenues
Product													$	53,120		$	30,884		$	965		$	84,969
Services														—			—			25,776			25,776

													$	53,120		$	30,884		$	26,741		$	110,745
	$	35,883		$	22,636		$	14,927		$	73,446

Gross profit (loss)	$	6,738		$	(1,738	)	$	1,388		$	6,388		$	6,651		$	(7,658	)	$	115		$	(892	)
Segment operating loss	$	(9,005	)	$	(13,352	)	$	(4,483	)	$	(26,840	)	$	(22,055	)	$	(28,509	)	$	(10,810	)	$	(61,374	)

Assets
December 31, 2009	$	143,043		$	83,365		$	55,270		$	281,678
March 31, 2010													$	155,354		$	106,030		$	48,983		$	310,367
September 30, 2009	$	138,930		$	70,537		$	56,007		$	265,474		$	138,930		$	70,537		$	56,007		$	265,474

~~related to the present value discounting of multi-year facility related restructuring liabilities. The total amount of the~~periods, and recorded an adjustment of ~~$1,221,000 was recorded as a~~$1,221,000. The restructuring ~~cost~~charges for the three months ended ~~December~~March 31, ~~2009. In addition,~~2010 were primarily related to general corporate support functions. Restructuring charges for the ~~Company recorded $117,000 of facility related restructuring costs during the three~~six months ended ~~December~~March 31, ~~2009~~2010 include $86,000 for the Global Customer Operations segment, with the balance related to ~~amortize the deferred discount on multi-year facility restructuring liabilities.~~general corporate support functions.

The Company recorded ~~a charge to operations~~restructuring charges of ~~$4,105,000 in~~$5,861,000 and $9,966,000 for the three and six months ended ~~December~~March 31, ~~2008.~~2009, respectively, in connection with its fiscal 2009 restructuring plan. These charges through the first half of fiscal 2009 consist primarily ~~relate to~~of severance costs ~~of $4,071,000 for~~associated with workforce reductions of ~~120~~approximately 400 employees in operations, service and administrative functions across all the main geographies in which the Company operates. The restructuring charges by segment for the ~~first quarter of fiscal year~~three months ended March 31, 2009 were: Critical Solutions — $2.5 million, Systems Solutions — $1.9 million and Global Customer Operations — ~~$2.7 million,~~$0.7 million. The restructuring charges by segment for the six months ended March 31, 2009 were: Critical Solutions ~~Group~~ — ~~$0.6~~$3.1 million, Systems Solutions — $2.4 million and ~~Systems Solutions Group~~Global Customer Operations — ~~$0.4~~$3.3 million. In addition, the Company incurred ~~$0.4~~$0.8 million and $1.2 million of restructuring charges for the three and six months ended March 31, 2009, respectively, that were related to general corporate functions that support all of its segments.

The activity for the three and six months ended ~~December~~March 31, ~~2009~~2010 and ~~2008~~2009 related to the Company’s restructuring-related accruals is summarized below (in thousands):


	Activity — Three Months Ended December 31, 2009									Activity — Three Months Ended March 31, 2010
	Balance							Balance		Balance							Balance
	September 30,							December 31,		December 31,							March 31,
	2009		Expense		Utilization			2009		2009		Expense		Utilization			2010
Facilities and other	$	6,289	$	1,338	$	(1,125	)	$	6,502	$	6,502	$	113	$	(1,119	)	$	5,496
Workforce-related		1,372		184		(1,009	)		547		547		371		(636	)		282

	$	7,661	$	1,522	$	(2,134	)	$	7,049	$	7,049	$	484	$	(1,755	)	$	5,778

Company incurred charges from UCI for products or services of $0.2 million and $0.3 million, respectively. At ~~December~~March 31, ~~2009~~2010 and September 30, 2009 the Company owed UCI ~~$0.2~~$0.0 million in connection with accounts payable for unpaid products and services.

The Company participates in a 50% joint venture with Yaskawa Electric Corporation (“Yaskawa”) ~~to form a joint venture~~ called Yaskawa Brooks Automation, Inc. (“YBA”) to exclusively market and sell Yaskawa’s semiconductor robotics products and Brooks’ automation hardware products to semiconductor customers in Japan. For the three months ended ~~December~~March 31, 2010 and 2009, the Company recorded income associated with YBA of $0.2 million and ~~2008,~~$0.0 million, respectively. For the six months ended March 31, 2010 and 2009, the Company recorded income (loss) associated with YBA of ($~~0.2)~~0.0) million and $0.0 million, respectively. At ~~December~~March 31, ~~2009,~~2010, the carrying value of YBA in the Company’s consolidated balance sheet was ~~$2.8~~$2.9 million. For the three months ended ~~December~~March 31, ~~2009~~2010 and ~~2008,~~2009, revenues earned by the Company from YBA were ~~$1.8~~$4.1 million and ~~$1.7~~$1.9 million, respectively. For the six months ended March 31, 2010 and 2009, revenues earned by the Company from YBA were $5.9 million and $3.6 million, respectively. The amount due from YBA included in accounts receivable at ~~December~~March 31, ~~2009~~2010 and September 30, 2009 was ~~$2.2~~$5.0 million and $2.4 million, respectively. For the three months and six months ended ~~December~~March 31, ~~2009 and 2008,~~2010, the Company ~~did not incur any~~incurred charges from YBA for products or ~~services.~~services of $0.1 million. For the three months and six months ended March 31, 2009, the Company incurred charges from YBA for products or services of $0.1 million and $0.4 million, respectively. At ~~December~~March 31, ~~2009~~2010 and September 30, 2009 the Company did not owe YBA any amount in connection with accounts payable for unpaid products and services.

These investments are accounted for using the equity method. Under this method of accounting, the Company records in income its proportionate share of the earnings of the joint ventures with a corresponding increase in the carrying value of the investment.

~~13.~~14. Fair Value Measurements

In September 2006, the FASB issued authoritative guidance for fair value measurements and disclosures, which defines fair value, establishes a framework for measuring fair value and expands the related disclosure requirements. This statement applies under other accounting pronouncements that require or permit fair value measurements. The statement indicates, among other things, that a fair value measurement assumes that the transaction to sell an asset or transfer a liability occurs in the principal market for the asset or liability or, in the absence of a principal market, the most advantageous market for the asset or liability. This guidance defines fair value based upon an exit price model.

The FASB amended the fair value measurement guidance to exclude accounting for leases and its related interpretive accounting pronouncements that address leasing transactions; the delay of the effective date of the measurement application to fiscal years beginning after November 15, 2008 for all non-financial assets and non-financial liabilities that are recognized or disclosed at fair value in the financial statements on a nonrecurring basis; and the determination of whether a market is active or inactive, and whether a transaction is distressed, is applicable to all assets and liabilities (i.e. financial and nonfinancial) and ~~will require~~requires enhanced disclosures.

The Company adopted the fair value measurement guidance as of October 1, 2008, with the exception of the application of the statement to non-recurring non-financial assets and non-financial liabilities. The Company adopted the fair value measurement guidance for non-recurring non-financial assets and non-financial liabilities on October 1, 2009.

The fair value measurement guidance also establishes a fair value hierarchy which requires an entity to maximize the use of observable inputs and minimize the use of unobservable inputs when measuring fair value. The standard describes three levels of inputs that may be used to measure fair value:


	Level 1		1 Quoted prices in active markets for identical assets or liabilities as of the reporting date. Active markets are those in which transactions for the asset and liability occur in sufficient frequency and volume to provide pricing information on an ongoing basis.


	Level 2		2 Observable inputs other than Level 1 prices, such as quoted prices for similar assets or liabilities; quoted prices in markets that are not active; or other inputs that are observable or can be corroborated by observable market data for substantially the full term of the assets or liabilities.

Cash Equivalents

Cash equivalents of ~~$24.7~~$22.0 million, consisting of Money Market Funds, are classified within Level 1 of the fair value hierarchy because they are valued using quoted market prices in active markets.

Available-For-Sale Securities

Available-for-sale securities of ~~$25.1~~$31.7 million, consisting of highly rated Corporate Bonds, are classified within Level 1 of the fair value hierarchy because they are valued using quoted market prices in active markets of identical assets or liabilities. Available-for-sale securities of ~~$39.1~~$45.4 million, consisting of Asset Backed Securities, Municipal Bonds, and Government Agencies are classified within Level 2 of the fair value hierarchy because they are valued using matrix pricing and benchmarking. Matrix pricing is a mathematical technique used to value securities by relying on the securities’ relationship to other benchmark quoted prices.

~~14.~~15. Contingencies

On August 22, 2006, an action captioned asMark Levy v. Robert J. Therrien and Brooks Automation, Inc., was filed in the United States District Court for the District of Delaware, seeking recovery, on behalf of Brooks, from Mr. Therrien (the Company’s former Chairman and CEO) under Section 16(b) of the Securities Exchange Act of 1934 for alleged “short-swing” profits earned by Mr. Therrien due to the loan and stock option exercise in November 1999, and a sale by Mr. Therrien of Brooks stock in March 2000. The complaint seeks disgorgement of all profits earned by Mr. Therrien on the transactions, attorneys’ fees and other expenses. On February 20, 2007, a second Section 16(b) action, concerning the same loan and stock option exercise in November 1999 discussed above and seeking the same remedy, was filed in the United States District Court of the District of Delaware, captionedAron Rosenberg v. Robert J. Therrien and Brooks Automation, Inc. On April 4, 2007, the court issued an order consolidating theLevyandRosenbergactions. On July 14, 2008, the court denied Mr. Therrien’s motion to dismiss this action. Discovery has commenced in this ~~matter and is currently ongoing.~~matter. It has been reported to the Company that the parties have reached an agreement in principle to settle this case, subject to the approval of the court and to the conclusion by the parties of necessary settlement processes and documents. Brooks is a nominal defendant in the consolidated action and any recovery in this action, less attorneys’ fees, would go to the Company.

~~15. Subsequent Event~~

On February 3, 2010, the Company entered into an agreement to sell certain intellectual property assets associated with factory automated material handling systems for $7.9 million. Under the terms of the agreement Brooks will retain the rights to use this intellectual property to support its existing installed base of factory automated material handling systems. The Company will record a gain of approximately $7.8 million on this sale during its second quarter of fiscal year 2010. The Company will receive $7.7 million of the proceeds from the sale during the second quarter of fiscal year 2010, and expects to receive the balance of $0.2 million during the second half of fiscal year 2010.

Overview

We are a leading provider of automation, vacuum and instrumentation solutions and are a highly valued business partner to original equipment manufacturers (OEM) and equipment users throughout the world. We serve markets where equipment productivity and availability is a critical factor for our customers’ success. Our largest served market is the semiconductor manufacturing industry, which represented 71% and ~~84%~~85% of our consolidated revenues for fiscal year 2009 and the first ~~quarter~~six months of fiscal year 2010, respectively. We also provide unique solutions to customers in data storage, advanced display, analytical instruments and industrial markets. We develop and deliver differentiated solutions that range from proprietary products to highly respected manufacturing services.

The demand for semiconductors and semiconductor manufacturing equipment is cyclical, resulting in periodic expansions and contractions. Demand for our products has been impacted by these cyclical industry conditions. During fiscal year 2006 and throughout most of fiscal year 2007, we benefited from an industry expansion. That cyclical expansion turned to a downturn in the fourth quarter of fiscal year 2007 that continued through the second quarter of fiscal year 2009. Our revenues for the ~~second quarter~~first half of fiscal year 2009 were ~~$37.3~~$110.7 million. Since that time, during a period of renewed industry expansion, our revenues have significantly increased in each fiscal quarter. Revenue for the first ~~quarter~~six months of fiscal year 2010 was ~~$106.2~~$254.6 million.

Throughout fiscal years 2008 and 2009, we implemented a number of cost reduction programs to align our cost structure with a reduced demand environment. ~~From the end of fiscal year 2007 through the end of fiscal year 2009, we reduced our headcount by approximately 40% and closed redundant facilities.~~ Our cost reduction efforts focused on actions that would decrease our overhead cost structure for the foreseeable future. Although we have added personnel ~~in recent months,~~during the first half of fiscal year 2010, these additions were made primarily to address increased production requirements. ~~We will continue to add personnel to address our increasing production levels. We~~At present, we do not ~~intend to~~anticipate significantly ~~increase~~increasing our overhead structure as our revenues recover.

In connection with our restructuring programs, we have realigned our management structure and our underlying internal financial reporting structure. Effective as of the beginning of our second quarter of 2009, we implemented a new internal reporting structure which includes three segments: Critical Solutions Group, Systems Solutions Group and Global Customer Operations. Financial results prior to this new management structure have been revised to reflect our current segment structure.

The Critical Solutions Group segment provides a variety of products critical to technology equipment productivity and availability. Those products include robots and robotic modules for atmospheric and vacuum applications and cryogenic vacuum pumping, thermal management and vacuum measurement solutions used to create, measure and control critical process vacuum applications.

The Systems Solutions Group segment provides a range of products and engineering and manufacturing services, which include our Extended Factory services. Our Extended Factory product ~~line~~offering provides services to build equipment front-end modules and other subassemblies which enable our customers to effectively develop and source high quality, high reliability, process tools for semiconductor and adjacent market applications.

The Global Customer Operations segment provides an extensive range of support services including on and off-site repair services, on and off-site diagnostic support services, and installation services to enable our customers to maximize process tool uptime and productivity. This segment also provides services and spare parts for our Automated Material Handling Systems (“AMHS”) product line. Revenues from the sales of spare parts that are not

related to a repair or replacement transaction, or are not AMHS products, are included within the product revenues of the other operating segments.

On ~~February 3,~~April 5, 2010, we ~~entered into an agreement to sell certain intellectual property assets associated with factory automated material handling systems for $7.9 million. Under~~announced the ~~terms~~appointment of Stephen S. Schwartz as the Company’s President as of April 5, 2010. Mr. Schwartz became a member of a newly formed Office of the ~~agreement we will retain the rights to use this intellectual property to support~~Chief Executive with Robert J. Lepofsky, Chief Executive Officer, and Martin S. Headley, Executive Vice President and Chief Financial Officer, where he plays a central role in developing and implementing our existing installed base of factory automated material handling systems. We will record a gain of approximately $7.8 million on this sale during our second quarter of fiscal year 2010. We will receive $7.7 million of the proceeds from the sale during the second quarter of fiscal year 2010, and expect to receive the balance of $0.2 million during the second half of fiscal year 2010.strategic objectives.

Three and Six Months Ended ~~December~~March 31, ~~2009,~~2010, Compared to Three and Six Months Ended ~~December~~March 31, ~~2008~~2009

Revenues

We reported revenues of ~~$106.2~~$148.4 million for the ~~first quarter of fiscal year~~three months ended March 31, 2010, compared to ~~$73.4~~$37.3 million in the same prior year period, a ~~44.6%~~297.7% increase. The total increase in revenues of ~~$32.8~~$111.1 million impacted all of our operating segments. Our Critical Solutions Group segment revenues increased by ~~$7.3~~$42.8 million, our System

Solutions Group segment revenues increased by ~~$24.5~~$64.4 million and our Global Customer Operations segment revenues increased by ~~$1.0~~$3.9 million. These increases were primarily the result of increased volume shipments in response to increasing demand for semiconductor capital equipment.

We reported revenues of $254.6 million for the six months ended March 31, 2010, compared to $110.7 million in the same prior year period, a 129.9% increase. The total increase in revenues of $143.9 million impacted all of our operating segments. Our Critical Solutions Group segment revenues increased by $50.1 million and our System Solutions Group segment revenues increased by $88.9 million. Additionally, our Global Customer Operations segment revenues increased by $4.9 million reflecting an increased active installed base of products for service. These increases were primarily the result of increased volume shipments in response to increasing demand for semiconductor capital equipment.

Our Critical Solutions Group segment reported revenues of ~~$43.2~~$60.0 million for the ~~first quarter of fiscal year~~three months ended March 31, 2010, an increase of ~~20.3%~~248.3% from ~~$35.9~~$17.2 million in the same prior year period. This segment reported revenues of $103.2 million for the six months ended March 31, 2010, an increase isof 94.3% from $53.1 million in the same prior year period. These increases are primarily attributable to a higher ~~volume~~volumes of shipments to semiconductor capital equipment ~~customers.~~customers, which increased 155.8% for the six months ended March 31, 2010 as compared to the same prior year period. This segment also experienced an increase ~~was partially offset by lower volume~~in revenues of ~~shipments of $2.3 million~~25.7% from non-semiconductor customers for the six months ended March 31, 2010 as compared to ~~non-semiconductor markets served by this segment.~~the same prior year period.

Our System Solutions Group segment reported revenues of ~~$47.1~~$72.6 million for the ~~first quarter of fiscal year~~three months ended March 31, 2010, a ~~108.1%~~779.9% increase from ~~$22.6~~$8.2 million in the same prior year period. This segment reported revenues of $119.7 million for the six months ended March 31, 2010, a 287.5% increase isfrom $30.9 million in the same prior year period. These increases are attributable to increased demand for semiconductor capital equipment. Included within this segment is our Extended Factory product ~~line.~~offering. Revenue ~~for~~from our Extended Factory product ~~line~~ was ~~substantially~~ the largest contributor to increased revenues in this ~~segment, increasing by $19.2 million for the first quarter of fiscal year 2010 as compared to the same prior year period.~~segment.

Our Global Customer Operations segment reported revenues of ~~$15.9~~$15.7 million for ~~first quarter of fiscal year~~the three months ended March 31, 2010, a ~~6.6%~~33.3% increase from ~~$14.9~~$11.8 million in the same prior year period. This segment reported revenues of $31.7 million for six months ended March 31, 2010, an 18.4% increase ~~is attributable~~from $26.7 million in the same prior year period. These increases are primarily related to ~~higher AMHS spare parts revenue of $0.7 million and~~ higher service contract and repair revenues of ~~$0.3 million.~~$3.5 million and $3.9 million for the three and six months ended March 31, 2010, respectively, as compared to the prior year periods. The balance of the increase relates to increased sales of AMHS spare parts. All service revenues included in our unaudited consolidated statements of operations, which include service contract and repair services, are related to our Global Customer Operations segment.

Gross Profit

Gross margin dollars increased to ~~$26.2~~$39.0 million for the ~~first quarter of fiscal year~~three months ended March 31, 2010, an increase of ~~310.9%~~240.1% from ~~$6.4~~a $27.8 million loss for the same prior year period. This increase was attributable to higher revenues of ~~$32.8~~$111.1 million, an intangible asset impairment charge of $20.5 million which reduced the prior year gross profit, a ~~$5.2~~$7.7 million reduction in charges for excess and obsolete inventory and $1.9 million of reduced amortization expense for completed technology intangible assets, due primarily to the impairment recorded for those assets during the second quarter of fiscal 2009. These decreases were partially offset by a less favorable product mix which reduced gross margin dollars by ~~$4.6~~$12.1 million. Gross margin dollars increased to $65.2 million for the six months ended March 31, 2010, an increase of 404.5% from a $21.4 million loss for the same prior year period. This increase was attributable to higher revenues of $143.9 million, an intangible asset impairment charge of $20.5 million which reduced the prior year gross profit, a $12.9 million reduction in charges for excess and obsolete inventory and $3.8 million of reduced amortization expense for completed technology intangible assets. These decreases were partially offset by a less favorable product mix which reduced gross margin dollars by $16.6 million.

Gross margin for the three and six months ended March 31, 2010 was reduced by $0.5 ~~million~~ and ~~$2.3~~$0.9 million, ~~for the first quarter of fiscal years 2010 and 2009,~~ respectively, for amortization of completed technology intangible assets, which relates primarily to the acquisition of Helix Technology Corporation (“Helix”) in October 2005. Amortization by operating segment for the three and six months ended March 31, 2010 was as follows: Critical Solutions Group — $0.4 million and $0.7 million, respectively; and, Global Customer Operations — $0.1 million and $0.2 million, respectively. Gross margin for the three and six months ended March 31, 2009 was reduced by $2.3 and $4.7 million, respectively, for amortization of

completed technology intangible assets. Amortization by operating segment for the three and six months ended March 31, 2009 was as follows: Critical Solutions Group — $1.0 million and $2.0 million, respectively; System Solutions Group — $0.1 million and $0.3 million, respectively; and Global Customer Operations — $1.2 million and $2.4 million, respectively.

Gross margin percentage increased to ~~24.7%~~26.3% for the ~~first quarter of fiscal year~~three months ended March 31, 2010, compared to ~~8.7%~~(74.5)% for the same prior year period. ~~This increase was~~Gross margin percentage increased to 25.6% for the six months ended March 31, 2010, compared to (19.3)% for the same prior year period. These increases are primarily attributable to higher absorption of indirect factory overhead on higher revenues. Other factors ~~increasing~~that increased gross margin percentage include the $20.5 million intangible asset impairment charge recorded in the prior year periods which reduced gross margin percentage by 55.0% for the three month period and 18.5% for the six month period, decreased charges for excess and obsolete inventory which increased gross margin percentage by ~~6.6%,~~19.4% for the three month period and 10.7% for the six month period and reduced amortization expense for completed technology intangible assets which increased gross margin percentage by ~~2.8%.~~1.3% for the three month period and 1.5% for the six month period. These increases in gross margin percentage were partially offset by a less favorable product mix from the rapid growth of our Extended Factory product offering which reduced gross margin percentage by ~~4.3%.~~8.2% and 6.5% for the three and six months ended March 31, 2010.

Gross margin ofdollars for our Critical Solutions Group segment increased to ~~$15.8~~$22.6 million for the ~~first quarter of fiscal year~~three months ended March 31, 2010, an increase of ~~134.1%~~260.2% from a $0.1 million loss in the same prior year period. Gross margin dollars for this segment increased to $38.3 million for the six months ended March 31, 2010, an increase of 476.3% from $6.7 million in the same prior year period. ~~This increase was~~These increases were attributable to higher revenues of ~~$7.3~~$42.8 million for the three month period and $50.1 million for the six month period, reduced charges for excess and obsolete inventory of ~~$1.7~~$1.1 million for the three month period and $2.9 million for the six month period and reduced amortization expense of $0.6 million for ~~completed technology intangible assets, due primarily to~~ the ~~impairment recorded for those assets during the second quarter of fiscal 2009. Gross margin~~three month period and $1.3 million for the ~~first quarter of fiscal years 2010 and 2009 was reduced by $0.4 million and $1.0 million, respectively, for completed technology amortization related to the Helix acquisition.~~six month period. Gross margin percentage was ~~36.5%~~37.6% for the ~~first quarter of fiscal year~~three months ended March 31, 2010 as compared to ~~18.8%~~(0.5)% in the same prior year period. ~~This increase is~~Gross margin percentage was 37.1% for the six months ended March 31, 2010 as compared to 12.5% in the same prior year period. These increases are primarily the result of higher absorption of indirect factory overhead on higher revenues. Other factors increasing gross margin percentage include decreased charges for excess and obsolete inventory which increased gross margin percentage by 5.1% for the three month period and 4.7%, for the six month period and reduced amortization expense for completed technology intangible assets which increased gross margin percentage by ~~1.9%.~~1.0% for the three month period and 1.2% for the six month period.

Gross margin ofdollars for our Systems Solutions Group segment increased to ~~$7.6~~$13.1 million for the ~~first quarter of fiscal year~~three months ended March 31, 2010, an increase of ~~534.7%~~320.7% from a ~~$1.7~~$5.9 million loss for the same prior year period. ~~This~~Gross margin dollars for this segment increased to $20.6 million for the six months ended March 31, 2010, an increase ~~was~~of 369.3% from a $7.7 million loss for the same prior year period. These increases were attributable to higher revenues of ~~$24.5~~$64.4 million for the three month period and $88.8 million for the six month period, decreased charges for excess and obsolete inventory of ~~$3.1~~$4.7 million for the three month period and ~~$0.2~~$7.8 million for the six month period and $0.1 million of reduced amortization expense for ~~completed technology intangible assets, due primarily to~~ the ~~impairment recorded for those assets during the second quarter of fiscal year 2009. Gross margin~~three month period and $0.3 million for the ~~first quarter of fiscal 2009 was reduced by $0.2 million for completed technology amortization.~~six month period. Gross margin percentage increased to ~~16.0%~~18.0% for the ~~first quarter of fiscal year~~three months ended March 31, 2010 as compared to ~~(7.7)~~(71.8)% in the same prior year period. ~~This increase was~~Gross margin percentage increased to 17.2% for the six months ended March 31, 2010 as compared to (24.8)% in the same prior year period. These increases were primarily attributable to higher absorption of indirect factory overhead on higher revenues. Other factors ~~increasing~~that led to the increase in gross margin percentage include decreased charges for excess and obsolete inventory which increased gross margin percentage by ~~12.4%~~52.1% for the three month period and 22.8% for the six month period and reduced amortization expense for completed technology intangible assets, which increased gross margin percentage by ~~0.7%.~~0.2% for both the three and six month periods. These increases in gross margin percentage were partially offset by a less favorable product mix which reduced gross margin percentage by ~~9.7%.~~16.7% for the three month period and 13.8% for the six month period. The less favorable product mix is attributable to ~~a $19.2 million increase~~increases in Extended Factory product sales which are less profitable than other products within this segment. Extended Factory product revenues were 65% of all sales within this segment for the first quarter of fiscal year 2010, and we expect this product will continue to generate a majority of the revenue for this segment in the near term.

Gross margin of our Global Customer Operations segment increased to ~~$2.9~~$3.3 million for the ~~first quarter of fiscal year~~three months ended March 31, 2010, an increase of ~~109.8%~~361.7% from the ~~$1.4~~$1.3 million loss in the same prior year period. Gross margin for this segment increased to $6.2 million for the six months ended March 31, 2010, as compared to $0.1 million in the same prior year period. ~~The increase was~~These increases were attributable to ~~reduced amortization expense of $1.1 million for completed technology intangible assets, due primarily to the impairment recorded for those assets during the second quarter of 2009, decreased~~a decrease in charges for excess and obsolete inventory of ~~$0.4~~$1.9 million for the three month period and ~~higher~~$2.3 million for the six month period and a reduction in amortization expense of $1.1 million for the three month period and $2.2 million for the six month period. The balance of the

increase relates primarily to increased revenues of ~~$1.0 million. Gross margin~~$3.9 million for the ~~first quarter of fiscal years 2010~~three month period and ~~2009 was reduced by $0.1~~$4.9 million ~~and $1.2 million, respectively,~~ for ~~completed technology amortization related to~~ the ~~Helix acquisition.~~six month period. Gross margin percentage ~~was 18.3%~~ for the ~~first quarter of fiscal year~~three months ended March 31, 2010 was 21.2% as compared to ~~9.3%~~(10.8)% in the same prior year period. ~~The increase~~Gross margin percentage was 19.7% for the six months ended March 31, 2010 as compared to 0.4% in the same prior year period. These increases in gross margin percentage ~~was primarily~~were attributable to ~~reduced amortization expense for completed technology intangible assets which increased gross margin percentage by 7.4%, and~~ decreased charges for excess and obsolete inventory which ~~decreased~~increased gross margin percentage by ~~2.6%.~~16.1% for the three month period and 8.5% for the six month period and reduced amortization expense increased gross margin percentage by 7.0% for the three month period and 6.9% for the six month period. The balance of the increase is primarily related to higher absorption of indirect overhead costs on higher revenues.

Research and Development

Research and development, or R&D, expenses for the ~~first quarter of fiscal year~~three months ended March 31, 2010 were ~~$7.5~~$7.7 million, essentially flat with the prior period. R&D expenses for the six months ended March 31, 2010 were $15.2 million, a decrease of ~~$1.8~~$1.7 million, compared to ~~$9.3~~$16.9 million in the same prior year period. This decrease is primarily related to lower labor related costs ~~of $1.7 million~~ associated with headcount reductions. Our headcount reductions were implemented to remove redundancies in our R&D infrastructure. We ~~will~~ continue to invest in R&D projects that enhance our product and service offerings.

Selling, General and Administrative

Selling, general and administrative, or SG&A expenses were ~~$19.0~~$20.8 million for the ~~first~~second quarter of fiscal year 2010, a decrease of ~~$8.6~~$4.4 million compared to ~~$27.6~~$25.2 million in the same prior year period. The decrease is primarily attributable to lower litigation costs of $3.6 million and $1.5 million of lower amortization of intangible assets, due primarily to the impairment recorded for those assets during the second quarter of 2009. The decreases in SG&A expenses were partially offset by higher depreciation expense of $0.5 million, which relates primarily to the Oracle ERP system which was placed in service in most of our U.S. based operations during the fourth quarter of fiscal year 2009. SG&A expenses were $39.8 million for the six months ended March 31, 2010, a decrease of $13.0 million compared to $52.8 million in the same prior year period. The decrease is primarily attributable to $5.4 million of reduced litigation costs, lower labor costs of ~~$3.7~~$3.2 million as we reduced our headcount to align our SG&A resources with our new management structure, a ~~$1.4~~$2.9 million reduction in amortization of intangible assets ~~primarily due to the impairment of intangible assets recorded in our second quarter of fiscal year 2009~~ and a ~~$1.9~~$0.9 million reduction in ~~litigation~~software maintenance costs. The decreases in SG&A expenses were partially offset by higher depreciation expense of $0.9 million, which relates primarily to the Oracle ERP system. We settled our litigation matters with the SEC during fiscal year 2008. ~~The total~~We have incurred minimal indemnification

costs for these litigation matters during the six months ended March 31, 2010. Our indemnification costs, net of insurance reimbursements, were ~~$(0.1)~~$3.6 million and ~~$1.8~~$5.4 million for the ~~first~~three and six month periods ended March 31, 2009.

Impairment Charges

We are required to test our goodwill for impairment at least annually. We conduct this test as of September 30^th of each fiscal year. Our test of goodwill at September 30, 2009 indicated that goodwill was not impaired. We have not tested other intangible assets since the end of the second quarter of fiscal ~~years 2010~~2009, since no events have occurred that would require an impairment assessment.

We implemented significant restructuring actions during the early part of fiscal year 2009, which led to a realignment of our management structure and our underlying internal financial reporting structure. As a result of these changes, we reallocated goodwill to each of our newly formed reporting units as of March 31, 2009. This reallocation, in conjunction with the weakness we were experiencing in the semiconductor markets at that time, indicated that a potential impairment may exist. As such, we tested our goodwill and other long-lived assets for impairment at March 31, 2009. For three of the five reporting units containing goodwill, we determined that the carrying amount of their net assets exceeded their respective fair values, indicating that a potential impairment existed for each of those three reporting units. After completing the second step of the goodwill impairment test, we recorded a goodwill impairment of $71.8 million as of March 31, 2009. We also tested our other long-lived assets for impairment as of March 31, 2009. As a result of this analysis, we determined that we had incurred an impairment loss of $35.1 million as of March 31, 2009, ~~respectively.~~and we allocated that loss among the long-lived assets of the impaired asset group based on the carrying value of each asset, with no asset reduced below its respective fair value. The impairment charge was allocated as follows: $19.6 million related to completed technology intangible assets; $1.2 million to trade name intangible assets; $13.4 million to customer relationship intangible assets and $0.9 million to property, plant and equipment. The impairment related to our completed technology intangible assets and our

property, plant and equipment which total $20.5 million, was reported as cost of sales, while the remaining $14.6 million of the impairment loss was reported separately as an operating expense.

Restructuring Charges

We recorded a restructuring charge of ~~$1.5~~$0.5 million and $2.0 million for the ~~first quarter of fiscal year 2010 which consisted of facility~~three and six month periods ended March 31, 2010. These charges include severance related ~~restructuring~~ costs of ~~$1.3~~$0.4 million and ~~$0.2 million of severance costs. These severance costs include $0.1~~$0.6 million for the ~~elimination~~three and six month periods, and facility related costs of ~~3 positions in our Global Customer Operations segment,~~$0.1 million and ~~$0.1~~$1.4 million for the three and six month periods. The severance costs consist primarily of costs to adjust severance provisions related to general corporate positions eliminated in prior periods.

~~During~~ The facility costs include $0.1 million and $0.2 million for the ~~preparation~~three and six months ended March 31, 2010 to amortize the deferred discount on multi-year facility restructuring liabilities. In addition, we revised the present value discounting of ~~our financial statements for~~multi-year facility related restructuring liabilities during the first quarter of fiscal year 2010 ~~we identified~~when certain accounting errors were identified in our prior period financial statements that, individually and in aggregate, are not material to our financial statements taken as a whole for any related prior ~~periods. The errors were related to the present value discounting of multi-year facility related restructuring liabilities. The total amount of the~~periods, and recorded an adjustment of $1.2 ~~million was recorded as a~~million. The restructuring ~~cost~~charges for the ~~first quarter of fiscal year 2010. In addition, we recorded~~three months ended March 31, 2010 were primarily related to general corporate support functions. Restructuring charges for the six months ended March 31, 2010 include $0.1 million ~~of facility~~for our Global Customer Operations segment, with the balance related ~~restructuring costs the first quarter of fiscal year 2010~~ to ~~amortize the deferred discount on multi-year facility restructuring liabilities.~~general corporate support functions.

We recorded ~~a charge~~restructuring charges of ~~$4.1~~$5.9 million and $10.0 million for the ~~first quarter of fiscal year~~three and six months ended March 31, 2009, ~~as an initial charge for~~respectively, in connection with our fiscal 2009 restructuring plan. ~~This charge consisted~~These charges through the first half of fiscal 2009 consist primarily of severance costs associated with workforce reductions of ~~120~~approximately 400 employees in operations, service and administrative functions across all the main geographies in which we operate. The restructuring charges by segment for the ~~first quarter of fiscal year~~three months ended March 31, 2009 were: Critical Solutions — $2.5 million, Systems Solutions — $1.9 million and Global Customer Operations — ~~$2.7 million,~~$0.7 million. The restructuring charges by segment for the six months ended March 31, 2009 were: Critical Solutions ~~Group~~ — ~~$0.6~~$3.1 million, Systems Solutions — $2.4 million and ~~Systems Solutions Group~~Global Customer Operations — ~~$0.4~~$3.3 million. In addition, we incurred ~~$0.4~~$0.8 million and $1.2 million of restructuring charges for the three and six months ended March 31, 2009, respectively, that were related to general corporate functions that support all of our segments.

Interest Income

Interest income was $0.3 million and $0.6 million for the ~~first quarter of fiscal year~~three and six month periods ended March 31, 2010, as compared to ~~$0.9~~$0.6 million and $1.5 million for the same prior year period. ~~Approximately $0.3 million of this decrease is~~These decreases are primarily due ~~to lower investment balances, with the balance of the decrease attributable~~ to lower interest rates on our investments.

Sale of Intellectual Property Rights

During the second quarter of fiscal year 2010, we sold certain patents and patents pending related to our AMHS product line. We recorded a gain of $7.8 million for this sale during the second quarter of 2010. The terms of the sale permit us to continue to use these patents to support our ongoing service and spare parts business included within our Global Customer Operations segment.

Loss on Investment

During the ~~first quarter of fiscal year~~six months ended March 31, 2010, we recorded a charge of $0.2 million for the sale of our minority equity investment in a closely-held Swiss public company. During the ~~first quarter of fiscal year~~six months ended March 31, 2009, we recorded a charge of $1.2 million to write down this investment to market ~~value as of December 31, 2008. As of December 31, 2009, we~~value. We no longer have an equity investment in this entity.

Other Expense, ~~net~~Net

Other expense, net of ~~$0.2~~$0.1 million for the ~~first quarter of fiscal year~~three months ended March 31, 2010 consists primarily of foreign exchange losses, offset partially by management fee income of $0.1 million. Other expense, net of ~~$0.0~~$0.1 million for the ~~first quarter of fiscal year~~three months ended March 31, 2009 consists primarily of foreign exchange losses, offset partially by management fee income of $0.2 million.

Other expense, net of $0.3 million ~~which has been fully offset by~~for the six months ended March 31, 2010 consists primarily of foreign exchange ~~losses.~~losses, offset partially by management fee income of $0.2 million. Other expense, net of $0.1 million for the six months ended March 31, 2009 consists of foreign exchange losses, offset partially by management fee income of $0.4 million.

Income Tax Provision (Benefit)

We recorded an income tax ~~provision~~benefit of ~~$0.6~~$2.8 million and $2.2 million for the ~~first quarter~~three and six month periods ended March 31, 2010. This benefit includes a $3.9 million expected refund from the carryback of ~~fiscal~~alternative minimum tax losses as a result of the Worker, Home Ownership and Business Assistance Act of 2009 which provides for 100% (previously 90%) of certain net operating loss carrybacks against alternative minimum taxable income. This benefit was partially offset by current year ~~2010~~alternative minimum taxes and ~~an income~~certain state taxes as well as international taxes. Our tax provision ~~of $0.4 million for the same prior year period. The provision for the first quarter of fiscal year 2010~~ is ~~substantially~~ impacted by foreign taxes arising from our international sales mix. ~~This provision is also attributable to U.S. Federal alternative minimum taxes and certain state income taxes.~~ The tax provision for the ~~first quarter of fiscal year~~three and six month periods ended March 31, 2009 is principally attributable to taxes on foreign income and interest related to unrecognized tax benefits. We continued to provide a full valuation allowance for our net deferred tax assets at ~~December~~March 31, ~~2009,~~2010, as we believe it is more likely than not that the future tax benefits from accumulated net operating losses and deferred taxes will not be realized.

Equity in Earnings (Losses) of Joint Ventures

Income ~~(loss)~~ associated with our 50% interest in ULVAC Cryogenics, Inc., a joint venture with ULVAC Corporation of Japan, was $0.0 million for both the three month periods ended March 31, 2010 and 2009. The income associated with our 50% interest in Yaskawa Brooks Automation, Inc., a joint venture with Yaskawa Electric Corporation of Japan was $0.2 million for the three months ended March 31, 2010 as compared to $0.0 million in the same prior year period.

Income (loss) associated with our 50% interest in ULVAC Cryogenics, Inc. was $(0.1) million for the ~~first quarter of fiscal year~~six months ended March 31, 2010, compared to $0.3 million in the same prior year period. The income (loss) associated with our 50% interest in Yaskawa Brooks Automation, Inc.~~, a joint venture with Yaskawa Electric Corporation of Japan~~ was ~~$(0.2)~~$(0.1) million for the ~~first quarter of fiscal year~~six months ended March 31, 2010 as compared to $0.0 million in the same prior year period.

Liquidity and Capital Resources

Our business is significantly dependent on capital expenditures by semiconductor manufacturers and OEMs that are, in turn, dependent on the current and anticipated market demand for semiconductors. Demand for semiconductors is cyclical and has historically experienced periodic downturns. This cyclicality makes estimates of future revenues, results of operations and net cash flows inherently uncertain.

At ~~December~~March 31, ~~2009,~~2010, we had cash, cash equivalents and marketable securities aggregating ~~$111.4~~$125.8 million. This amount was comprised of ~~$47.2~~$48.6 million of cash and cash equivalents, ~~$38.0~~$35.8 million of investments in short-term marketable securities and ~~$26.2~~$41.4 million of investments in long-term marketable securities.

Cash and cash equivalents were ~~$47.2~~$48.6 million at ~~December~~March 31, ~~2009,~~2010, a decrease of ~~$12.8~~$11.4 million from September 30, 2009. This decrease was primarily due to ~~$14.1~~$27.1 million of purchases in marketable securities, net of maturities. This decrease was partially offset by ~~$1.5~~$9.3 million of cash provided by operating ~~activities.~~activities and $7.8 million of proceeds from the sale of intellectual property rights.

Cash provided by operating activities was ~~$1.5~~$9.3 million for the ~~first quarter of fiscal year~~six months ended March 31, 2010, and was comprised of a net ~~loss~~income of ~~$2.9~~$18.1 million, which includes ~~$7.0~~$13.8 million of net non-cash related charges such as ~~$4.8~~$9.5 million of depreciation and amortization and ~~$1.5~~$3.6 million of stock-based ~~compensation.~~compensation which was partially offset by $7.8 million from our gain on sale of intellectual property rights. Further, cash provided by operations was reduced by net increases in working capital of ~~$2.6~~$14.7 million, consisting primarily of ~~$14.8~~$29.3 million of increases in accounts receivable and ~~$5.2~~$19.7 million of increases in inventory. The increases in accounts receivable and inventory were caused by a ~~65.7%~~129.9% increase in revenues for the ~~first quarter of fiscal year~~six months ended March 31, 2010 as compared to the ~~fourth quarter~~first six months of fiscal year 2009. ~~Additionally,~~In addition, we paid approximately $3.0 million in annual incentive compensation payments during the first quarter of fiscal year 2010 related to the prior fiscal year. Our other current assets have also increased as of March 31, 2010 to reflect the $3.9 million of refundable taxes for the carryback of alternative minimum tax losses. These increases in working capital were partially offset by ~~$19.9~~$40.4 million of increases in accounts payable and ~~$1.2~~$1.1 million of higher deferred revenues.

�� Cash used in investing activities was ~~$14.4~~$21.1 million for the ~~first quarter of fiscal year~~six months ended March 31, 2010, and is principally comprised of net purchases of marketable securities of ~~$14.1~~$27.1 million, the purchase of intellectual property related intangible assets for $0.9 million and ~~$0.5~~$1.2 million of capital expenditures. These uses of cash were partially offset

by $7.8 million of proceeds from our sale of intellectual property rights and $0.2 million of proceeds from our sale of a minority equity investment in a closely-held Swiss public company. Our capital expenditures for the ~~first quarter of fiscal year~~six months ended March 31, 2009 were ~~$5.1~~$9.1 million, including ~~$3.0~~$6.2 million in expenditures related to our Oracle ERP implementation. We implemented the Oracle ERP system in most of our U.S. operations in July 2009. ~~We are currently evaluating~~

Cash provided by financing activities for the ~~timing~~six months ended March 31, 2010 and ~~cost~~2009 is comprised entirely of proceeds from the sale of common stock to ~~implement this system in~~employees through our ~~international locations.~~employee stock purchase plan.

At ~~December~~March 31, ~~2009,~~2010, we had approximately $0.5 million of letters of credit outstanding.

We believe that we have adequate resources to fund our currently planned working capital and capital expenditure requirements for the next twelve months. However, the cyclical nature of our served markets and uncertainty with the current global economic environment makes it difficult for us to predict future liquidity requirements with certainty. We may be unable to obtain any required additional financing on terms favorable to us, if at all. If adequate funds are not available on acceptable terms, we may be unable to successfully develop or enhance products, respond to competitive pressure or take advantage of acquisition opportunities, any of which could have a material adverse effect on our business.

Recently Enacted Accounting Pronouncements

In September 2006, the Financial Accounting Standards Board (“FASB”) issued authoritative guidance for Fair Value Measurements and Disclosures which defines fair value, establishes a framework for measuring fair value and expands disclosures about assets and liabilities measured at fair value in the financial statements. In February 2008, the FASB issued authoritative guidance which ~~allows~~allowed for the delay of the effective date for fair value measurements for one year for all non-financial assets and non-financial liabilities, except for items that are recognized or disclosed at fair value in the financial statements on a recurring basis (at least annually). In April 2009, the FASB issued additional authoritative guidance in determining whether a market is active or inactive, and whether a transaction is distressed, is applicable to all assets and liabilities (i.e., financial and non-financial) and ~~will require~~requires enhanced disclosures. This standard was effective beginning with our fourth quarter of fiscal 2009. The measurement and disclosure requirements related to financial assets and financial liabilities were effective for us beginning on October 1, 2008. See Note ~~13.~~14. On October 1, 2009 we adopted the fair value measurement standard for all non-financial assets and non-financial liabilities, which had no impact on our financial position or results of operations.

In December 2007, the FASB revised the authoritative guidance for Business Combinations, which significantly changes the accounting for business combinations in a number of areas including the treatment of contingent consideration, pre-acquisition contingencies, transaction costs, restructuring costs and income taxes. On October 1, 2009 we adopted this standard prospectively and will apply the standard to any business combination with an acquisition date after October 1, 2009.

In December 2007, the FASB issued authoritative guidance regarding Consolidation, which establishes accounting and reporting standards for noncontrolling interests in a subsidiary and for the deconsolidation of a subsidiary. This standard clarifies that a noncontrolling interest in a subsidiary is an ownership interest in the consolidated entity that should be reported as equity in the consolidated financial statements. The amount of net income attributable to the noncontrolling interest will be included in consolidated net income on the face of the income statement. Further, it clarifies that changes in a parent’s ownership interest in a subsidiary that do not result in deconsolidation are equity transactions if the parent retains its controlling financial interest. In addition, this standard requires that a parent recognize a gain or loss in net income when a subsidiary is deconsolidated. On October 1, 2009 we adopted this standard retrospectively, which did not have a material impact on our financial position or results of operations.

In April 2008, the FASB issued authoritative guidance regarding the determination of the useful life of intangible assets. This guidance amends the factors that should be considered in developing renewal or extension assumptions used to determine the useful life of a recognized intangible asset. It also improves the consistency between the useful life of a recognized intangible asset and the period of expected cash flows used to measure the fair value of the asset. On October 1, 2009 we adopted this standard, which had no impact on our financial position or results of operations.

In June 2008, the FASB issued authoritative guidance regarding whether instruments granted in share-based payment transactions are participating securities, which classifies unvested share-based payment awards that contain nonforfeitable rights to dividends or dividend equivalents (whether paid or unpaid) as participating securities and requires them to be included in the computation of earnings per share pursuant to the two-class method. All prior-period earnings per share data presented are to be adjusted retrospectively (including interim financial statements, summaries of earnings, and selected financial data) to conform with the provisions of this guidance. On October 1, 2009 we adopted this standard, which had no impact on our financial position or results of operations.

In December 2008, the FASB issued authoritative guidance regarding Compensation — Retirement Benefits, which requires enhanced disclosures about the plan assets of a company’s defined benefit pension and other postretirement plans. The enhanced disclosures are intended to provide users of financial statements with a greater understanding of: (1) how investment allocation decisions are made, including the factors that are pertinent to an understanding of investment policies and strategies; (2) the major categories of plan assets; (3) the inputs and valuation techniques used to measure the fair value of plan assets; (4) the effect of fair value measurements using significant unobservable inputs (Level 3) on changes in plan assets for the period; and (5) significant concentrations of risk within plan assets. This standard will be effective for us for the fiscal year ending September 30, 2010. We are currently evaluating the potential impact of this guidance on our future disclosures.

interest in a VIE, and requires ongoing assessment of whether an entity is a VIE and whether an interest in a VIE makes the holder the primary beneficiary of the VIE. This guidance is effective for fiscal years beginning after November 15, 2009. We are currently evaluating the potential impact of this standard on our financial position and results of operations.

In September 2009, the FASB issued authoritative guidance on revenue arrangements with multiple deliverables. This guidance provides another alternative for establishing fair value for a deliverable. When vendor specific objective evidence or third-party evidence for deliverables in an arrangement cannot be determined, companies will be required to develop a best estimate of the selling price for separate deliverables and allocate arrangement consideration using the relative selling price method. This guidance is effective October 1, 2010, and early adoption is permitted. We are currently evaluating the potential impact of this guidance on our financial position and results of operations.

Item 3.Quantitative and Qualitative Disclosure About Market Risk

We are exposed to a variety of market risks, including changes in interest rates affecting the return on our cash and cash equivalents, short-term and long-term investments and fluctuations in foreign currency exchange rates.

Interest Rate Exposure

As our cash and cash equivalents consist principally of money market securities, which are short-term in nature, our exposure to market risk related to interest rate fluctuations for these investments is not significant. Our short-term and long-term investments consist mostly of highly rated corporate debt securities, and as such, market risk to these investments is not significant. During the ~~three~~six months ended ~~December~~March 31, ~~2009,~~2010, the unrealized loss on marketable securities was ~~$51,000.~~$188,000. A hypothetical 100 basis point change in interest rates would result in an annual change of approximately $1.2 million in interest income earned.

Currency Rate Exposure

We have transactions and balances denominated in currencies other than the U.S. dollar. Most of these transactions or balances are denominated in Euros and a variety of Asian currencies. Sales in currencies other than the U.S. dollar were ~~18.0%~~17% of our total sales for the three months ended ~~December~~March 31, ~~2009.~~2010. These foreign sales were made primarily by our foreign subsidiaries, which have cost structures that substantially align with the currency of sale.

In the normal course of our business, we have short-term advances between our legal entities that are subject to foreign currency exposure. These short-term advances were approximately ~~$13.4~~$17.1 million at ~~December~~March 31, ~~2009,~~2010, and relate to the Euro and a variety of Asian currencies. A majority of our foreign currency loss of ~~$0.2~~$0.5 million for the ~~three~~

six months ended ~~December~~March 31, ~~2009~~2010 relates to the currency fluctuation on these advances between the time the transaction occurs and the ultimate settlement of the transaction. A hypothetical 10% change in foreign exchange rates at ~~December~~March 31, ~~2009~~2010 would result in a ~~$1.3~~$1.7 million change in our net income (loss). We mitigate the impact of potential currency translation losses on these short-term inter company advances by the timely settlement of each transaction, generally within 30 days.

Item 4.Controls and Procedures

Evaluation of Disclosure Controls and Procedures. As of the end of the period covered by this report, and pursuant to Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, the Company’s management, including our chief executive officer and chief financial officer has concluded that our disclosure controls and procedures are effective.

Change in Internal Controls. There were no changes in our internal control over financial reporting that occurred during our most recent fiscal quarter that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

PART II. OTHER INFORMATION

Item 1.Legal Proceedings

On August 22, 2006, an action captioned asMark Levy v. Robert J. Therrien and Brooks Automation, Inc., was filed in the United States District Court for the District of Delaware, seeking recovery, on behalf of Brooks, from Mr. Therrien (the Company’s former Chairman and CEO) under Section 16(b) of the Securities Exchange Act of 1934 for alleged “short-swing” profits earned by Mr. Therrien due to the loan and stock option exercise in November 1999, and a sale by Mr. Therrien of Brooks stock in March 2000. The complaint seeks disgorgement of all profits earned by Mr. Therrien on the transactions, attorneys’ fees and other expenses. On February 20, 2007, a second Section 16(b) action, concerning the same loan and stock option exercise in November 1999 discussed above and seeking the same remedy, was filed in the United States District Court of the District of Delaware, captionedAron Rosenberg v. Robert J. Therrien and Brooks Automation, Inc. On April 4, 2007, the court issued an order consolidating theLevyandRosenbergactions. On July 14, 2008, the court denied Mr. Therrien’s motion to dismiss this action. Discovery has commenced in this ~~matter and is currently ongoing.~~matter. It has been reported to us that the parties have reached an agreement in principle to settle this case, subject to the approval of the court and to the conclusion by the parties of necessary settlement processes and documents. Brooks is a nominal defendant in the consolidated action and any recovery in this action, less attorneys’ fees, would go to the Company.

Item 2.Unregistered Sales of Equity Securities and Use of Proceeds

The following table provides information concerning shares of our Common Stock $0.01 par value purchased in connection with the forfeiture of shares to satisfy the employees’ obligations with respect to withholding taxes in connection with the vesting of shares of restricted stock during the three months ended ~~December~~March 31, ~~2009.~~2010. These purchases were made pursuant to the Amended and Restated 2000 Equity Incentive Plan.

Maximum
Number (or
Approximate
Total Number of Dollar Value) of
Total Shares Purchased as Shares that May Yet
Number Part of Publicly be Purchased Under
of Shares Average Price Paid Announced Plans the Plans or
Period Purchased per Share or Programs Programs
October 1 — 31, 2009 1,146 $ 6.88 1,146 $ —
November 1 — 30, 2009 37,869 7.76 37,869 —
December 1 — 31, 2009 — — — —

Total 39,015 $ 7.73 39,015 $ —

Total Number of
Total Shares Purchased as
Number Part of Publicly
of Shares Average Price Paid Announced Plans
Period Purchased per Share or Programs
January 1 — 31, 2010 — $ — —
February 1 — 28, 2010 28,865 8.14 28,865
March 1 — 31, 2010 98,468 8.61 98,468

Total 127,333 $ 8.50 127,333

Item 5.Other Information

The Annual Meeting of the stockholders of the Company was held on February 4, 2010. At this meeting, the stockholders were asked to and did vote on the following proposals:


	PAGE NUMBER
PART I. FINANCIAL INFORMATION
Item 1. Consolidated Financial Statements		3
Consolidated Balance Sheets as of ~~December~~March 31, ~~2009~~2010 (unaudited) and September 30, 2009		3
Consolidated Statements of Operations for the three and six months ended ~~December~~March 31, ~~2009~~2010 and ~~2008~~2009 (unaudited)		4
Consolidated Statements of Cash Flows for the ~~three~~six months ended ~~December~~March 31, ~~2009~~2010 and ~~2008~~2009 (unaudited)		5
Notes to Consolidated Financial Statements (unaudited)		6
Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations		16
Item 3. Quantitative and Qualitative Disclosure about Market Risk		2224
Item 4. Controls and Procedures		2225
PART II. OTHER INFORMATION
Item 1. Legal Proceedings		2325
Item 2. Unregistered Sales of Equity Securities and Use of Proceeds		2325
Item 5. Other Information		25
Item 6. Exhibits		2326
Signatures		2427
EX-10.1
EX-31.01 ~~Section 302 Certification of Chief Executive Officer~~
EX-31.02 ~~Section 302 Certification of Chief Financial Officer~~
EX-32 ~~Section 906 Certification of Chief Executive Officer and Chief Financial Officer~~


Activity — Three Months Ended December 31, 2008
Balance						Balance
September 30,						December 31,
2008	Accruals		Settlements			2008
$8,174	$	3,085	$	(3,321	)	$	7,938


Activity — Three Months Ended March 31, 2009
Balance			Balance
December 31,			March 31,
2008	Accruals	Settlements	2009
$7,938	$ 1,874	$ (3,145)	$ 6,667


Activity — Six Months Ended March 31, 2010
Balance			Balance
September 30,			March 31,
2009	Accruals	Settlements	2010
$5,698	$ 6,450	$ (5,026)	$ 7,122


Activity — Six Months Ended March 31, 2009
Balance			Balance
September 30,			March 31,
2008	Accruals	Settlements	2009
$8,174	$ 4,959	$ (6,466)	$ 6,667


				Weighted-
				Average	Weighted		Aggregate
	Number of			Remaining	Average		Intrinsic Value
	Options			Contractual Term	Exercise Price		(In Thousands)
Outstanding at September 30, 2009		1,189,897			$	17.54
Forfeited/expired		(59,175	)			14.20

Outstanding at December 31, 2009		1,130,722		1.3 years	$	17.71	$	28
Vested and unvested expected to vest at December 31, 2009		1,129,477		1.3 years	$	17.72	$	28
Options exercisable at December 31, 2009		1,105,722		1.3 years	$	17.82	$	28


Level 3		3 Unobservable inputs that are supported by little or no market activity and that are significant to the fair value of the assets or liabilities.


			Fair Value Measurements at Reporting Date Using								Fair Value Measurements at Reporting Date Using
			Quoted Prices in								Quoted Prices in
			Active Markets for		Significant Other		Significant				Active Markets for		Significant Other		Significant
	December 31,		Identical Assets		Observable Inputs		Unobservable Inputs		March 31,		Identical Assets		Observable Inputs		Unobservable Inputs
Description	2009		(Level 1)		(Level 2)		(Level 3)		2010		(Level 1)		(Level 2)		(Level 3)
Assets
Cash Equivalents	$	24,656	$	24,656	$	—	$	—	$	22,029	$	22,029	$	—	$	—
Available-for-sale securities		64,195		25,143		39,052		—		77,139		31,686		45,453		—

Total Assets	$	88,851	$	49,799	$	39,052	$	—	$	99,168	$	53,715	$	45,453	$	—


							Maximum
							Number (or
							Approximate
					Total Number of		Dollar Value) of
	Total				Shares Purchased as		Shares that May Yet
	Number				Part of Publicly		be Purchased Under
	of Shares		Average Price Paid		Announced Plans		the Plans or
Period	Purchased		per Share		or Programs		Programs
October 1 — 31, 2009		1,146	$	6.88		1,146	$	—
November 1 — 30, 2009		37,869		7.76		37,869		—
December 1 — 31, 2009		—		—		—		—

Total		39,015	$	7.73		39,015	$	—


	Votes For		Withheld		Broker Non-Vote
A. Clinton Allen		43,712,168		9,161,068		6,720,986
Robert J. Lepofsky		44,131,460		8,741,776		6,720,986
Joseph R. Martin		44,138,955		8,734,281		6,720,986
John K. McGillicuddy		43,275,045		9,598,191		6,720,986
Krishna G. Palepu		42,987,188		9,886,048		6,720,986
C. S. Park		43,913,835		8,959,401		6,720,986
Kirk P. Pond		44,134,901		8,738,335		6,720,986
Alfred Woollacott, III		43,303,087		9,570,149		6,720,986
Mark S. Wrighton		43,270,895		9,602,341		6,720,986


Exhibit No.		Description
10.01		Employment Agreement, effective as of April 5, 2010, by and between Brooks Automation, Inc. and Stephen S. Schwartz.

31.01		Rule 13a-14(a), 15d-14(a) Certification.

31.02		Rule 13a-14(a), 15d-14(a) Certification.

32		Section 1350 Certifications.


		BROOKS AUTOMATION, INC.
~~DATE: February 5, 2010~~	~~/s/Martin S. Headley~~
	~~Martin S. Headley~~
	~~Executive Vice President and Chief Financial Officer~~ ~~(Principal Financial Officer)~~


DATE: ~~February 5,~~May 6, 2010		/s/Martin S. Headley Martin S. Headley
		Executive Vice President and Chief Financial Officer
		(Principal Financial Officer)

DATE: May 6, 2010		/s/Timothy S. Mathews Timothy S. Mathews
	~~Timothy S. Mathews~~
	Vice President and Corporate Controller
		(Principal Accounting Officer)