Alnylam Pharmaceuticals (ALNY) 10-K20 Feb 142013 FY Annual reportFinancial data

Company Profile

Document_and_Entity_Informatio

Document and Entity Information (USD $)	12 Months Ended
Document and Entity Information (USD $)	Dec. 31, 2013	Jan. 31, 2014	Jun. 28, 2013
Document Information [Line Items]	'	'	'
Document Type	'10-K	'	'
Amendment Flag	'false	'	'
Document Period End Date	31-Dec-13	'	'
Document Fiscal Year Focus	'2013	'	'
Document Fiscal Period Focus	'FY	'	'
Trading Symbol	'ALNY	'	'
Entity Registrant Name	'ALNYLAM PHARMACEUTICALS, INC.	'	'
Entity Central Index Key	'0001178670	'	'
Current Fiscal Year End Date	'--12-31	'	'
Entity Well-known Seasoned Issuer	'Yes	'	'
Entity Current Reporting Status	'Yes	'	'
Entity Voluntary Filers	'No	'	'
Entity Filer Category	'Large Accelerated Filer	'	'
Entity Common Stock, Shares Outstanding	'	63,916,814	'
Entity Public Float	'	'	$1,915,005,225

Consolidated_Balance_Sheets

Consolidated Balance Sheets (USD $)	Dec. 31, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012
Current assets:	'	'
Cash and cash equivalents	$53,169	$51,405
Marketable securities	192,701	71,407
Billed and unbilled collaboration receivables	4,248	104
Prepaid expenses and other current assets	3,910	2,641
Total current assets	254,028	125,557
Marketable securities	104,602	103,416
Investment in equity securities of Regulus Therapeutics Inc.	45,452	38,748
Property and equipment, net	16,448	19,799
Total assets	420,530	287,520
Current liabilities:	'	'
Accounts payable	5,896	4,420
Accrued expenses	14,160	11,558
Deferred rent	1,112	950
Deferred revenue	32,696	31,417
Total current liabilities	53,864	48,345
Deferred rent, net of current portion	2,925	4,248
Deferred revenue, net of current portion	93,394	100,874
Total liabilities	150,183	153,467
Commitments and contingencies (Note 6)	'	'
Stockholders' equity:	'	'
Preferred stock, $0.01 par value per share, 5,000,000 shares authorized and no shares issued and outstanding at December 31, 2013 and 2012	'	'
Common stock, $0.01 par value per share, 125,000,000 shares authorized; 63,741,573 shares issued and outstanding at December 31, 2013; 52,489,936 shares issued and outstanding at December 31, 2012	637	525
Additional paid-in capital	846,228	624,876
Accumulated other comprehensive income	19,717	15,662
Accumulated deficit	-596,235	-507,010
Total stockholders' equity	270,347	134,053
Total liabilities and stockholders' equity	$420,530	$287,520

Consolidated_Balance_Sheets_Pa

Consolidated Balance Sheets (Parenthetical) (USD $)	Dec. 31, 2013	Dec. 31, 2012
Preferred stock, par value	$0.01	$0.01
Preferred stock, shares authorized	5,000,000	5,000,000
Preferred stock, shares issued	'	'
Preferred stock, shares outstanding	'	'
Common stock, par value	$0.01	$0.01
Common stock, shares authorized	125,000,000	125,000,000
Common stock, shares issued	63,741,573	52,489,936
Common stock, shares outstanding	63,741,573	52,489,936

Consolidated_Statements_of_Com

Consolidated Statements of Comprehensive Loss (USD $)	12 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Dec. 31, 2013		Dec. 31, 2012		Dec. 31, 2011
Net revenues from collaborators	$47,167		$66,725		$82,757
Operating expenses:	'		'		'
Research and development	112,957	[1]	86,569	[1]	99,295	[1]
General and administrative	27,152	[1]	44,612	[1]	38,280	[1]
Restructuring of Tekmira license agreement	'		65,000		'
Total operating expenses	140,109		196,181		137,575
Loss from operations	-92,942		-129,456		-54,818
Other income (expense):	'		'		'
Equity in loss of joint venture (Regulus Therapeutics Inc.)	'		-4,522		-3,505
Gain on issuance of stock by Regulus Therapeutics Inc.	'		16,084		'
Interest income	1,069		977		1,205
Other (expense) income	-47		331		-531
Total other income (expense)	1,022		12,870		-2,831
Loss before income taxes	-91,920		-116,586		-57,649
Benefit from income taxes	2,695		10,572		0
Net loss	-89,225		-106,014		-57,649
Net loss per common share - basic and diluted	($1.45)		($2.11)		($1.36)
Weighted average common shares used to compute basic and diluted net loss per common share	61,551		50,286		42,410
Comprehensive loss:	'		'		'
Net loss	-89,225		-106,014		-57,649
Unrealized gain (loss) on marketable securities, net of tax	4,055		15,827		-879
Comprehensive loss	($85,170)		($90,187)		($58,528)

[1]	Non-cash stock-based compensation expenses included in operating expenses are as follows: Research and development $ 14,369 $ 8,041 $ 10,921 General and administrative 6,334 4,319 5,755

Consolidated_Statements_of_Com1

Consolidated Statements of Comprehensive Loss (Parenthetical) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Non-cash stock-based compensation expenses included in operating expenses are as follows:	'	'	'
Research and development	$14,369	$8,041	$10,921
General and administrative	$6,334	$4,319	$5,755

Consolidated_Statements_of_Sto

Consolidated Statements of Stockholders' Equity (USD $)	Total	Common Stock	Additional Paid-in Capital	Accumulated Other Comprehensive Income (Loss)	Accumulated Deficit
In Thousands, except Share data	Total	Common Stock	Additional Paid-in Capital	Accumulated Other Comprehensive Income (Loss)	Accumulated Deficit
Balance at Dec. 31, 2010	$158,233	$423	$500,443	$714	($343,347)
Balance (in shares) at Dec. 31, 2010	'	42,343,423	'	'	'
Exercise of common stock options (in shares)	'	16,800	'	'	'
Exercise of common stock options	103	'	103	'	'
Issuance of common stock under other types of equity plans (in shares)	'	124,815	'	'	'
Issuance of common stock under other types of equity plans	1,023	2	1,021	'	'
Issuance of restricted stock, net of cancellations and tax withholdings (in shares)	'	236,904	'	'	'
Issuance of restricted stock, net of cancellations and tax withholdings	'	2	-2	'	'
Stock-based compensation expense	16,676	'	16,676	'	'
Joint venture stock-based compensation (Regulus Therapeutics Inc.)	370	'	370	'	'
Tax benefit from stock-based compensation	120	'	120	'	'
Other comprehensive income	-879	'	'	-879	'
Net loss	-57,649	'	'	'	-57,649
Balance at Dec. 31, 2011	117,997	427	518,731	-165	-400,996
Balance (in shares) at Dec. 31, 2011	'	42,721,942	'	'	'
Exercise of common stock options (in shares)	'	661,909	'	'	'
Exercise of common stock options	6,402	7	6,395	'	'
Issuance of common stock under other types of equity plans (in shares)	'	97,459	'	'	'
Issuance of common stock under other types of equity plans	879	1	878	'	'
Issuance of restricted stock, net of cancellations and tax withholdings (in shares)	'	383,626	'	'	'
Issuance of restricted stock, net of cancellations and tax withholdings	-519	4	-523	'	'
Issuance of common stock, net of offering costs (in shares)	'	8,625,000	'	'	'
Issuance of common stock, net of offering costs	86,800	86	86,714	'	'
Stock-based compensation expense	12,360	'	12,360	'	'
Joint venture stock-based compensation (Regulus Therapeutics Inc.)	321	'	321	'	'
Other comprehensive income	15,827	'	'	15,827	'
Net loss	-106,014	'	'	'	-106,014
Balance at Dec. 31, 2012	134,053	525	624,876	15,662	-507,010
Balance (in shares) at Dec. 31, 2012	'	52,489,936	'	'	'
Exercise of common stock options (in shares)	2,031,916	2,031,916	'	'	'
Exercise of common stock options	27,994	20	27,974	'	'
Issuance of common stock under other types of equity plans (in shares)	'	60,180	'	'	'
Issuance of common stock under other types of equity plans	1,184	1	1,183	'	'
Tax withholdings and cancellations of restricted stock, net of issuances of new awards, shares	'	-40,459	'	'	'
Tax withholdings and cancellations of restricted stock, net of issuances of new awards	-1,989	-1	-1,988	'	'
Issuance of common stock, net of offering costs (in shares)	'	9,200,000	'	'	'
Issuance of common stock, net of offering costs	173,572	92	173,480	'	'
Stock-based compensation expense	20,703	'	20,703	'	'
Other comprehensive income	4,055	'	'	4,055	'
Net loss	-89,225	'	'	'	-89,225
Balance at Dec. 31, 2013	$270,347	$637	$846,228	$19,717	($596,235)
Balance (in shares) at Dec. 31, 2013	'	63,741,573	'	'	'

Consolidated_Statements_of_Cas

Consolidated Statements of Cash Flows (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Cash flows from operating activities:	'	'	'
Net loss	($89,225)	($106,014)	($57,649)
Adjustments to reconcile net loss to net cash used in operating activities:	'	'	'
Depreciation and amortization	10,229	9,035	5,125
Non-cash stock-based compensation	20,703	12,360	16,676
Charge for 401(k) company stock match	449	364	488
Equity in loss of joint venture (Regulus Therapeutics Inc.)	'	4,522	3,505
Tax benefit from stock-based compensation	'	'	120
Other than temporary impairment on equity securities	'	'	595
Realized gain on sale of marketable securities	'	-255	'
Gain on issuance of stock by joint venture	'	-16,084	'
Benefit from intraperiod tax allocation on marketable securities	-2,695	-10,572	'
Changes in operating assets and liabilities:	'	'	'
Proceeds from landlord tenant improvements	204	1,780	'
Billed and unbilled collaboration receivables	-4,144	1,364	1,982
Income taxes receivable	'	'	10,669
Prepaid expenses and other assets	-1,356	1,780	2,731
Accounts payable	1,832	-1,736	-3,512
Accrued expenses and other	1,547	-3,591	2,457
Deferred revenue	-6,201	-8,562	-70,255
Net cash used in operating activities	-68,657	-115,609	-87,068
Cash flows from investing activities:	'	'	'
Purchases of property and equipment	-4,006	-8,348	-1,291
Increase in restricted cash	'	-162	'
Purchases of marketable securities	-364,305	-277,129	-293,115
Sales and maturities of marketable securities	237,806	289,013	376,365
Net cash (used in) provided by investing activities	-130,505	3,374	81,959
Cash flows from financing activities:	'	'	'
Proceeds from exercise of stock options and other types of equity	28,743	6,971	738
Proceeds from issuance of common stock, net of offering costs	173,572	86,800	'
Payments for repurchase of common stock for employee tax withholding	-1,389	-359	'
Net cash provided by financing activities	200,926	93,412	738
Net increase (decrease) in cash and cash equivalents	1,764	-18,823	-4,371
Cash and cash equivalents, beginning of period	51,405	70,228	74,599
Cash and cash equivalents, end of period	53,169	51,405	70,228
Supplemental disclosure of cash flows:	'	'	'
Cash (paid for income taxes) proceeds from income tax refunds	-11	-17	10,657
Supplemental disclosure of noncash investing activities:	'	'	'
Fixed asset expenditures included in accounts payable and accrued expenses	161	1,441	'
Repurchase of common stock for employee tax withholding in accrued expenses	$600	'	'

Nature_Of_Business

Nature Of Business	12 Months Ended
	Dec. 31, 2013
Nature Of Business	'
	1	NATURE OF BUSINESS
	Alnylam Pharmaceuticals, Inc. (the “Company” or “Alnylam”) commenced operations on June 14, 2002 as a biopharmaceutical company seeking to develop and commercialize novel therapeutics based on RNA interference (“RNAi”). Alnylam is focused on discovering, developing and commercializing RNAi therapeutics by establishing strategic alliances with leading pharmaceutical and life sciences companies, establishing and maintaining a strong intellectual property position in the RNAi field, generating revenues through licensing agreements, and ultimately developing and commercializing RNAi therapeutics for its own account. The Company has devoted substantially all of its efforts to business planning, research and development, acquiring, filing and expanding intellectual property rights, recruiting management and technical staff, and raising capital.

Summary_of_Significant_Account

Summary of Significant Accounting Policies	12 Months Ended
Summary of Significant Accounting Policies	Dec. 31, 2013
Summary of Significant Accounting Policies	'
	2	SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES
	Basis of Presentation and Principles of Consolidation
	The accompanying consolidated financial statements reflect the operations of the Company and its wholly-owned subsidiaries. All intercompany accounts and transactions have been eliminated.
	Reclassifications
	Certain reclassifications have been made to prior years’ consolidated financial statements to conform to the 2013 presentation.
	Use of Estimates
	The preparation of financial statements in conformity with accounting principles generally accepted in the United States of America (“GAAP”) requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and the disclosure of contingent assets and liabilities at the date of the consolidated financial statements and the reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates.
	Concentrations of Credit Risk and Significant Customers
	Financial instruments that potentially expose the Company to concentrations of credit risk consist primarily of cash, cash equivalents and fixed income marketable securities. At December 31, 2013 and 2012, substantially all of the Company’s cash, cash equivalents and fixed income marketable securities were invested in money market mutual funds, commercial paper, corporate notes and U.S. government securities through highly rated financial institutions. Investments are restricted, in accordance with the Company’s investment policy, to a concentration limit per issuer.
	In recent periods, the Company’s revenues from collaborations have been generated from primarily F. Hoffmann-La Roche Ltd and certain of its affiliates (collectively, “Roche”) (which assigned its rights and obligations to Arrowhead Research Corporation (“Arrowhead”) in 2011), Takeda Pharmaceutical Company Limited (“Takeda”), Cubist Pharmaceuticals, Inc. (“Cubist”), Monsanto Company (“Monsanto”) and The Medicines Company (“MDCO”). For the year ended December 31, 2013, the composition of the Company’s billed and unbilled collaboration receivables was primarily composed of an amount due from Genzyme Corporation (“Genzyme”) based upon the initiation of a Phase 3 clinical trial. For the year ended December 31, 2012, the composition of the Company’s billed and unbilled collaboration receivables was entirely composed of amounts due from the U.S. Government for the wind-down of completed government contracts.

	The following table summarizes customers that represent greater than 10% of the Company’s net revenues from collaborators, for the periods indicated:


			Year Ended
			December 31,
			2013				2012				2011
	Takeda			47	%			33	%			27	%
	Cubist			21	%			*	%			*	%
	Monsanto			12	%			*	%			*	%
	Roche/Arrowhead			*	%			56	%			68	%
	The following table summarizes customers with amounts due that represent greater than 10% of the Company’s billed and unbilled collaboration receivables balance, at the periods indicated:


			At December 31,
			2013				2012
	Genzyme			94	%			*	%
	U.S. Government			*	%			100	%


	*	Represents 10% or less
	Fair Value Measurements
	The fair value is the price that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date. The following tables present information about the Company’s assets that are measured at fair value on a recurring basis at December 31, 2013 and 2012, and indicate the fair value hierarchy of the valuation techniques the Company utilized to determine such fair value. In general, fair values determined by Level 1 inputs utilize quoted prices (unadjusted) in active markets for identical assets or liabilities. Fair values determined by Level 2 inputs utilize data points that are observable, such as quoted prices (adjusted), interest rates and yield curves. Fair values determined by Level 3 inputs utilize unobservable data points for the asset or liability, and include situations where there is little, if any, market activity for the asset or liability. The fair value hierarchy level is determined by the lowest level of significant input. Financial assets and liabilities measured at fair value on a recurring basis are summarized as follows, in thousands:


	Description		At				Quoted				Significant				Significant
			December 31,				Prices in				Observable				Unobservable
			2013				Active				Inputs				Inputs
							Markets				(Level 2)				(Level 3)
							(Level 1)
	Cash equivalents		$	32,571			$	32,571			$	—			$	—
	Marketable securities (fixed income):
	Corporate notes			228,462				—				228,462				—
	U.S. Government obligations			56,863				—				56,863				—
	Commercial paper			11,978				—				11,978				—
	Marketable securities (Regulus equity holdings)			45,452				45,452				—				—

	Total		$	375,326			$	78,023			$	297,303			$	—



	Description		At				Quoted				Significant				Significant
			December 31,				Prices in				Observable				Unobservable
			2012				Active				Inputs				Inputs
							Markets				(Level 2)				(Level 3)
							(Level 1)
	Cash equivalents		$	50,213			$	50,213			$	—			$	—
	Marketable securities (fixed income):
	Corporate notes			91,523				—				91,523				—
	U.S. Government obligations			60,661				—				60,661				—
	Commercial paper			22,639				—				22,639				—
	Marketable securities (Regulus equity holdings)			38,748				—				38,748				—

Total		$	263,784			$	50,213			$	213,571			$	—

For the year ended December 31, 2013, the Company transferred $45.5 million of marketable securities (equity holdings in Regulus Therapeutics Inc. (“Regulus”)) from Level 2 to Level 1 due to the increased volume in average daily trading on the NASDAQ stock market for these instruments. For the year ended December 31, 2012, there were no transfers between Level 1 and Level 2 financial assets. The carrying amounts reflected in the Company’s consolidated balance sheets for cash, billed and unbilled collaboration receivables, other current assets, accounts payable and accrued expenses approximate fair value due to their short-term maturities.
Investments in Marketable Securities
The Company invests its excess cash balances in short-term and long-term marketable debt and equity securities. The Company classifies its investments in marketable debt securities as either held-to-maturity or available-for-sale based on facts and circumstances present at the time it purchased the securities. At each balance sheet date presented, the Company classified all of its investments in debt and equity securities as available-for-sale. The Company reports available-for-sale investments at fair value at each balance sheet date and includes any unrealized holding gains and losses (the adjustment to fair value) in accumulated other comprehensive income (loss), a component of stockholders’ equity. Realized gains and losses are determined using the specific identification method and are included in other income. If any adjustment to fair value reflects a decline in the value of the investment, the Company considers all available evidence to evaluate the extent to which the decline is “other than temporary” and, if so, marks the investment to market through a charge to its consolidated statements of comprehensive loss. The Company did not record any impairment charges related to its fixed income marketable securities during the years ended December 31, 2013, 2012 or 2011. During 2011, the Company recorded an impairment charge of $0.6 million related to its former investment in equity securities of Tekmira Pharmaceuticals Corporation (“TPC”), as the decrease in the fair value of this investment was deemed to be other than temporary. The Company’s marketable securities are classified as cash equivalents if the original maturity, from the date of purchase, is 90 days or less, and as marketable securities if the original maturity, from the date of purchase, is in excess of 90 days. The Company’s cash equivalents are composed of money market funds.

In the fourth quarter of 2012, the Company began accounting for its investment in Regulus as an available-for-sale marketable security. Intraperiod tax allocation rules require the Company to allocate its provision for income taxes between continuing operations and other categories of earnings, such as other comprehensive income. In periods in which the Company has a year-to-date pre-tax loss from continuing operations and pre-tax income in other categories of earnings, such as other comprehensive income, the Company must allocate the tax provision to the other categories of earnings. The Company then records a related tax benefit in continuing operations. The following tables summarize the fair value, accumulated other comprehensive income and intraperiod tax allocation regarding the Company’s investment in Regulus available-for-sale marketable securities at December 31, 2013 and 2012, and for the activity recorded in the year, in thousands:


Description		At				During Twelve				Balance at
		December 31,				Months Ended				December 31,
		2012				December 31,				2013
						2013
Carrying value		$	12,449			$	—			$	12,449
Accumulated other comprehensive income, before tax			26,299				6,704				33,003

Investment in equity securities of Regulus Therapeutics Inc., as reported		$	38,748			$	6,704			$	45,452

Accumulated other comprehensive income, before tax		$	26,299			$	6,704			$	33,003
Intraperiod tax allocation recorded as a benefit from income taxes			(10,572	)			(2,695	)			(13,267	)

Accumulated other comprehensive income, net of tax		$	15,727			$	4,009			$	19,736

The Company obtains fair value measurement data for its marketable securities from independent pricing services. The Company performs validation procedures to ensure the reasonableness of this data. This includes meeting with the independent pricing services to understand the methods and data sources used. Additionally, the Company performs its own review of prices received from the independent pricing services by comparing these prices to other sources and confirming those securities are trading in active markets.
The following tables summarize the Company’s marketable securities, other than its holdings in Regulus noted above, at December 31, 2013 and 2012, in thousands:


		December 31, 2013
		Amortized				Gross				Gross				Fair Value
		Cost				Unrealized				Unrealized
						Gains				Losses
Commercial paper (Due within 1 year)		$	11,983			$	—			$	(5	)		$	11,978
Corporate notes (Due within 1 year)			154,175				33				(46	)			154,162
Corporate notes (Due after 1 year through 2 years)			74,312				23				(35	)			74,300
U.S. Government obligations (Due within 1 year)			26,553				8				—				26,561
U.S. Government obligations (Due after 1 year through 2 years)			30,300				2				—				30,302

Total		$	297,323			$	66			$	(86	)		$	297,303

		December 31, 2012
		Amortized				Gross				Gross				Fair Value
		Cost				Unrealized				Unrealized
						Gains				Losses
Commercial paper (Due within 1 year)		$	22,650			$	1			$	(12	)		$	22,639
Corporate notes (Due within 1 year)			41,249				23				(4	)			41,268
Corporate notes (Due after 1 year through 2 years)			50,322				5				(72	)			50,255
U.S. Government obligations (Due within 1 year)			7,500				—				—				7,500
U.S. Government obligations (Due after 1 year through 2 years)			53,168				2				(9	)			53,161

Total		$	174,889			$	31			$	(97	)		$	174,823


Estimated Liability for Development Costs
The Company records accrued liabilities related to expenses for which service providers have not yet billed the Company with respect to products or services that the Company has received, specifically related to ongoing pre-clinical studies and clinical trials. These costs primarily relate to third-party clinical management costs, laboratory and analysis costs, toxicology studies and investigator fees. The Company has multiple product candidates in concurrent pre-clinical studies and clinical trials at multiple clinical sites throughout the world. In order to ensure that the Company has adequately provided for ongoing pre-clinical and clinical development costs during the period in which the Company incurs such costs, the Company maintains an accrual to cover these expenses. The Company updates the estimate for this accrual on at least a quarterly basis. The assessment of these costs is a subjective process that requires judgment. Upon settlement, these costs may differ materially from the amounts accrued in the Company’s consolidated financial statements. The Company’s historical accrual estimates have not been materially different from the Company’s actual costs.
Revenue Recognition
The Company has entered into collaboration agreements with leading pharmaceutical and life sciences companies, including Novartis Pharma AG and one of its affiliates (together, “Novartis”), Roche, Takeda, Kyowa Hakko Kirin Co., Ltd. (“Kyowa Hakko Kirin”), Cubist, Monsanto, Genzyme and MDCO. The terms of the Company’s collaboration agreements typically include non-refundable license fees, funding of research and development, payments based upon achievement of clinical and pre-clinical development milestones, regulatory milestones, manufacturing services, sales milestones and royalties on product sales.
In January 2011, the Company adopted new authoritative guidance on revenue recognition for multiple element arrangements. The guidance, which applied to multiple element arrangements entered into or materially modified on or after January 1, 2011, amended the criteria for separating and allocating consideration in a multiple element arrangement by modifying the fair value requirements for revenue recognition and eliminating the use of the residual method. The fair value of deliverables under the arrangement may be derived using a “best estimate of selling price” if vendor specific objective evidence and third-party evidence is not available. Deliverables under the arrangement could be considered separate units of accounting provided that (i) a delivered item has value to the customer on a standalone basis and (ii) if the arrangement includes a general right of return relative to the delivered item, delivery or performance of the undelivered item is considered probable and substantially in the control of the vendor. The new guidance did not change the criteria for standalone value. As a biotechnology entity with unique and specialized delivered and undelivered performance obligations, the Company has been unable to demonstrate standalone value in its multiple element arrangements. For example, the Company applied the new rules to collaborations executed with Monsanto and Genzyme during 2012, but it was unable to demonstrate standalone value. In addition, the Company has not materially modified any of its multiple element arrangements. As such, the Company has continued to account for license and collaboration agreements under previously issued revenue recognition guidance for multiple element arrangements, as described below.
Non-refundable license fees are recognized as revenue upon delivery of the license only if the Company has a contractual right to receive such payment, the contract price is fixed or determinable, the collection of the resulting receivable is reasonably assured and the Company has no further performance obligations under the license agreement. Multiple element arrangements, such as license and development arrangements, are analyzed to determine whether the deliverables, which often include a license and performance obligations such as research and steering committee services, can be separated or whether they must be accounted for as a single unit of accounting. The Company recognizes upfront license payments as revenue upon delivery of the license only if the license has standalone value and the fair value of the undelivered performance obligations, typically including research and/or steering committee services, can be determined. If the fair value of the undelivered performance obligations can be determined, such obligations are accounted for separately as such obligations are fulfilled. If the license is considered to either not have standalone value or have standalone value but the fair value of any of the undelivered performance obligations cannot be determined, the arrangement would then be accounted for as a single unit of accounting and the license payments and payments for performance obligations are recognized as revenue over the estimated period of when the performance obligations are performed.

Whenever the Company determines that an arrangement should be accounted for as a single unit of accounting, the Company determines the period over which the performance obligations will be performed and revenue will be recognized. Revenue is recognized using either a proportional performance or straight-line method. The Company recognizes revenue using the proportional performance method when the level of effort required to complete its performance obligations under an arrangement can be reasonably estimated and such performance obligations are provided on a best-efforts basis. Direct labor hours or full-time equivalents are typically used as the measure of performance. The amount of revenue recognized under the proportional performance method is determined by multiplying the total payments under the contract, excluding royalties and payments contingent upon achievement of milestones, by the ratio of level of effort incurred to date to estimated total level of effort required to complete the Company’s performance obligations under the arrangement. Revenue is limited to the lesser of the cumulative amount of payments received or the cumulative amount of revenue earned, as determined using the proportional performance method, as of the period ending date.
If the Company cannot reasonably estimate the level of effort to complete its performance obligations under an arrangement, the Company recognizes revenue under the arrangement on a straight-line basis over the period the Company is expected to complete its performance obligations. Revenue is limited to the lesser of the cumulative amount of payments received or the cumulative amount of revenue earned, as determined using the straight-line method, as of the period ending date.
Significant management judgment is required in determining the level of effort required under an arrangement and the period over which the Company is expected to complete its performance obligations under an arrangement. Steering committee services that are not inconsequential or perfunctory and that are determined to be performance obligations are combined with other research services or performance obligations required under an arrangement, if any, in determining the level of effort required in an arrangement and the period over which the Company expects to complete its aggregate performance obligations.
Many of the Company’s collaboration agreements entitle it to additional payments upon the achievement of performance-based milestones. These milestones are generally categorized into three types; development milestones which are generally based on the advancement of the Company’s pipeline and initiation of clinical trials, regulatory milestones which are generally based on the submission, filing or approval of regulatory applications such as a new drug application in the United States, and commercialization milestones which are generally based on meeting specific thresholds of sales in certain geographic areas. If the achievement of a milestone is considered probable at the inception of the collaboration, the related milestone payment is included with other collaboration consideration, such as upfront fees and research funding, in the Company’s revenue model. Milestones that are tied to regulatory approval are not considered probable of being achieved until such approval is received. Milestones tied to counter-party performance are not included in the Company’s revenue model until the performance conditions are met.
The Company performs an assessment to determine whether a substantive milestone exists at the inception of its collaborative arrangements. In evaluating if a milestone is substantive, the Company considers whether uncertainty exists as to the achievement of the milestone event at the inception of the arrangement, the achievement of the milestone involves substantive effort and can only be achieved based in whole or part on the performance or the occurrence of a specific outcome resulting from the Company’s performance, the amount of the milestone payment appears reasonable either in relation to the effort expected to be expended or to the projected enhancement of the value of the delivered items, there is any future performance required to earn the milestone, and the consideration is reasonable relative to all deliverables and payment terms in the arrangement. When a substantive milestone is achieved, the accounting rules permit the Company to recognize revenue related to the milestone payment in its entirety.
To date, the Company has not recorded any substantive milestones under its collaborations because the Company has not identified any milestones that meet the required criteria listed above. The Company has deferred recognition of payments for achievement of non-substantive milestones and recognized revenue over the estimated period of performance applicable to each collaborative arrangement. As these milestones are achieved, the Company will recognize as revenue a portion of the milestone payment, which is equal to the percentage of the performance period completed when the milestone is achieved, multiplied by the amount of the milestone payment, upon achievement of such milestone. The Company will recognize the remaining portion of the milestone payment over the remaining performance period under the proportional performance method or on a straight-line basis.
For revenue generating arrangements where the Company, as a vendor, provides consideration to a licensor or collaborator, as a customer, the Company applies the accounting standard that governs such transactions. This standard addresses the accounting for revenue arrangements where both the vendor and the customer make cash payments to each other for services and/or products. A payment to a customer is presumed to be a reduction of the selling price unless the Company receives an identifiable benefit for the payment and it can reasonably estimate the fair value of the benefit received. Payments to a customer that are deemed a reduction of selling price are recorded first as a reduction of revenue, to the extent of both cumulative revenue recorded to date and probable future revenues, which include any unamortized deferred revenue balances, under all arrangements with such customer, and then as an expense. Payments that are not deemed to be a reduction of selling price are recorded as an expense.
The Company evaluates its collaborative agreements for proper classification in its consolidated statements of comprehensive loss based on the nature of the underlying activity. Transactions between collaborators recorded in the Company’s consolidated statements of comprehensive loss are recorded on either a gross or net basis, depending on the characteristics of the collaborative relationship. The Company generally reflects amounts due under its collaborative agreements related to cost-sharing of development activities as a reduction of research and development expense.
Amounts received prior to satisfying the above revenue recognition criteria are recorded as deferred revenue in the accompanying consolidated balance sheets. Although the Company follows detailed guidelines in measuring revenue, certain judgments affect the application of its revenue policy. For example, in connection with the Company’s existing collaboration agreements, the Company has recorded on its balance sheet short-term and long-term deferred revenue based on its best estimate of when such revenue will be recognized. Short-term deferred revenue consists of amounts that are expected to be recognized as revenue in the next 12 months. Amounts that the Company expects will not be recognized within the next 12 months are classified as long-term deferred revenue. However, this estimate is based on the Company’s current operating plan and, if its operating plan should change in the future, the Company may recognize a different amount of deferred revenue over the next 12-month period.
The estimate of deferred revenue also reflects management’s estimate of the periods of the Company’s involvement in certain of its collaborations. The Company’s performance obligations under these collaborations consist of participation on steering committees and the performance of other research and development services. In certain instances, the timing of satisfying these obligations can be difficult to estimate. Accordingly, the Company’s estimates may change in the future. Such changes to estimates would result in a change in revenue recognition amounts. If these estimates and judgments change over the course of these agreements, it may affect the timing and amount of revenue that the Company recognizes and records in future periods. At December 31, 2013, the Company had short-term and long-term deferred revenue of $32.7 million and $93.4 million, respectively, related to its collaborations.
Income Taxes
The Company uses the asset and liability method of accounting for income taxes. Under the asset and liability method, deferred tax assets and liabilities reflect the impact of temporary differences between amounts of assets and liabilities for financial reporting purposes and such amounts as measured under enacted tax laws. A valuation allowance is required to offset any net deferred tax assets if, based upon the available evidence, it is more likely than not that some or all of the deferred tax asset will not be realized.
The Company accounts for uncertain tax positions using a “more-likely-than-not” threshold for recognizing and resolving uncertain tax positions. The evaluation of uncertain tax positions is based on factors that include, but are not limited to, changes in tax law, the measurement of tax positions taken or expected to be taken in tax returns, the effective settlement of matters subject to audit, new audit activity and changes in facts or circumstances related to a tax position. The Company’s policy is to accrue interest and penalties related to unrecognized tax positions in income tax expense. As of December 31, 2013, the Company has not recorded significant interest and penalty expense related to uncertain tax positions.
Research and Development Costs
The Company expenses research and development costs as incurred. Included in research and development costs are wages, benefits and other operating costs, facilities, supplies, external services, clinical trial and manufacturing costs, and overhead directly related to the Company’s research and development operations, as well as costs to acquire technology licenses.
The Company has entered into several license agreements for rights to utilize certain technologies. The terms of the licenses may provide for upfront payments, annual maintenance payments, milestone payments based upon certain specified events being achieved and royalties on product sales. The Company charges costs to acquire and maintain licensed technology that has not reached technological feasibility and does not have alternative future use to research and development expense as incurred. During the years ended December 31, 2013, 2012 and 2011, the Company charged to research and development expense costs associated with license fees of $8.0 million, $5.7 million and $1.4 million, respectively.
Accounting for Stock-Based Compensation
The Company has stock incentive plans and an employee stock purchase plan under which it grants equity instruments. The Company accounts for all stock-based awards granted to employees at their fair value and generally recognizes compensation expense over the vesting period of the award. Determining the amount of stock-based compensation to be recorded requires the Company to develop estimates of fair values of stock options as of the grant date. The Company calculates the grant date fair values using the Black-Scholes valuation model. The Company’s expected stock price volatility assumption is based on a combination of the historical and implied volatility of the Company’s publicly traded stock.
For stock-based awards granted to non-employees, the Company generally recognizes compensation expense over the vesting period of the award, which is generally the period during which services are rendered by such non-employees. At the end of each financial reporting period prior to vesting, the Company re-measures the value of these stock-based awards (as calculated using the Black-Scholes option-pricing model) using the then-current fair value of the Company’s common stock. Stock options granted by the Company to non-employees, other than members of the Company’s Board of Directors and Scientific Advisory Board members, generally vest over the service period.
The fair value of restricted stock awards granted to employees is based upon the quoted closing market price per share on the date of grant, adjusted for assumed forfeitures. Expense is recognized over the vesting period, commencing when the Company determines that it is probable that the awards will vest.
For performance-based stock awards, expense is first recorded when the Company determines that the achievement of such performance conditions is deemed probable. This determination requires significant judgment by management. At the probable date, the Company records a cumulative expense catch-up, with remaining expense amortized over the remaining service period.
Comprehensive Loss
Comprehensive loss is comprised of net loss and certain changes in stockholders’ equity that are excluded from net loss. The Company includes foreign currency translation adjustments in other comprehensive loss for Alnylam Europe AG (“Alnylam Europe”) as the functional currency is not the United States dollar. The Company includes unrealized gains and losses on certain marketable securities in other comprehensive loss.
Net Loss Per Common Share
The Company computes basic net loss per common share by dividing net loss by the weighted average number of common shares outstanding. The Company computes diluted net loss per common share by dividing net loss by the weighted average number of common shares and dilutive potential common share equivalents then outstanding. Potential common shares consist of shares issuable upon the exercise of stock options (using the treasury stock method), and unvested restricted stock awards. Because the inclusion of potential common shares would be anti-dilutive for all periods presented, diluted net loss per common share is the same as basic net loss per common share.
The following table sets forth for the periods presented the potential common shares (prior to consideration of the treasury stock method) excluded from the calculation of net loss per common share because their inclusion would be anti-dilutive, in thousands:


		December 31,
		2013				2012				2011
Options to purchase common stock			8,713				8,932				9,779
Unvested restricted common stock			500				604				312

			9,213				9,536				10,091

Segment Information
The Company operates in a single reporting segment, the discovery, development and commercialization of RNAi therapeutics.
Subsequent Events
The Company evaluated all events or transactions that occurred after December 31, 2013 up through the date these consolidated financial statements were issued. During this period, the Company did not have any material recognized subsequent events. However, the Company did have the following nonrecognized subsequent events, which are more fully described in Note 12, “Subsequent Events”:

	•		In January 2014, the Company entered into a stock purchase agreement with Sirna Therapeutics, Inc. (“Sirna”), Merck Sharp & Dohme Corp. (“Merck”), and, for limited purposes, Merck & Co., Inc., pursuant to which the Company will purchase from Merck all of Merck’s right, title and interest in and to all of the outstanding shares of common stock, par value $0.01 per share, of Sirna (the “Sirna Common Stock”). See Note 12.

	•		In January 2014, the Company and Genzyme entered into a new global strategic collaboration agreement to develop and commercialize the Company’s current and future genetic medicine pipeline principally in territories outside of North America and Western Europe, subject to certain broader rights. See Note 12.
Recent Accounting Pronouncements
In February 2013, the Financial Accounting Standards Board (“FASB”) issued amendments to the accounting guidance for presentation of comprehensive income to improve the reporting of reclassifications out of accumulated other comprehensive income. The amendments did not change the current requirements for reporting net income or other comprehensive income, but require an entity to provide information about the amounts reclassified out of accumulated other comprehensive income by component. In addition, an entity is now required to present, either on the face of the statement where the net income is presented or in the notes, significant amounts reclassified out of accumulated other comprehensive income by the respective line items of net income but only if the amount reclassified is required under GAAP to be reclassified to net income in its entirety in the same reporting period. For other amounts that are not required under GAAP to be reclassified in their entirety to net income, an entity is required to cross-reference to other disclosures required under GAAP that provide additional detail about these amounts. For public companies, these amendments were effective prospectively for reporting periods beginning after December 15, 2012. The Company adopted this guidance on January 1, 2013. Other than a change in presentation, the adoption of this guidance did not have a material impact on the Company’s consolidated financial statements.

In July 2013, the FASB issued new accounting guidance specific to income taxes. The new guidance requires an entity to present an unrecognized tax benefit and a net operating loss carryforward, a similar tax loss, or a tax credit carryforward on a net basis as part of a deferred tax asset, unless the unrecognized tax benefit is not available to reduce the deferred tax asset component or would not be utilized for that purpose, then a liability would be recognized. The updated accounting guidance is effective for fiscal years beginning after December 15, 2013. The Company does not expect the adoption of this guidance to have a material impact on the Company’s consolidated financial statements.

Significant_Agreements

Significant Agreements

12 Months Ended

Dec. 31, 2013

Significant Agreements

SIGNIFICANT AGREEMENTS

The following table summarizes the Company’s total consolidated net revenues from collaborators, for the periods indicated, in thousands:

Year Ended December 31,

2013

2012

2011

Takeda

21,973

22,248

Cubist

9,721

2,777

2,467

Monsanto

5,640

1,954

—

MDCO

4,604

—

Roche/Arrowhead

—

37,318

55,978

Other

5,229

2,703

2,064

Total net revenues from collaborators

47,167

66,725

82,757

Product Alliances

Genzyme Alliance

In January 2014, the Company entered into a global, strategic collaboration with Genzyme to discover, develop and commercialize RNAi therapeutics as genetic medicines to treat orphan diseases (the “2014 Genzyme Collaboration”). The 2014 Genzyme Collaboration is governed by a Master Collaboration Agreement, dated January 11, 2014, by and between the Company and Genzyme (including the License Terms appended thereto, the “Master Agreement”), which will become effective upon closing of the equity transaction, described below under Note 12, “Subsequent Events.” Once effective, the Master Agreement will supersede and replace the previous collaboration between the Company and Genzyme entered into in October 2012 to develop and commercialize RNAi therapeutics targeting targeting transthyretin (“TTR”) for the treatment of transthyretin-mediated amyloidosis (“ATTR”) (the “2012 Genzyme Agreement”).

In consideration for the rights granted to Genzyme under the 2012 Genzyme Agreement, Genzyme paid the Company an upfront cash payment of $22.5 million. The Company was also entitled to receive certain milestone payments under the 2012 Genzyme Agreement. In the fourth quarter of 2013, the Company earned a milestone of $7.0 million based upon the completion of a successful patisiran Phase 2 clinical trial and a milestone of $4.0 million based upon the initiation of the Phase 3 clinical trial for patisiran.

Under the 2012 Genzyme Agreement, the parties agreed to collaborate in the development of licensed products, with Genzyme assuming primary responsibility for the development and commercialization of licensed products in the Genzyme territory and the Company retaining primary responsibility for the development and commercialization of licensed products in the rest of the world. The collaboration between Genzyme and the Company was governed by a joint steering committee comprised of an equal number of representatives from each party. Genzyme was responsible, at its expense, for all development activities under the development plan reasonably necessary for the regulatory approval and commercialization of an RNAi therapeutic for the treatment of ATTR in the Genzyme territory.

The Company determined that the deliverables under the 2012 Genzyme Agreement included the license, the joint steering committee and any additional TTR-specific RNAi therapeutic compounds that comprised the ALN-TTR program. The Company also determined that, pursuant to the accounting guidance governing revenue recognition on multiple element arrangements, the license and undelivered joint steering committee and any additional TTR-specific RNAi therapeutic compounds did not have standalone value due to the specialized nature of the services to be provided by the Company. In addition, while Genzyme had the ability to grant sublicenses, it could not sublicense all or substantially all of its rights under the 2012 Genzyme Agreement. The uniqueness of the Company’s services and the limited sublicense right were indicators that standalone value was not present in the arrangement. Therefore the deliverables were not separable and, accordingly, the license and undelivered services were treated as a single unit of accounting. Because the Company was unable to reasonably estimate our period of performance under the Genzyme agreement, as the Company was unable to estimate the timeline of deliverables related to the option granted to Genzyme for any additional compounds, the Company deferred all revenue under the 2012 Genzyme Agreement until the Company was able to reasonably estimate its period of performance. The Company was unable to reasonably estimate the period of performance under the 2012 Genzyme Agreement, as it was unable to estimate the timeline of its deliverables related to the deliverable for any additional TTR-specific RNAi therapeutic compounds. Through Decembe 31, 2013, the Company has deferred all revenue under the 2012 Genzyme Agreement. At December 31, 2013, deferred revenue under the 2012 Genzyme Agreement was $33.5 million. The Company expects that the $33.5 million received under the 2012 Genzyme Agreement, which is currently included in deferred revenue, will be accounted for in conjunction with the 2014 Genzyme Collaboration.

The Medicines Company Alliance

In February 2013, the Company and MDCO entered into a license and collaboration agreement (the “MDCO Agreement”) pursuant to which the Company granted to MDCO an exclusive, worldwide license to develop, manufacture and commercialize RNAi therapeutics targeting proprotein convertase subtilisin/kexin type 9 (“PCSK9”), including ALN-PCS02 and ALN-PCSsc, for the treatment of hypercholesterolemia and other human diseases (collectively, “ALN-PCS Licensed Products”). ALN-PCS02 is an intravenously administered RNAi therapeutic for which the Company completed a Phase 1 clinical trial, and ALN-PCSsc is a subcutaneously administered RNAi therapeutic currently in pre-clinical development. In consideration for the rights granted to MDCO under the MDCO Agreement, MDCO paid the Company an upfront cash payment of $25.0 million. Upon achievement of certain milestones, the Company will be entitled to receive milestone payments, up to an aggregate of $180.0 million, including up to $30.0 million in specified development milestones, $50.0 million in specified regulatory milestones and $100.0 million in specified commercialization milestones. In addition, the Company will be entitled to royalties ranging from the low- to high- teens based on annual worldwide net sales, if any, of ALN-PCS Licensed Products by MDCO, its affiliates and sublicensees, subject to reduction under specified circumstances. The Company could potentially earn the next development milestone payment of $10.0 million under the MDCO Agreement based upon the initiation of an ALN-PCSsc Phase 1 clinical trial. For purposes of potential future revenue recognition, the Company does not believe this milestone or any future milestones are substantive. Due to the uncertainty of pharmaceutical development and the high historical failure rates generally associated with drug development, the Company may not receive any milestone or royalty payments from MDCO.

Under the MDCO Agreement, the parties will collaborate in the further development of ALN-PCS Licensed Products. The Company will retain responsibility for the development of ALN-PCS Licensed Products until Phase 1 Completion (as defined in the MDCO Agreement) at its cost, up to an agreed upon initial development cost cap. MDCO will assume all other responsibility for the development and commercialization of ALN-PCS Licensed Products, at its sole cost. Initially the collaboration included the development of both ALN-PCS02 and ALN-PCSsc in parallel. In October 2013, the parties announced the selection of ALN-PCSsc for ongoing development, in accordance with the terms of the MDCO Agreement. The collaboration between MDCO and the Company will be governed by a joint steering committee that will be comprised of an equal number of representatives from each party. The Company will be solely responsible for obtaining supply of finished product reasonably required for the conduct of its obligations through Phase 1 Completion, and supplying MDCO with finished product reasonably required for the first Phase 2 clinical trial of an ALN-PCS Licensed Product conducted by MDCO, at the Company’s expense, provided such costs do not exceed the development costs cap, subject to certain exceptions. After such time, MDCO will have the sole right and responsibility to manufacture and supply ALN-PCS Licensed Product for development and commercialization under the MDCO development plan, subject to the terms of the MDCO Agreement. The Company also has obligations under the MDCO Agreement to transfer certain technology to MDCO.

Unless terminated earlier in accordance with the terms of the agreement, the MDCO Agreement expires on a licensed product-by-licensed product and country-by-country basis upon expiration of the last royalty term for any licensed product in any country, where a royalty term is defined as the latest to occur of (1) the expiration of the last valid claim of patent rights covering a licensed product, (2) the expiration of the Regulatory Exclusivity, as defined in the MDCO Agreement, and (3) the twelfth anniversary of the first commercial sale of the licensed product in such country. The Company estimates that its fundamental RNAi patents covering licensed products under the MDCO Agreement will expire both in and outside of the United States generally between 2015 and 2023. The Company also estimates that its ALN-PCS product-specific patents covering licensed products under the MDCO Agreement in the United States and elsewhere will expire at the end of 2033. These patent rights are subject to potential patent term extensions and/or supplemental protection certificates extending such terms in countries where such extensions may become available. In addition, more patent filings relating to the collaboration may be made in the future.

Either party may terminate the MDCO Agreement in the event the other party fails to cure a material breach or upon patent-related challenges by the other party. The Company may terminate the agreement in the event that a lead licensed product has not been designated by the joint steering committee within a designated time period. In addition, MDCO has the right to terminate the agreement without cause at any time upon four months’ prior written notice.

The Company has determined that the significant deliverables under the MDCO Agreement include the license, the joint steering committee, technology transfer obligations, development activities through Phase 1 Completion and supply of product for a Phase 2 clinical trial. The Company also determined that, pursuant to the accounting guidance governing revenue recognition on multiple element arrangements, the license and collective undelivered activities and services do not have standalone value due to the specialized nature of the activities and services to be provided by the Company. In addition, while MDCO has the ability to grant sublicenses, it must receive the Company’s prior written consent to sublicense all or substantially all of its rights. The uniqueness of the Company’s services and the limited sublicense right are indicators that standalone value is not present in the arrangement. Therefore the deliverables are not separable and, accordingly, the license and undelivered services are being treated as a single unit of accounting. When multiple deliverables are accounted for as a single unit of accounting, the Company bases its revenue recognition pattern on the final deliverable. Under the MDCO Agreement, all deliverables are expected to be completed within five years. The Company is recognizing revenue under the MDCO Agreement on a straight-line basis over five years. The Company is not utilizing a proportional performance model since it is unable to reasonably estimate the level of effort to fulfill these obligations, primarily because the effort required under the development activities is largely unknown.

The Company received the upfront payment of $25.0 million from MDCO in February 2013, which was initially recorded as deferred revenue. As future milestones are achieved, if any, the Company will recognize as revenue a portion of the milestone payment equal to the percentage of the performance period completed when the milestone is achieved, multiplied by the amount of the milestone payment. At December 31, 2013, deferred revenue under the MDCO Agreement was $20.5 million.

Cubist Alliance

In January 2009, the Company entered into a license and collaboration agreement with Cubist (the “Cubist Agreement”) to develop and commercialize therapeutic products based on certain of the Company’s RNAi technology for the treatment of RSV infection. Licensed products initially included ALN-RSV01, as well as several other second-generation RNAi-based RSV inhibitors. In consideration for the rights granted to Cubist under the Cubist Agreement, in January 2009, Cubist paid the Company an upfront cash payment of $20.0 million. Under the terms of the Cubist Agreement, the Company and Cubist shared responsibility for developing licensed products in North America and each was responsible for one-half of the related development costs, subject to certain exceptions. In February 2013, Cubist notified the Company that it would not exercise its opt-in right for ALN-RSV01. In light of this determination, the Company and Cubist mutually agreed to terminate the license and collaboration agreement. As of the termination date, the parties have no further rights and obligations under the Cubist Agreement, as amended, notwithstanding anything to the contrary in the Cubist Agreement, as amended.

Under the Cubist Agreement, the last element to be delivered was the development and manufacturing services, which had an expected life of approximately eight years. The Company was recognizing the upfront payment of $20.0 million on a straight-line basis over approximately eight years because the Company was unable to reasonably estimate the level of effort to fulfill its performance obligations, and therefore, could not utilize a proportional performance model. As a result of the termination of the Cubist Agreement in February 2013 and the end of the Company’s performance obligations thereunder, the Company recognized the remaining deferred revenue of $9.7 million during 2013.

Platform Alliances

Monsanto Alliance

In August 2012, the Company and Monsanto entered into a license and collaboration agreement (the “Monsanto Agreement”), pursuant to which the Company granted to Monsanto a worldwide, exclusive, royalty bearing right and license, including the right to grant sublicenses, to the Company’s RNAi platform technology and intellectual property controlled by the Company as of the date of the Monsanto Agreement or during the 30 months thereafter, in the field of agriculture. The Monsanto Agreement also includes the transfer of technology from the Company to Monsanto and a collaborative research project (the “Monsanto Discovery Collaboration”). Under the Monsanto Agreement, Monsanto will be the Company’s exclusive collaborator in the agriculture field for a ten-year period (the “Exclusivity Period”).

In consideration for the rights granted to Monsanto under the Monsanto Agreement, Monsanto paid the Company $29.2 million in upfront cash payments. Monsanto is also required to make near-term milestone payments to the Company upon the achievement of specified technology transfer and patent-related milestones. The Company is also entitled to receive additional funding for collaborative research efforts. In the aggregate, the Company can earn up to $5.0 million in potential future milestone payments and research funding under the Monsanto Agreement. In addition, Monsanto is required to pay to the Company a percentage of specified fees from certain sublicense agreements Monsanto may enter into that include access to the Company’s intellectual property, as well as low single-digit royalty payments on worldwide, net sales by Monsanto, its affiliates and sublicensees of certain Licensed Products (as defined in the Monsanto Agreement), if any. In December 2012, the Company received a milestone payment of $1.5 million of the $5.0 million in potential milestone payments under the Monsanto Agreement based upon the achievement of a specified patent-related event. In August 2013, the Company received an additional milestone payment of $2.5 million based upon the completion of technology transfer activities. The Company could potentially earn the next and final milestone payment of $1.0 million under the Monsanto Agreement in connection with the Monsanto Discovery Collaboration. For purposes of potential future revenue recognition, the Company does not believe this milestone or any future milestones are substantive. Due to the uncertainty of the application of RNAi technology in the field of agriculture, the Company may not receive any additional milestone payments or any royalty payments from Monsanto.

The term of the Monsanto Agreement generally ends upon the expiration of the last-to-expire patent licensed under the agreement. The Company estimates that its fundamental RNAi patents licensed under the Monsanto Agreement will expire both in and outside the United States generally between 2016 and 2025, subject to any potential patent term extensions and/or supplemental protection certificates extending such term extensions in countries where such extensions may become available. Monsanto may terminate the Monsanto Agreement in its entirety upon 30-days’ prior written notice to the Company, provided, however, that Monsanto is required to continue to make royalty payments to the Company if any royalties were payable on net sales of a Licensed Product during the previous 24 months. The Monsanto Agreement may also be terminated by either party in the event the other party fails to cure a material breach under the agreement.

The Company determined that the significant deliverables under the Monsanto Agreement include the license, the technology transfer activities and the services that the Company will be obligated to perform under the Monsanto Discovery Collaboration. The Company also determined that, pursuant to the accounting guidance governing revenue recognition on multiple element arrangements, the license and undelivered technical transfer activities and Monsanto Discovery Collaboration services do not have standalone value due to the specialized nature of the services to be provided by the Company. In addition, while Monsanto has the ability to grant sublicenses, it cannot grant access to certain of the Company’s proprietary technology. The uniqueness of the Company’s services and the limited sublicense right are indicators that standalone value is not present in the arrangement. Therefore the deliverables are not separable and, accordingly, the license and undelivered technical transfer activities and Monsanto Discovery Collaboration services are being treated as a single unit of accounting. When multiple deliverables are accounted for as a single unit of accounting, the Company bases its revenue recognition model on the final deliverable. Under the Monsanto Agreement, the last deliverable to be completed is the Monsanto Discovery Collaboration, which must be completed within five years. The Company is recognizing revenue under the Monsanto Agreement on a straight-line basis over five years. The Company is not utilizing a proportional performance model since it is unable to reasonably estimate the level of effort to fulfill these obligations, primarily because the effort required under the Monsanto Discovery Collaboration is largely unknown.

The Company received a payment of $29.2 million from Monsanto in August 2012, which was initially recorded as deferred revenue. Under the terms of the Monsanto Agreement, in the event that during the Exclusivity Period Monsanto loses certain patent rights, and such loss has a material adverse effect on the Licensed Products, then the Company would be required to pay Monsanto up to $5.0 million as liquidated damages, and Monsanto’s royalty obligations to the Company under the Monsanto Agreement would be reduced or, under certain circumstances, terminated. The Company has the right to cure any such loss of patent rights under the Monsanto Agreement. The Company has determined that this amount is not fixed and determinable and therefore, the Company has excluded this amount from its revenue model and is deferring the recognition of $5.0 million of revenue. The Company will continue to reassess when this amount can be considered fixed and determinable. If the achievement of a milestone is considered probable at the inception of the collaboration, the Company’s policy is to include the related payment in its revenue model. The Company concluded that the receipt of the technology transfer payment of $2.5 million was probable, and therefore included this amount in the Company’s revenue model. As future milestones are achieved, if any, the Company will recognize as revenue a portion of the milestone payment equal to the percentage of the performance period completed when the milestone is achieved, multiplied by the amount of the milestone payment. At December 31, 2013, deferred revenue under the Monsanto Agreement was $25.6 million.

Takeda Alliance

In May 2008, the Company entered into a license and collaboration agreement (the “Takeda Agreement”) with Takeda to pursue the development and commercialization of RNAi therapeutics. Under the Takeda Agreement, the Company granted to Takeda a non-exclusive, worldwide, royalty-bearing license to the Company’s intellectual property, including delivery-related intellectual property, controlled by the Company as of the date of the agreement or during the five years thereafter, to develop, manufacture, use and commercialize RNAi therapeutics, subject to the Company’s existing contractual obligations to third parties. The license initially is limited to the fields of oncology and metabolic disease and may be expanded at Takeda’s option to include other therapeutic areas, subject to specified conditions.

In consideration for the rights granted to Takeda under the Takeda Agreement, Takeda agreed to pay the Company $150.0 million in upfront and near-term technology transfer payments. In addition, the Company has the option, exercisable until the start of Phase 3 development, to opt-in under a 50-50 profit sharing agreement to the development and commercialization in the United States of up to four Takeda licensed products, and would be entitled to opt-in rights for two additional products for each additional field expansion, if any, elected by Takeda under the Takeda Agreement. In June 2008, Takeda paid the Company an upfront payment of $100.0 million and agreed to pay to the Company an additional $50.0 million upon achievement of specified technology transfer milestones. Of this $50.0 million, $20.0 million was paid to the Company in October 2008, $20.0 million was paid to the Company in March 2010, and $10.0 million was paid to the Company in March 2011 (collectively, the “Technology Transfer Milestones”). If Takeda elects to expand its license to additional therapeutic areas, Takeda will be required to pay the Company $50.0 million for each additional field selected, if any. In addition, for each RNAi therapeutic product developed by Takeda, its affiliates and sublicensees, the Company is entitled to receive specified development, regulatory and commercialization milestone payments, totaling up to $171.0 million per product, together with up to a double-digit percentage royalty payment based on worldwide annual net sales, if any. The potential future milestone payments per product include up to $26.0 million for the achievement of specified development milestones, up to $40.0 million for the achievement of specified regulatory milestones and up to $105.0 million for the achievement of specified commercialization milestones. The Company could potentially earn the next milestone payment of $2.0 million under the Takeda Agreement based upon the achievement of a specified pre-clinical event by Takeda for an RNAi therapeutic product. For purposes of potential future revenue recognition, the Company does not believe this milestone or any future milestones are substantive. Due to the uncertainty of pharmaceutical development and the high historical failure rates generally associated with drug development, the Company may not receive any additional milestone payments or any royalty payments from Takeda.

Pursuant to the Takeda Agreement, the Company and Takeda are also collaborating on the research of RNAi therapeutics directed to one or two disease targets agreed to by the parties (the “Research Collaboration”), subject to the Company’s existing contractual obligations with third parties. Takeda also has the option, subject to certain conditions, to collaborate with the Company on the research and development of RNAi drug delivery technology for targets agreed to by the parties. In addition, the Company has a right of first negotiation to participate with Takeda in the development and commercialization of licensed products in the United States. The collaboration is governed by a joint technology transfer committee (the “JTTC”), a joint research collaboration committee (the “JRCC”) and a joint delivery collaboration committee (the “JDCC”), each of which is comprised of an equal number of representatives from each party.

The term of the Takeda Agreement generally ends upon the later of (1) the expiration of the Company’s last-to-expire patent covering a licensed product and (2) the last-to-expire term of a profit sharing agreement in the event the Company elects to enter into such an agreement. The Takeda Agreement may be terminated by either party in the event the other party fails to cure a material breach under the agreement. In addition, Takeda may terminate the agreement on a licensed product-by-licensed product or country-by-country basis upon 180-days’ prior written notice to the Company, provided, however, that Takeda is required to continue to make royalty payments to the Company for the duration of the royalty term with respect to a licensed product.

The Company has determined that the deliverables under the Takeda Agreement include the license, the joint committees (the JTTC, JRCC and JDCC), the technology transfer activities and the services that the Company will be obligated to perform under the Research Collaboration. The Company also determined that, pursuant to the accounting guidance governing revenue recognition on multiple element arrangements, the license and undelivered services (i.e., the joint committees and the Research Collaboration) are not separable and, accordingly, the license and services are being treated as a single unit of accounting. When multiple deliverables are accounted for as a single unit of accounting, the Company bases its revenue recognition pattern on the final deliverable. Under the Takeda Agreement, the last elements to be delivered are the JDCC and JTTC services, each of which has a life of no more than seven years.

The Company is recognizing the upfront payment of $100.0 million and the Technology Transfer Milestones of $50.0 million, the receipt of which the Company believed was probable at the commencement of the collaboration, on a straight-line basis over seven years because the Company is unable to reasonably estimate the level of effort to fulfill these obligations, primarily because the effort required under the Research Collaboration is largely unknown, and therefore, cannot utilize a proportional performance model. As future milestones are achieved, if any, the Company will recognize as revenue a portion of the milestone payment equal to the percentage of the performance period completed when the milestone is achieved, multiplied by the amount of the milestone payment. At December 31, 2013, deferred revenue under the Takeda Agreement was $30.8 million.

Roche/Arrowhead Alliance

In July 2007, the Company and, for limited purposes, Alnylam Europe, entered into a license and collaboration agreement (the “LCA”) with Roche. Under the LCA, which became effective in August 2007, the Company granted Roche a non-exclusive license to the Company’s intellectual property, including delivery-related intellectual property existing as of the date of the LCA, to develop and commercialize therapeutic products that function through RNAi, subject to the Company’s existing contractual obligations to third parties. In November 2010, Roche announced the discontinuation of certain activities in research and early development, including its RNAi research efforts. In October 2011, Arrowhead announced its acquisition of RNA therapeutics assets from Roche, including the LCA. As a result of this acquisition, Arrowhead owns all of the rights and obligations of Roche under the LCA. The license is initially limited to four therapeutic areas, and may be expanded to include additional therapeutic areas upon payment to the Company by Arrowhead of an additional $50.0 million for each additional therapeutic area, if any.

In consideration for the rights the Company granted under the LCA, Roche paid the Company $273.5 million in upfront cash payments. In addition, in exchange for the Company’s contributions under the LCA, for each RNAi therapeutic product developed by Arrowhead, its affiliates or sublicensees under the LCA, the Company is entitled to receive milestone payments upon achievement of specified development, regulatory and commercialization events, totaling up to an aggregate of $100.0 million per therapeutic target, together with a single-digit percentage royalty payment based on worldwide annual net sales, if any. The potential future milestone payments for each therapeutic target include up to $17.5 million for the achievement of specified development milestones, up to $62.5 million for the achievement of specified regulatory milestones and up to $20.0 million for the achievement of specified commercialization milestones. The Company could potentially earn the next development milestone payment of $1.0 million under the LCA based upon the initiation of the first Phase 1 clinical trial by Arrowhead for an RNAi therapeutic product. For purposes of potential future revenue recognition, the Company does not believe this milestone or any future milestones are substantive. Due to the uncertainty of pharmaceutical development and the high historical failure rates generally associated with drug development, the Company may not receive any milestone or royalty payments from Arrowhead. Under the LCA, the Company and Roche also established a discovery collaboration in October 2009 (“Discovery Collaboration”), subject to the Company’s existing contractual obligations to third parties.

The term of the LCA generally ends upon the later of ten years from the first commercial sale of a licensed product and the expiration of the last-to-expire patent covering a licensed product. Arrowhead may terminate the LCA, on a licensed product-by-licensed product, licensed patent-by-licensed patent, and country-by-country basis, upon 180-days’ prior written notice, but is required to continue to make milestone and royalty payments to the Company if any royalties were payable on net sales of a terminated licensed product during the previous 12 months. The LCA may also be terminated by either party in the event the other party fails to cure a material breach under the LCA.

In July 2007, the Company executed a common stock purchase agreement (the “Common Stock Purchase Agreement”) with Roche Finance Ltd, an affiliate of Roche. In connection with the execution of the LCA and the Common Stock Purchase Agreement, the Company also executed a share purchase agreement (the “Alnylam Europe Purchase Agreement”) with Alnylam Europe and Roche Beteiligungs GmbH, an affiliate of Roche (“Roche Germany”). Under the terms of the Alnylam Europe Purchase Agreement, the Company sold substantially all of the non-intellectual property assets of Alnylam Europe to Roche Germany for an aggregate purchase price of $15.0 million.

In summary, the Company received upfront payments totaling $331.0 million under the Roche alliance, which included an upfront payment under the LCA of $273.5 million, $42.5 million under the Common Stock Purchase Agreement and $15.0 million under the Alnylam Europe Purchase Agreement. The Company initially recorded $278.2 million of these proceeds as deferred revenue in connection with this alliance.

The Company determined that the deliverables under these agreements included the license, the Alnylam Europe assets and employees, the steering committees (joint steering committee and future technology committee) and the services under the Discovery Collaboration. The Company also determined that, pursuant to the accounting guidance governing revenue recognition on multiple element arrangements, the license and assets of Alnylam Europe are not separable from the undelivered services (i.e., the steering committees and Discovery Collaboration) and, accordingly the license and the services were treated as a single unit of accounting. When multiple deliverables are accounted for as a single unit of accounting, the Company bases its revenue recognition pattern on the final deliverable. Under the Arrowhead alliance, the steering committee services and the Discovery Collaboration services are the final deliverables and all such services ended, contractually, in August 2012, five years from the effective date of the LCA.

The Company recognized the revenue related to these agreements on a straight-line basis over five years because the Company could not reasonably estimate the total level of effort required to complete its service obligations under the LCA, and therefore, could not utilize a proportional performance model. At December 31, 2013, there was no remaining deferred revenue under the LCA as the Company recognized all remaining Roche/Arrowhead revenue during the quarter ended September 30, 2012. The Company will recognize future milestones under the LCA, if any, when such milestones are achieved.

Discovery and Development Alliances

Isis Collaboration and License Agreement

In April 2009, the Company and Isis amended and restated their existing strategic collaboration and license agreement (as amended and restated, the “Amended and Restated Isis Agreement”), originally entered into in March 2004, to extend the broad cross-licensing arrangement regarding double-stranded RNAi that was established in 2004, pursuant to which Isis granted the Company licenses to its current and future patents and patent applications relating to chemistry and to RNA-targeting mechanisms for the research, development and commercialization of double-stranded RNA (“dsRNA”) products. The Company has the right to use Isis technologies in its development programs or in collaborations and Isis agreed not to grant licenses under these patents to any other organization for the discovery, development and commercialization of dsRNA products designed to work through an RNAi mechanism, except in the context of a collaboration in which Isis plays an active role. The Company granted Isis non-exclusive licenses to its current and future patents and patent applications relating to RNA-targeting mechanisms and to chemistry for research use. The Company also granted Isis the non-exclusive right to develop and commercialize dsRNA products developed using RNAi technology against a limited number of targets. In addition, the Company granted Isis non-exclusive rights to research, develop and commercialize single-stranded RNA products. In August 2012, the Company and Isis amended the Amended and Restated Isis Agreement to provide for the discovery, development and commercialization of dsRNA products by the Company or its sublicensees in the field of agriculture.

In 2004, under the terms of the original Isis agreement, the Company paid Isis an upfront license fee of $5.0 million. The Company also agreed to pay Isis milestone payments, totaling up to approximately $3.4 million, upon the occurrence of specified development and regulatory events, and low single-digit royalties on sales, if any, for each product that the Company or a collaborator develops using Isis intellectual property. In addition, the Company agreed to pay to Isis a percentage of specified fees from strategic collaborations the Company may enter into that include access to Isis’ intellectual property.

Isis agreed to pay the Company, per therapeutic target, a license fee of $0.5 million, milestone payments totaling approximately $3.4 million, payable upon the occurrence of specified development and regulatory events, and low single-digit royalties on sales, if any, for each product developed by Isis or a collaborator that utilizes the Company’s intellectual property. Isis has the right to elect up to ten non-exclusive target licenses under the agreement and has the right to purchase one additional non-exclusive target per year during the term of the collaboration.

The term of the Amended and Restated Isis Agreement generally ends upon the expiration of the last-to-expire patent licensed thereunder, whether such patent is a patent licensed by the Company to Isis, or vice versa. As the license will include additional patents, if any, filed to cover future inventions, if any, the date of expiration cannot be determined at this time.

During the years ended December 31, 2013, 2012 and 2011, as a result of certain payments received by the Company in connection with the MDCO, Monsanto and Genzyme alliances, the Company paid $0.7 million, $2.5 million and zero to Isis, respectively. These license fees were charged to research and development expense.

Property_and_Equipment_Net

Property and Equipment, Net	12 Months Ended
Property and Equipment, Net	Dec. 31, 2013
Property and Equipment, Net	'
	4	PROPERTY AND EQUIPMENT, NET
	Property and equipment consist of the following at December 31, 2013 and 2012, in thousands:


					December 31,
			Useful Life		2013			2012
	Laboratory equipment			5 years	$	22,729		$	21,201
	Computer equipment and software			3 years		4,261			4,203
	Furniture and fixtures			5 years		1,793			1,793
	Leasehold improvements			*		28,953			19,862
	Construction in progress			—		28			8,209

						57,764			55,268
	Less: accumulated depreciation					(41,316	)		(35,469	)

					$	16,448		$	19,799


	*	Shorter of asset life or lease term
	During the years ended December 31, 2013, 2012 and 2011, the Company recorded $6.1 million, $4.6 million and $5.0 million, respectively, of depreciation expense related to its property and equipment.

2012_Restructuring

2012 Restructuring

12 Months Ended

Dec. 31, 2013

2012 Restructuring

2012 RESTRUCTURING

In January 2012, the Company’s Board of Directors approved, and the Company implemented, a strategic corporate restructuring pursuant to which the Company reduced its overall workforce by approximately 33%, to approximately 115 employees. During the three months ended March 31, 2012, the Company substantially completed the implementation of the strategic corporate restructuring and recorded $3.9 million of restructuring-related costs in operating expenses, including employee severance, benefits and related costs. The Company paid substantially all of these restructuring costs during 2012. The Company did not incur any additional significant costs associated with this restructuring and does not expect to incur any additional significant costs in the future.

The following table summarizes the components of the Company’s restructuring expenses recorded in operating expenses and in current liabilities, in thousands:

Original

(Reversals) or

Amounts Paid

Amounts

Charges

Adjustments to

Through

Accrued at

and Amounts

Charges

December 31,

Accrued

2013

Employee severance, benefits and related costs

3,909

(179

)

3,730

—

Commitments_and_Contingencies

Commitments and Contingencies	12 Months Ended
Commitments and Contingencies	Dec. 31, 2013
Commitments and Contingencies	'
	6	COMMITMENTS AND CONTINGENCIES
	Purchase Commitments
	The Company has future purchase commitments totaling $62.7 million at December 31, 2013, of which $33.6 million is expected to be incurred in 2014 and $29.1 million is expected to be incurred past 2014. These commitments are related to purchase orders, clinical and pre-clinical agreements, and other purchase commitments for goods or services that the Company is likely to continue, regardless of the fact that they were cancelable at December 31, 2013.
	Technology License Commitments
	The Company has licensed from third parties the rights to use certain technologies in its research processes as well as in any products the Company may develop including these licensed technologies. In accordance with the related license agreements, the Company is required to make certain fixed payments to the licensor or a designee of the licensor over various agreement terms. Many of these agreement terms are consistent with the remaining lives of the underlying intellectual property that the Company has licensed. At December 31, 2013, the Company was committed to make the following fixed, estimated and cancelable payments under existing license agreements, in thousands:


	Year Ending December 31,
	2014		$	7,533
	2015			694
	2016			649
	2017			669
	2018			729
	Thereafter			7,196

	Total		$	17,470

	Operating Leases
	The Company leases office and laboratory space located at 300 Third Street, Cambridge, Massachusetts (the “Premises”) for its corporate headquarters and primary research facility under a non-cancelable operating lease agreement (the “Third Street Lease”) with ARE-MA Region No. 28 LLC (the “Landlord”). Under the Third Street Lease, the Company leases a total of approximately 129,000 square feet of office and laboratory space at the Premises. The term of the Third Street Lease expires in September 2016. The Company has the option to extend the Third Street Lease for two successive five-year extensions.
	The Company separately agreed, with the Landlord’s consent, to sublease a portion of the Premises consisting of 34,014 square feet (the “Subleased Premises) beginning on September 1, 2010 pursuant to a sublease agreement between the Company and sanofi-aventis U.S. Inc. (“sanofi”) dated August 3, 2010 (the “Sublease”). In November 2011, the Company and sanofi entered into a first amendment to the Sublease, pursuant to which the Company agreed, with the Landlord’s consent, to extend the Sublease of the Subleased Premises through September 30, 2016 (the Sublease, as so amended by the first amendment, the “Amended Sublease”). Pursuant to the terms of the Amended Sublease, sanofi had an option to terminate the Amended Sublease as of December 31, 2013, with advance notice and payment of a termination fee to the Company. In connection with the execution of the Amended Sublease, the Company and the Landlord entered into an amendment to the Third Street Lease (the Third Street Lease, as so amended, the “Amended Third Street Lease”) to, among other things, change the allocation as between the Company and the Landlord of Excess Income (as defined in the Amended Third Street Lease) received by the Company in connection with any assignment or subletting of any or all of the Premises (including the Subleased Premises). In March 2013, sanofi notified the Company that it was exercising its right to terminate Amended Sublease as of December 31, 2013. As a result of this early termination, sanofi paid the Company a termination fee. The Company does not believe that the termination of the sanofi sublease was material to its business. In December 2013, the Company agreed, with the Landlord’s consent, to sublease a portion of the Premises consisting of approximately 18,000 square feet through September 30, 2016 pursuant to a sublease agreement between the Company and a third party.
	On February 10, 2012, the Company entered into a non-cancelable real property lease agreement (“the BMR Lease”) with BMR-Fresh Pond Research Park LLC (“BMR”) for the Company’s manufacturing facility. Under the BMR Lease, the Company leases approximately 15,000 square feet of office and laboratory space located at 665 Concord Avenue, Cambridge, Massachusetts. The term of the BMR Lease expires August 31, 2017. The Company has the option to extend the BMR Lease for two successive five-year extensions.
	From 2004 through 2008, the Company received $7.3 million in leasehold improvement incentives from the Landlord in connection with the Third Street Lease. In addition, the Company received $0.2 million and $1.8 million in leasehold improvement incentives from BMR during the years ended December 31, 2013 and 2012, respectively. These leasehold improvement incentives are being accounted for as a reduction in rent expense ratably over the Amended Third Street Lease and BMR Lease terms. The balance from these leasehold improvement incentives is included in current portion of deferred rent and deferred rent, net of current portion in the consolidated balance sheets at December 31, 2013 and 2012.
	Total rent expense, including operating expenses, under the Company’s real property leases was $4.9 million, $6.4 million and $6.5 million for the years ended December 31, 2013, 2012 and 2011, respectively.
	Future minimum payments under the Company’s non-cancelable leases are approximately as follows, in thousands:


	Year Ending December 31,
	2014		$	6,303
	2015			6,550
	2016			5,192
	2017			364
	2018			—

	Total		$	18,409

	Litigation
	University of Utah Litigation
	On March 22, 2011, The University of Utah (“Utah”) filed a civil complaint in the United States District Court for the District of Massachusetts against the Company, Max Planck Gesellschaft Zur Foerderung Der Wissenschaften e.V. and Max Planck Innovation GmbH (together, “Max Planck”), the Whitehead Institute for Biomedical Research (“Whitehead”), the Massachusetts Institute of Technology (“MIT”) and the University of Massachusetts (“UMass”), claiming a professor at Utah is the sole inventor or, in the alternative, a joint inventor, of the Tuschl patents. Utah did not serve the original complaint on the Company or the other defendants. On July 6, 2011, Utah filed an amended complaint alleging substantially the same claims against the Company, Max Planck, Whitehead, MIT and UMass. The amended complaint was served on the Company on July 14, 2011. Utah is seeking changes to the inventorship of the Tuschl patents, unspecified damages and other relief. On October 31, 2011, the Company, Max Planck, Whitehead, MIT and UMass filed a motion to dismiss. Also on October 31, 2011, UMass filed a motion to dismiss on separate grounds, which the Company, Max Planck, Whitehead and MIT have joined. On December 31, 2011, Utah filed a second amended complaint dropping UMass as a defendant and adding as defendants several UMass officials. In June 2012, the Court denied both motions to dismiss. The Company, Max Planck, Whitehead, MIT and UMass filed an appeal of the Court’s ruling on the motion to dismiss for lack of jurisdiction and a motion requesting that the Court stay the case pending the outcome of the appeal. In July 2012, the Court stayed discovery in the case pending the outcome of the defendants’ appeal. Oral arguments in the appeal were heard in early March 2013 in the United States Court of Appeals for the Federal Circuit (the “CAFC”). In August 2013, the CAFC affirmed the lower Court’s ruling, in a split decision. The Company believes the majority made an error in law when affirming the lower Court’s decision, and in September 2013, the Company filed a petition with the CAFC for rehearing or rehearing en banc. In October 2013, the CAFC invited Utah to file an answer to the petition. In November 2013, the CAFC denied the Company’s petition for rehearing or rehearing en banc and remanded the case back to the lower Court. In February 2014, the Company filed a petition for writ of certiorari from the Supreme Court and a motion to stay the lower Court proceedings pending a decision from the Supreme Court on the Company’s petition. The Company is awaiting the Courts’ decisions.
	Although the Company believes it has meritorious defenses and intends to vigorously defend itself in this matter, litigation is subject to inherent uncertainty and a court could ultimately rule against the Company. In addition, the defense of litigation and related matters are costly and may divert the attention of the Company’s management and other resources that would otherwise be engaged in other activities. The Company has not recorded an estimate of the possible loss associated with this legal proceeding due to the uncertainties related to both the likelihood and the amount of any possible loss or range of loss.
	The Company’s accounting policy for accrual of legal costs is to recognize such expenses as incurred.
	Tekmira Settlement Agreement
	On November 12, 2012, the Company, TPC, Protiva Biotherapeutics, Inc., a wholly owned subsidiary of TPC (“Protiva,” and together with TPC, “Tekmira”) and Acuitas Therapeutics Inc. (formerly AlCana Technologies, Inc.) (“Acuitas”) entered into a settlement agreement and general release resolving all ongoing litigation, as well as a patent interference proceeding between the Company and Protiva. The terms of the settlement agreement include mutual releases and dismissal with prejudice of all claims and counterclaims in the following litigation between the parties: (i) Tekmira Pharmaceuticals Corp., et al. v. Alnylam Pharmaceuticals, Inc., et al., Civ. A. No. 11-1010-BLS2, pending in the Business Litigation Section of the Massachusetts Superior Court for Suffolk County; (ii) Tekmira Pharmaceuticals Corp. v. Michael Hope, et al., No. S117660, pending in the Supreme Court of British Columbia, Canada; (iii) Alnylam Pharmaceuticals, Inc., et al. v. Tekmira Pharmaceuticals Corp., Civ. A. No. 1:12-CV-10087, pending in the United States District Court for the District of Massachusetts; and (iv) Alnylam Pharmaceuticals, Inc., et al. v. Tekmira Pharmaceuticals Corp., Court File No. T-1783-12, pending in the Federal Court of Canada. In addition, as part of the settlement agreement, the parties agreed to a covenant not to sue one another in the future on matters released under the settlement agreement, as well as substantial liquidated damages to be paid by any party that breaches such covenant. The parties have also agreed to resolve any future disputes that may arise over the next three years through binding arbitration.
	Pursuant to the settlement agreement, the Company and Tekmira also agreed to resolve the interference proceeding declared by the United States Board of Patent Appeals and Interferences between the Company and Protiva, captioned Protiva Biotherapeutics, Inc. v. Alnylam Pharmaceuticals, Inc., Patent Interference No. 105792.
	Contemporaneously with the execution of the settlement agreement, the Company and Tekmira restructured their contractual relationship and entered into a cross-license agreement that supersedes the prior license and manufacturing agreements among the Company, TPC and Protiva. In connection with this restructuring, the Company incurred a $65.0 million charge to operating expenses for the year ended December 31, 2012. Specifically, the Company made a one-time payment of $30.0 million to Tekmira for the termination of, and its release from, all of its obligations under the manufacturing agreement with TPC, including without limitation the obligations to obtain materials and/or services from TPC. Further, the Company elected to buy-down certain future potential milestone and royalty payments due to Tekmira for certain of the Company’s RNAi therapeutics, formulated using LNP technology. Specifically, pursuant to the cross-license agreement, the Company made a one-time payment of $35.0 million to Tekmira, which amount constituted payment for the termination of the 2008 license agreements with TPC and Protiva and the parties’ rights and obligations thereunder, as well as the buy-down of certain milestone payments and the significant reduction of royalty rates for ALN-VSP, ALN-PCS02 and ALN-TTR02 (“patisiran”). In addition, under the 2012 cross-license agreement, the Company was obligated to pay TPC an aggregate of $10.0 million in contingent milestone payments related to advancement of ALN-VSP and patisiran, which now represent the only potential milestones due to Tekmira for ALN-VSP, ALN-PCS02 and patisiran lipid nanoparticle (“LNP”)-based RNAi therapeutics. In the fourth quarter of 2013, the Company paid TPC $5.0 million in connection with the initiation of the patisiran Phase 3 clinical trial. With respect to the second $5.0 million milestone, in August 2013, the Company initiated binding arbitration proceedings to resolve a disagreement with TPC regarding the achievement by TPC of this milestone under the parties cross-license agreement relating to the manufacture of ALN-VSP clinical trial material for use in China. The Company’s policy is to expense these potential milestones when incurred and record them as research and development expense. A description of the Company’s cross-license agreement with Tekmira is included in Part I, Item 1, “ —Delivery-Related Licenses and Collaborations—Tekmira,” of this annual report on Form 10-K.
	Indemnifications
	Licensor indemnification — In connection with the Company’s license agreements with Max Planck relating to the Tuschl I and Tuschl II patent applications, the Company is required to indemnify Max Planck for certain damages arising in connection with the intellectual property rights licensed under the agreements. Under the Max Planck indemnification agreement, the Company is responsible for paying the costs of any litigation relating to the license agreements or the underlying intellectual property rights, including the costs associated with certain litigation regarding the Tuschl patents, which was settled during 2011. In connection with the Company’s research agreement with Acuitas, the Company agreed to indemnify Acuitas for certain legal costs, subject to certain exceptions and limitations, associated with the Tekmira litigation described above. These indemnification costs were charged to general and administrative expense. The Company is also a party to a number of agreements entered into in the ordinary course of business, which contain typical provisions that obligate the Company to indemnify the other parties to such agreements upon the occurrence of certain events. Such indemnification obligations are usually in effect from the date of execution of the applicable agreement for a period equal to the applicable statute of limitations.
	The maximum potential future liability of the Company under any such indemnification provisions is uncertain. However, to date, other than certain costs associated with certain previously settled litigation related to the Tuschl patents and the Tekmira litigation described above, the Company has not incurred material costs to defend lawsuits or settle claims related to these indemnification provisions. The Company has determined that the estimated aggregate fair value of its potential liabilities under all such indemnification provisions is minimal and has not recorded any liability related to such indemnification provisions at December 31, 2013 or 2012.

Stockholders_Equity

Stockholders' Equity	12 Months Ended
	Dec. 31, 2013
Stockholders' Equity	'
	7	STOCKHOLDERS’ EQUITY
	Preferred Stock
	The Company has authorized up to 5,000,000 shares of preferred stock, $0.01 par value per share, for issuance. The preferred stock will have such rights, preferences, privileges and restrictions, including voting rights, dividend rights, conversion rights, redemption privileges and liquidation preferences, as shall be determined by the Company’s Board of Directors upon its issuance. At December 31, 2013 and 2012, there were no shares of preferred stock outstanding.
	Stockholder Rights Agreement
	On July 13, 2005, the Board of Directors of the Company declared a dividend of one right (collectively, the “Rights”) to buy one one-thousandth of a share of newly designated Series A Junior Participating Preferred Stock (“Series A Junior Preferred Stock”) for each outstanding share of the Company’s common stock to stockholders of record at the close of business on July 26, 2005. Initially, the Rights are not exercisable and will be attached to all certificates representing outstanding shares of common stock. The Rights will expire at the close of business on July 13, 2015 unless earlier redeemed or exchanged. Until a Right is exercised, the holder thereof will have no rights as a stockholder of the Company, including the right to vote or to receive dividends. Subject to the terms and conditions of the rights agreement (the “Rights Agreement”), the Rights will become exercisable upon the earlier of (1) ten business days following the later of (a) the first date of a public announcement that a person or group (an “Acquiring Person”) acquires, or obtained the right to acquire, beneficial ownership of 20% or more of the outstanding shares of common stock of the Company or (b) the first date on which an executive officer of the Company has actual knowledge that an Acquiring Person has become such or (2) ten business days following the commencement of a tender offer or exchange offer that would result in a person or group beneficially owning more than 20% of the outstanding shares of common stock of the Company. Each Right entitles the holder to purchase one one-thousandth of a share of Series A Junior Preferred Stock at an initial purchase price of $80.00 in cash, subject to adjustment. In the event that any person or group becomes an Acquiring Person, unless the event causing the 20% threshold to be crossed is a Permitted Offer (as defined in the Rights Agreement), each Right not owned by the Acquiring Person will entitle its holder to receive, upon exercise, that number of shares of common stock of the Company (or in certain circumstances, cash, property or other securities of the Company) which equals the exercise price of the Right divided by 50% of the current market price (as defined in the Rights Agreement) per share of such common stock at the date of the occurrence of the event. In the event that, at any time after any person or group becomes an Acquiring Person, (i) the Company is consolidated with, or merged with and into, another entity and the Company is not the surviving entity of such consolidation or merger (other than a consolidation or merger which follows a Permitted Offer) or if the Company is the surviving entity, but shares of its outstanding common stock are changed or exchanged for stock or securities (of any other person) or cash or any other property, or (ii) more than 50% of the Company’s assets or earning power is sold or transferred, each holder of a Right (except Rights which previously have been voided as set forth in the Rights Agreement) shall thereafter have the right to receive, upon exercise, that number of shares of common stock of the acquiring company which equals the exercise price of the Right divided by 50% of the current market price of such common stock at the date of the occurrence of the event.
	Public Offerings
	In February 2012, the Company sold an aggregate of 8,625,000 shares of its common stock through an underwritten public offering at a price to the public of $10.75 per share. As a result of this offering, the Company received aggregate net proceeds of approximately $86.8 million, after deducting underwriting discounts and commissions and other estimated offering expenses of approximately $5.9 million.
	In January 2013, the Company sold an aggregate of 9,200,000 shares of its common stock through an underwritten public offering at a price to the public of $20.13 per share. As a result of this offering, the Company received aggregate net proceeds of approximately $173.6 million, after deducting underwriting discounts and commissions and other estimated offering expenses of approximately $11.6 million.

Stock_Incentive_Plans

Stock Incentive Plans	12 Months Ended
Stock Incentive Plans	Dec. 31, 2013
Stock Incentive Plans	'
	8	STOCK INCENTIVE PLANS
	Stock Plans
	In June 2009, the Company’s stockholders approved an amendment and restatement of the Company’s 2004 Stock Incentive Plan (the “Amended and Restated 2004 Plan”), which replaced the Company’s 2004 Stock Incentive Plan, as amended (the “2004 Plan”). At December 31, 2013, the Amended and Restated 2004 Plan provided for the granting of stock options to purchase up to 12,366,485 shares of common stock. Prior to the adoption of the Amended and Restated 2004 Plan, the Company was authorized to grant both stock options and restricted stock awards under the 2004 Plan. As of the effective date of the Amended and Restated 2004 Plan, the Company may only grant stock options under the Amended and Restated 2004 Plan, provided that the terms and conditions of any restricted stock awards outstanding under the 2004 Plan will continue to be governed by the Amended and Restated 2004 Plan.
	In June 2009, the Company’s stockholders also approved the Company’s 2009 Stock Incentive Plan (the “2009 Plan”). The 2009 Plan provides for the granting of stock options, restricted stock awards and units, stock appreciation rights and other stock-based awards. In June 2013, the Company’s stockholders approved an amendment to the 2009 Plan, which increased the number of shares of common stock authorized for issuance from 2,200,000 to 5,900,000. The 2009 Plan has a fungible share pool. Any award that is not a full value award is counted against the authorized share limits specified in the 2009 Plan as one share for each share of common stock subject to the award, and all full value awards, defined in the 2009 Plan as restricted stock awards or other stock-based awards, are counted as one and a half shares for each one share of common stock subject to such full value award. In addition, the 2009 Plan includes a non-employee director stock option program under which each eligible non-employee director is entitled to (1) a grant of an option to purchase 30,000 shares of common stock upon his or her initial appointment to the Board of Directors, or such other amount as the Board of Directors deems appropriate, and (2) a subsequent annual grant of an option to purchase 15,000 shares of common stock based on continued service, made on the date of each annual meeting of stockholders, provided the non-employee director has served as a director for at least six months and is serving as a director immediately prior to and following such annual meeting. The chairman of the audit committee will receive an additional annual grant of an option to purchase 10,000 shares of common stock based on continued service and the chairman of the science and technology committee will receive an additional annual grant of an option to purchase 15,000 shares of common stock based on continued service. Stock options granted by the Company to non-employee directors upon their appointment to the Board of Directors vest as to one-third of such shares on each of the first, second and third anniversaries of the date of grant, and those granted at each year’s annual meeting at which they serve as a director vest in full on the first anniversary of the date of grant.
	At December 31, 2013, an aggregate of 11,369,175 shares of common stock were reserved for issuance under the Company’s stock plans, including outstanding stock options to purchase 8,713,395 shares of common stock, 2,426,811 shares of common stock available for additional equity awards and 228,969 shares available for future grant under the Company’s 2004 Employee Stock Purchase Plan (the “2004 Purchase Plan”). Each option shall expire within ten years of issuance. Stock options granted by the Company to employees generally vest as to 25% of the shares on the first anniversary of the grant date and 6.25% of the shares at the end of each successive three-month period until fully vested.
	Stock-Based Compensation
	The Company recorded $14.1 million, $9.0 million and $14.8 million of stock-based compensation expense for the years ended December 31, 2013, 2012 and 2011, respectively, related to employee stock options and the 2004 Purchase Plan.
	The Company accounts for non-employee grants as an expense over the vesting period of the underlying stock options. At the end of each financial reporting period prior to vesting, the Company re-measures the value of these stock options (as calculated using the Black-Scholes option-pricing model) using the then-current fair value of the Company’s common stock. The Company recognized $3.2 million, $1.0 million and $0.4 million of non-employee stock-based compensation expense for the years ended December 31, 2013, 2012 and 2011, respectively.
	In October 2010, the Company granted 113,370 shares of restricted stock of the Company to certain employees. These restricted stock awards were valued at $1.4 million on the grant date. These restricted stock awards vested ratably over an approximate three-year period. In May 2011, the Company granted an aggregate of 229,806 shares of performance-based restricted stock awards to its employees, excluding the Company’s leadership team. These restricted stock awards were valued at $2.3 million on the grant date and had a contractual term of five years. The vesting of these awards was predicated on the Company’s achievement of certain clinical development goals. These awards have vested in full due to the achievement of these goals in 2011 and 2013. In January 2012, as part of its post-restructuring retention program, the Company granted an aggregate of 508,928 shares of restricted stock to its retained employees, excluding the Company’s chief executive officer and president and chief operating officer. These restricted stock awards were valued at $5.3 million on the grant date and vest in full on the second anniversary of the grant date. The Company recognized an aggregate of $3.4 million, $2.4 million and $1.5 million of stock-based compensation expense related to all of these restricted stock awards for the years ended December 31, 2013, 2012 and 2011, respectively.

	Valuation Assumptions for Stock Options
	The fair value of stock options at date of grant, based on the following assumptions, was estimated using the Black-Scholes option-pricing model. The Company’s expected stock-price volatility assumption is based on the historical volatility of the Company’s publicly traded stock. The expected life assumption is based on the Company’s historical data. The dividend yield assumption is based on the fact that the Company has never paid cash dividends and has no present intention to pay cash dividends. The risk-free interest rate used for each grant is equal to the zero coupon rate for instruments with a similar expected life. The Company has applied an annual forfeiture rate of 8.2% to all unvested employee stock options and restricted stock at December 31, 2013 based on an analysis of its historical forfeitures. The Company will record additional expense if the actual forfeitures are lower than estimated and will record a recovery of prior expense if the actual forfeitures are higher than estimated.


			2013			2012			2011
	Risk-free interest rate			1.0-2.0	%		0.8-1.0	%		1.2-2.6	%
	Expected dividend yield			—			—			—
	Expected option life			5.6 years			5.6-5.9 years			5.8-5.9 years
	Expected volatility			55-56	%		57	%		55-57	%
	At December 31, 2013, there was $31.8 million of unearned compensation expense remaining related to unvested employee stock options to be recognized as expense over a weighted-average period of approximately three years.
	Stock Option Activity
	The following table summarizes the activity of the Company’s stock option plans:


			Number of			Weighted			Weighted			Aggregate
			Options			Average			Average			Intrinsic
						Exercise			Remaining			Value
						Price			Contractual			(in thousands)
									Term (in years)
	Outstanding, December 31, 2012			8,931,583		$	15.71
	Granted			1,849,104		$	54.23
	Exercised			(2,031,916	)	$	13.96
	Cancelled			(35,376	)	$	21.56

	Outstanding, December 31, 2013			8,713,395		$	24.26			6.5		$	348,864

	Exercisable at December 31, 2013			5,324,421		$	18.21			5		$	245,378
	Vested or expected to vest at December 31, 2013			7,650,775		$	20.06			6.1		$	338,514
	The weighted average fair value of stock options granted was $26.33, $8.68 and $7.68 per share for the years ended December 31, 2013, 2012 and 2011, respectively. The intrinsic value of stock options exercised was $57.9 million, $4.8 million and $40,000 for the years ended December 31, 2013, 2012 and 2011, respectively.

	Restricted Stock Awards
	The following table summarizes the activity of the Company’s restricted stock awards:


			Number of			Weighted
			Awards			Average
						Grant Date
						Fair Value
	Unvested at December 31, 2012			603,760		$	9.37
	Granted			1,966		$	61.03
	Vested			(105,093	)	$	10.58
	Forfeited			(1,121	)	$	10.23

	Unvested at December 31, 2013			499,512		$	10.69

	The total grant date fair value of restricted stock awards that vested during the years ended December 31, 2013, 2012 and 2011 was $1.1 million, $1.5 million and $0.5 million, respectively. At December 31, 2013, there remained $0.3 million of unearned compensation expense related to unvested restricted stock awards to be recognized as expense over a weighted-average period of approximately one month.
	Employee Stock Purchase Plan
	In 2004, the Company adopted the 2004 Purchase Plan with 315,789 shares authorized for issuance. In June 2010, the Company’s stockholders approved an amendment to the 2004 Purchase Plan, which increased the shares authorized for issuance from 315,789 shares to 715,789 shares. Under the 2004 Purchase Plan, each offering period is six months, at the end of which employees may purchase shares of common stock through payroll deductions made over the term of the offering. The per-share purchase price at the end of each offering period is equal to the lesser of 85% of the closing price of the common stock at the beginning or end of the offering period. The Company issued 45,141, 73,590 and 79,038 shares during the years ended December 31, 2013, 2012 and 2011, respectively, and at December 31, 2013, 228,969 shares were available for issuance under the 2004 Purchase Plan.
	The weighted average fair value of stock purchase rights granted as part of the 2004 Purchase Plan was $11.49, $2.82 and $3.46 per share for the years ended December 31, 2013, 2012 and 2011, respectively. The fair value was estimated using the Black-Scholes option-pricing model. The Company used a weighted-average stock-price volatility of 55%, expected option life assumption of six months and a risk-free interest rate of 0.1%. The Company recorded $0.3 million, $0.2 million and $0.3 million of stock-based compensation expense for the years ended December 31, 2013, 2012 and 2011, respectively, related to the 2004 Purchase Plan.

Income_Taxes

Income Taxes	12 Months Ended
Income Taxes	Dec. 31, 2013
Income Taxes	'
	9	INCOME TAXES
	The domestic and foreign components of loss before income taxes are as follows, in thousands:


			2013			2012			2011
	Domestic		$	(81,109	)	$	(116,400	)	$	(57,481	)
	Foreign			(10,811	)		(186	)		(168	)

	Loss before income taxes		$	(91,920	)	$	(116,586	)	$	(57,649	)


	Deferred income taxes reflect the tax effects of temporary differences between the carrying amounts of assets and liabilities for financial reporting and income tax purposes. The Company establishes a valuation allowance when uncertainty exists as to whether all or a portion of the net deferred tax assets will be realized. Components of the net deferred tax (liability) asset at December 31, 2013 and 2012 are as follows, in thousands:


			2013			2012
	Deferred tax assets:
	Net operating loss carryforwards		$	124,797		$	102,819
	Research and development credits			23,902			17,443
	AMT credits			788			788
	Foreign tax credits			3,196			3,196
	Capitalized research and development and start-up costs			16,214			16,102
	Deferred revenue			37,273			30,776
	Deferred compensation			21,706			24,804
	Intangible assets			2,210			2,540
	Partnership interest			689			7,118
	Other			4,885			4,173

	Total deferred tax assets			235,660			209,759
	Deferred tax liabilities:
	Intangible assets			(7	)		(38	)
	Unrealized gain on available-for-sale securities			(13,267	)		(10,572	)
	Gain on issuance of stock by Regulus			—			(6,466	)
	Deferred tax asset valuation allowance			(222,393	)		(192,721	)

	Net deferred tax liability		$	(7	)	$	(38	)

	The benefit from income taxes for the years ended December 31, 2013, 2012 and 2011 are as follows, in thousands:


			2013			2012			2011
	U.S.:
	Current		$	34		$	52		$	52
	Deferred			(2,695	)		(10,572	)		—

	Total U.S.			(2,661	)		(10,520	)		52

	Foreign:
	Current			—			—			—
	Deferred			(34	)		(52	)		(52	)

	Total Foreign			(34	)		(52	)		(52	)

	Benefit from income taxes		$	(2,695	)	$	(10,572	)	$	—


	The Company’s effective income tax rate differs from the statutory federal income tax rate as follows for the years ended December 31, 2013, 2012 and 2011:


			2013			2012			2011
	At U.S. federal statutory rate			35	%		35	%		35	%
	State taxes, net of federal effect			4.3			4.9			4.6
	Stock compensation			0.8			(0.7	)		(3.3	)
	Tax credits			8.5			4.2			3.7
Orphan drug credit addback			(2.7	)		—			—
Other permanent items			(0.3	)		(1.6	)		(0.2	)
Foreign rate differential			(4.1	)		(0.1	)		(0.1	)
Valuation allowance			(38.5	)		(32.6	)		(39.7	)

Effective income tax rate			3	%		9.1	%		—	%

The Company has evaluated the positive and negative evidence bearing upon the realizability of its deferred tax assets. The Company has concluded, in accordance with the applicable accounting standards, that it is more likely than not that the Company may not realize the benefit of all of its deferred tax assets. Accordingly, the Company has recorded a valuation allowance against the deferred tax assets that management believes will not be realized. The Company reevaluates the positive and negative evidence on a quarterly basis. The valuation allowance increased by $29.7 million, $38.3 million and $23.0 million for the years ended December 31, 2013, 2012 and 2011 respectively, due primarily to additional operating losses and deferred revenue. Increases to the valuation allowance were partially offset by decreases related to the Company’s partnership interest in Regulus.
For the years ended December 31, 2013 and 2012, the Company recorded a tax benefit of $2.7 million and $10.6 million, respectively. For the year ended December 31, 2011, the Company recorded a provision for income taxes of zero. For the years ended December 31, 2013 and 2012, the Company recorded unrealized gains on its investments in available-for-sale securities in other comprehensive income. The benefit of $2.7 million and $10.6 million for the years ended December 31, 2013 and 2012, respectively, is due to the recognition of corresponding income tax expense associated with the increase in the value of the Company’s investment in Regulus that the Company carried at fair market value during the same period. The corresponding income tax expense has been recorded in other comprehensive income. Intraperiod tax allocation rules require the Company to allocate its provision for income taxes between continuing operations and other categories of earnings, such as other comprehensive income. In periods in which the Company has a year-to-date pre-tax loss from continuing operations and pre-tax income in other categories of earnings, such as other comprehensive income, the Company must allocate the tax provision to the other categories of earnings. The Company then records a related tax benefit in continuing operations.
The deferred tax assets above exclude $26.6 million of net operating losses and $0.5 million of federal and state research and development credits related to tax deductions from the exercise of stock options subsequent to the adoption of the 2006 accounting standard on stock-based compensation. This amount represents an excess tax benefit and has not been included in the gross deferred tax assets.
At December 31, 2013, the Company had federal and state net operating loss carryforwards of $372.4 million and $441.6 million, respectively, to reduce future taxable income that will expire at various dates through 2033. At December 31, 2013, federal and state research and development credit carryforwards were $20.8 million and $6.8 million, respectively, available to reduce future tax liabilities that expire at various dates through 2033. At December 31, 2013, foreign tax credit carryforwards were $3.2 million available to reduce future tax liabilities that expire in 2017. At December 31, 2013, alternative minimum tax credits of $0.8 million are available to reduce future regular tax liabilities to the extent such regular tax less other non-refundable credits exceeds the tentative minimum tax. Ownership changes, as defined in the Internal Revenue Code, including those resulting from the issuance of common stock in connection with the Company’s public offerings, may limit the amount of net operating loss that can be utilized to offset future taxable income or tax liability. The Company has determined that based on the value of the Company, in the event there was an annual limitation under Section 382, all net operating loss and tax credit carryforwards would still be available to offset taxable income.
At December 31, 2013, the Company had no unrecognized tax benefits that, if recognized, would favorably impact the Company’s effective income tax rate in future periods. A reconciliation of the beginning and ending amount of unrecognized tax benefits is as follows, in thousands:


Balance at December 31, 2011		$	128
Subtractions for tax positions related to the prior years			(128	)

Balance at December 31, 2012			—
Subtractions for tax positions related to the prior years			—

Balance at December 31, 2013		$	—

The tax years 2010 through 2013 remain open to examination by major taxing jurisdictions to which the Company is subject, which are primarily in the United States, as carryforward attributes generated in years past may still be adjusted upon examination by the Internal Revenue Service or state tax authorities if they have or will be used in a future period. In July 2011, the Internal Revenue Service completed its audits of the Company’s 2008 and 2009 tax years. The Company did not record any tax expense related to these audits. The Company has not recorded any interest and penalties on any unrecognized tax benefits since its inception.

Regulus

Regulus	12 Months Ended
Regulus	Dec. 31, 2013
Regulus	'
	10	REGULUS
	In September 2007, the Company and Isis established Regulus, a company focused on the discovery, development and commercialization of microRNA therapeutics, a potential new class of drugs to treat the pathways of human disease. Regulus, which initially was established as a limited liability company, converted to a C corporation in January 2009 and changed its name to Regulus Therapeutics Inc. Regulus operates as an independent company with a separate board of directors, scientific advisory board and management team.
	In consideration for the Company’s and Isis’ initial interests in Regulus, each party granted Regulus exclusive licenses to its intellectual property for certain microRNA therapeutic applications as well as certain patents in the microRNA field. In addition, the Company made an initial cash contribution to Regulus of $10.0 million, resulting in the Company and Isis making approximately equal aggregate initial capital contributions to Regulus. In March 2009, the Company and Isis each purchased $10.0 million of Series A preferred stock of Regulus.
	From the formation of Regulus in September 2007 to October 2012, the Company accounted for its interest in Regulus using the equity method of accounting. The Company reviewed the consolidation guidance that defines a variable interest entity (“VIE”), and concluded that Regulus qualified as a VIE during such time period. The Company did not consolidate Regulus as the Company lacked the power to direct the activities that could significantly impact the economic success of this entity.

	Summary results of Regulus’ statements of comprehensive loss for the nine months ended September 30, 2012 and the year ended December 31, 2011 are presented in the tables below, in thousands:


			Nine months ended			Year ended
			September 30,			December 31,
			2012			2011
	Statements of Comprehensive Loss Data:
	Net revenues		$	9,462		$	13,789
	Operating expenses			17,733			20,926

	Loss from operations			(8,271	)		(7,137	)
	Other (expense) income			(2,289	)		(259	)
	Income tax benefit (expense)			28			(206	)

	Net loss		$	(10,532	)	$	(7,602	)

	Under the equity method of accounting, the Company was required to recognize losses up to the amount of Regulus’ debt, which was guaranteed by the Company. This resulted in a negative carrying amount. In October 2012, Regulus completed an initial public offering, resulting in the Company’s ownership percentage decreasing from approximately 44% to 17% of Regulus’ outstanding common stock. Upon the completion of the Regulus’ initial public offering, the Company’s debt guarantee was terminated.
	Based upon the Company’s ownership percentage of 17% after the initial public offering, as well as a review of qualitative factors, the Company did not believe that it had the ability to exercise significant influence over the operating decisions and financial policies of Regulus and therefore discontinued the equity method of accounting for Regulus at September 30, 2012. The Company determined that the period between September 30, 2012 and the date on which Regulus’ closed its initial public offering was immaterial for additional equity method accounting. Accordingly, beginning October 10, 2012, the Company accounted for its investment in Regulus as an available-for-sale marketable security due to its readily determinable fair value. At December 31, 2012, the fair value of the Regulus equity securities was $38.7 million. As a result of the issuance of additional common stock by Regulus, the Company recognized a gain of $16.1 million. This amount was recorded as other income in the Company’s consolidated statements of comprehensive loss for the year ended December 31, 2012. The Company’s carrying amount in Regulus increased to $12.4 million following the initial public offering, which became the initial basis of its investment in Regulus under the accounting standard for marketable securities. In addition, the Company recorded $15.7 million as an unrealized gain in other comprehensive income, net of an intraperiod tax benefit of $10.6 million. The Company has historically classified the equity method investment amount in the financial statement caption “Investment in joint venture (Regulus Therapeutics Inc.)” on the Company’s consolidated balance sheets. For the purposes of the 2012 balance sheet, this amount is zero and the Company has reclassified the 2011 balance of $0.6 million to the financial statement caption “Other assets.”

Quarterly_Financial_Data

Quarterly Financial Data	12 Months Ended
Quarterly Financial Data	Dec. 31, 2013
Quarterly Financial Data	'
	11	QUARTERLY FINANCIAL DATA (UNAUDITED)
	The following information has been derived from unaudited consolidated financial statements that, in the opinion of management, include all recurring adjustments necessary for a fair statement of such information.


			Three Months Ended
			March 31,			June 30,			September 30,			December 31,
			2013			2013			2013			2013
			(In thousands, except per share data)
	Revenues		$	18,642		$	8,687		$	8,991		$	10,847
	Operating expenses			28,446			29,999			41,225			40,439
	Net loss			(9,013	)		(18,169	)		(29,686	)		(32,357	)
	Net loss per common share — basic and diluted		$	(0.15	)	$	(0.29	)	$	(0.48	)	$	(0.51	)
	Weighted average common shares — basic and diluted			59,173			61,661			62,416			62,909


			Three Months Ended
			March 31,			June 30,			September 30,			December 31,
			2012			2012			2012			2012
			(In thousands, except per share data)
	Revenues		$	20,587		$	20,884		$	16,759		$	8,495
	Operating expenses			31,480			32,951			34,906			96,844
	Net loss			(11,368	)		(12,956	)		(19,502	)		(62,188	)
	Net loss per common share — basic and diluted		$	(0.25	)	$	(0.25	)	$	(0.38	)	$	(1.20	)
	Weighted average common shares — basic and diluted			46,210			51,280			51,542			51,821
	The increase in operating expenses for the three months ended December 31, 2012 resulted from a $65.0 million charge to operating expenses in connection with the restructuring of the Company’s license agreement with Tekmira in November 2012. This increase in operating expenses was offset by a gain in other income of $16.1 million and a tax benefit of $10.6 million recorded as part of the Company’s accounting for the Regulus initial public offering.

Subsequent_Events

Subsequent Events	12 Months Ended
	Dec. 31, 2013
Subsequent Events	'
	12	SUBSEQUENT EVENTS
	Acquisition of Sirna Therapeutics
	On January 10, 2014, the Company entered into a Stock Purchase Agreement (the “Sirna Agreement”) with Sirna, Merck and, for limited purposes, Merck & Co., Inc., pursuant to which the Company will purchase from Merck all of Merck’s right, title and interest in and to all of the Sirna Common Stock. Sirna possesses intellectual property and RNAi assets including pre-clinical therapeutic candidates, chemistry, and siRNA-conjugate and other delivery technologies that the Company intends to integrate into its platform for delivery of RNAi therapeutics. The Company will not acquire any employees, manufacturing or other facilities, developed processes or clinical-stage assets as part of the acquisition of Sirna.
	In consideration for the Sirna Common Stock, the Company will (i) pay Merck $25.0 million in cash and (ii) issue to Merck 2,520,044 shares of the Company’s common stock, par value $0.01 per share (“Company Common Stock”), having a value of $150.0 million as calculated under the terms of the Sirna Agreement on the date of execution. In addition, Merck is eligible to receive the following consideration from the Company: (i) up to an aggregate of $10.0 million upon the achievement by the Company or its Related Parties (as defined in the Agreement) of specified regulatory milestones for RNAi products covered by Sirna intellectual property (“Company Products”), and (ii) up to an aggregate of $105.0 million upon the achievement by the Company or its Related Parties of specified development and regulatory ($40.0 million) and commercial ($65.0 million) milestones associated with the clinical development progress of certain pre-clinical candidates discovered by Sirna (“Sirna Products”), together with low single-digit royalties for Company Products and single-digit royalties for Sirna Products, in each case based on annual worldwide net sales, if any, by the Company and its Related Parties of any such products.
	Under the Sirna Agreement, Merck also agreed not to dispose of (i) any shares of Company Common Stock beneficially owned for a period of six months following the closing date (the “Initial Lock-Up”), subject to certain limited exceptions, and (ii) 50% of the shares of Company Common Stock beneficially owned for a period of six additional months following the termination of the Initial Lock-Up (the “Subsequent Lock-Up”). During and following the expiration of the Subsequent Lock-Up, Merck will be permitted to sell such shares of Company Common Stock subject to certain limitations, including certain volume and manner of sale restrictions.
	The Sirna Agreement contains customary representations, warranties, and covenants of the parties thereto. Subject to customary closing conditions, including the expiration or early termination of the applicable pre-merger waiting period under the Hart-Scott-Rodino Antitrust Improvements Act of 1976, the transaction is expected to close during the first quarter of 2014.
	2014 Genzyme Collaboration
	On January 11, 2014, the Company entered into the 2014 Genzyme Collaboration. The 2014 Genzyme Collaboration is governed by a Master Collaboration Agreement, dated January 11, 2014, by and between the Company and Genzyme (including the License Terms appended thereto, the “Master Agreement”), which will become effective upon closing of the Equity Transaction (as defined below) (the “Effective Date”) and will supersede and replace the 2012 Genzyme Agreement.
	The 2014 Genzyme Collaboration is structured as an exclusive relationship for the worldwide development and commercialization of RNAi therapeutics in the field of genetic medicines, which includes the Company’s current and future genetic medicine programs that reach Human Proof-of-Principal (POP) Study Completion (as defined in the Master Agreement) (“Human POP”) by the end of 2019 (collectively, “Genzyme Collaboration Products”), subject to extension to the end of 2021 in various circumstances. The Company will retain product rights in North America and Western Europe, while Genzyme will obtain exclusive rights to develop and commercialize Genzyme Collaboration Products in the rest of the world (the “Genzyme Territory”), together with certain broader co-development/co-promote or worldwide rights for certain products. Genzyme’s rights are structured as an opt-in that is triggered upon achievement of Human POP. The Company maintains development control for all programs prior to Genzyme’s opt-in and maintains development and commercialization control after Genzyme’s opt-in for all programs in its territory.
	Upon the Effective Date, Genzyme will opt-in to patisiran, an RNAi therapeutic currently in a Phase 3 clinical trial for the treatment of ATTR patients with Familial Amyloidotic Polyneuropathy, for the Genzyme Territory, and the Company will retain full product rights in North America and Western Europe. The Company and Genzyme have also agreed to expand their current collaboration on ALN-TTRsc, an RNAi therapeutic currently in a Phase 2 clinical trial for the treatment of ATTR patients with TTR amyloid cardiomyopathy, where the parties will co-develop and co-promote ALN-TTRsc in North America and Western Europe. The Company will maintain development and commercialization control with ALN-TTRsc and Genzyme will develop and commercialize the product in the Genzyme Territory.
	In addition to its regional rights for the Company’s current and future genetic medicine programs in the Genzyme Territory, Genzyme will have the right to either (i) co-develop and co-promote ALN-AT3 for the treatment of hemophilia and other rare bleeding disorders in the Company’s territory, with the Company maintaining development and commercialization control, or (ii) obtain a global license to ALN-AS1 for the treatment of hepatic porphyrias. Genzyme will exercise this selection right upon Human POP for the ALN-AT3 and ALN-AS1 programs. Finally, Genzyme will have the right for a global license to a single, future genetic medicine program that is not one of the currently defined genetic medicine programs. The Company will retain global rights to any RNAi therapeutic genetic medicine program that does not reach Human POP by the end of 2019, subject to certain limited exceptions. Under the terms of the Master Agreement, the Company retains full rights to all current and future RNAi therapeutic programs outside of the field of genetic medicines, including the right to form new collaborations.
	In consideration for the rights granted to Genzyme under the Master Agreement, Genzyme will be required to make payments to the Company for each Genzyme Collaboration Product upon the achievement of specified development, regulatory and commercial milestones for each (i) regional (e.g., patisiran) and co-developed/co-promoted (e.g., ALN-TTRsc) Genzyme Collaboration Product totaling up to $75.0 million and (ii) global Genzyme Collaboration Product up to $200.0 million, and to pay tiered double-digit royalties up to twenty percent for each regional and global Genzyme Collaboration Product based on annual net sales, if any, of each Genzyme Collaboration Product by Genzyme, its affiliates and sublicensees. The Company could potentially earn the next development milestone payment of $25.0 million under the 2014 Genzyme Collaboration based upon the initiation of the first global Phase 3 clinical trial. In the case of co-developed/co-promoted Genzyme Collaboration Products, the parties will share profits equally and the Company will book product sales in North America and Western Europe.
	Under the Master Agreement, the parties will collaborate in the development of option products, with the Company leading development for all programs prior to Genzyme’s opt-in and also leading development and commercialization for all programs in the Company’s territory after Genzyme’s opt-in. Development costs for Genzyme Collaboration Products once Genzyme exercises an option (or as of the Effective Date for patisiran and ALN-TTRsc) will be shared between Genzyme and the Company as follows, subject to the provisions of the relevant License Terms: (a) for all regional Genzyme Collaboration Products, Genzyme shall be responsible for twenty percent of the global development costs, (b) for all co-develop/co-promote Genzyme Collaboration Products, Genzyme shall be responsible for fifty percent of the global development costs, and (c) for all global Genzyme Collaboration Products, Genzyme shall be responsible for one hundred percent of global development costs. If Genzyme does not exercise its option to license rights to a particular program, the Company will retain the exclusive right to develop and commercialize such program throughout the world, including the right to sublicense to third parties.
	The 2014 Genzyme Collaboration will be governed by an alliance joint steering committee that will be comprised of an equal number of representatives from each party. There will also be additional committees to manage various aspects of each regional, co-developed/co-promoted and global program. The Company and Genzyme intend to enter into supply agreements to provide for supply of Genzyme Collaboration Products to Genzyme for clinical studies, and, at Genzyme’s request, commercial sales. Genzyme also has certain rights to manufacture Genzyme Collaboration Products. Additionally, Genzyme has certain limited opt-out rights, as specified in the Master Agreement, upon which products revert fully back to the Company with no further obligations to Genzyme.
	In addition, under the Master Agreement, the Company and Genzyme have agreed to enter into exclusive discussions and negotiations regarding a potential collaboration around the delivery of small interfering RNAs (“siRNAs”) to the central nervous system (“CNS”) with the objective of enabling the discovery of siRNAs for the treatment of CNS disorders.
	The Master Agreement (including the License Terms appended thereto) contains certain termination provisions, including for material breach by the other party. Unless terminated earlier pursuant to its terms, the Master Agreement will terminate upon the last to expire of any of the option periods under the Master Agreement or the License Terms appended thereto.
	In consideration for the rights granted to Genzyme under the Master Agreement and pursuant to the terms of a Stock Purchase Agreement, dated January 11, 2014, by and between Genzyme and the Company, the Company has agreed to sell to Genzyme 8,766,338 shares of its common stock, par value $0.01 per share (the “Common Stock”), and Genzyme agreed to pay $700.0 million in aggregate cash consideration to the Company (the “Equity Transaction”). This sale does not involve a public offering and is therefore exempt from registration under Section 4(a)(2) of the Securities Act of 1933, as amended. Subject to customary closing conditions, including the expiration or early termination of the applicable pre-merger waiting period under the Hart-Scott-Rodino Antitrust Improvements Act of 1976, the Equity Transaction is expected to close during the first quarter of 2014. Following the closing of the Equity Transaction, Genzyme will beneficially own approximately 12% of the Company’s outstanding common stock.
	As a condition to the closing of the Equity Transaction, Genzyme will enter into an investor agreement with the Company (the “Investor Agreement”). Under the Investor Agreement, until the earlier of the fifth anniversary of the expiration or earlier termination of the Collaboration and the date on which Genzyme and its affiliates cease to beneficially own at least 5% of the Company’s outstanding common stock, Genzyme and its affiliates will be bound by certain “standstill” provisions. The standstill provisions include agreements not to acquire more than 30% of the Company’s outstanding common stock, call stockholder meetings, nominate directors other than those approved by the Company’s Board of Directors, subject to certain limited exceptions, or propose or support a proposal to acquire the Company.
	Further, Genzyme will agree to vote, and cause its affiliates to vote, all shares of the Company’s voting securities they are entitled to vote, up to a maximum of 20% of the Company’s outstanding common stock, in a manner either as recommended by the Company’s Board of Directors or proportionally with the votes cast by other stockholders of the Company, except with respect to certain change of control transactions or liquidation or dissolution of the Company. Until Genzyme owns less than 7.5% of the Company’s outstanding common stock, subject to Genzyme’s limited right to maintain its ownership percentage as described below, if the Company issues common stock or securities convertible into or exercisable for common stock to a third party that holds at least 30% of the Company’s outstanding common stock or, in connection with a collaboration or license transaction, to a third party that will initially hold at least the percentage of the Company’s outstanding common stock represented by the shares purchased by Genzyme at the closing of the Equity Transaction, the Company will offer Genzyme an opportunity to amend the standstill and voting provisions in the Investor Agreement to be consistent with the terms provided to such third party.

Summary_of_Significant_Account1

Summary of Significant Accounting Policies (Policies)	12 Months Ended
Summary of Significant Accounting Policies (Policies)	Dec. 31, 2013
Basis of Presentation and Principles of Consolidation	'
	Basis of Presentation and Principles of Consolidation
	The accompanying consolidated financial statements reflect the operations of the Company and its wholly-owned subsidiaries. All intercompany accounts and transactions have been eliminated.
Reclassifications	'
	Reclassifications
	Certain reclassifications have been made to prior years’ consolidated financial statements to conform to the 2013 presentation.
Use of Estimates	'
	Use of Estimates
	The preparation of financial statements in conformity with accounting principles generally accepted in the United States of America (“GAAP”) requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities and the disclosure of contingent assets and liabilities at the date of the consolidated financial statements and the reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates.
Concentrations of Credit Risk and Significant Customers	'
	Concentrations of Credit Risk and Significant Customers
	Financial instruments that potentially expose the Company to concentrations of credit risk consist primarily of cash, cash equivalents and fixed income marketable securities. At December 31, 2013 and 2012, substantially all of the Company’s cash, cash equivalents and fixed income marketable securities were invested in money market mutual funds, commercial paper, corporate notes and U.S. government securities through highly rated financial institutions. Investments are restricted, in accordance with the Company’s investment policy, to a concentration limit per issuer.
	In recent periods, the Company’s revenues from collaborations have been generated from primarily F. Hoffmann-La Roche Ltd and certain of its affiliates (collectively, “Roche”) (which assigned its rights and obligations to Arrowhead Research Corporation (“Arrowhead”) in 2011), Takeda Pharmaceutical Company Limited (“Takeda”), Cubist Pharmaceuticals, Inc. (“Cubist”), Monsanto Company (“Monsanto”) and The Medicines Company (“MDCO”). For the year ended December 31, 2013, the composition of the Company’s billed and unbilled collaboration receivables was primarily composed of an amount due from Genzyme Corporation (“Genzyme”) based upon the initiation of a Phase 3 clinical trial. For the year ended December 31, 2012, the composition of the Company’s billed and unbilled collaboration receivables was entirely composed of amounts due from the U.S. Government for the wind-down of completed government contracts.

	The following table summarizes customers that represent greater than 10% of the Company’s net revenues from collaborators, for the periods indicated:


			Year Ended
			December 31,
			2013			2012			2011
	Takeda			47	%		33	%		27	%
	Cubist			21	%		*	%		*	%
	Monsanto			12	%		*	%		*	%
	Roche/Arrowhead			*	%		56	%		68	%
	The following table summarizes customers with amounts due that represent greater than 10% of the Company’s billed and unbilled collaboration receivables balance, at the periods indicated:


			At December 31,
			2013			2012
	Genzyme			94	%		*	%
	U.S. Government			*	%		100	%


	*	Represents 10% or less
Fair Value Measurements	'
	Fair Value Measurements
	The fair value is the price that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date. The following tables present information about the Company’s assets that are measured at fair value on a recurring basis at December 31, 2013 and 2012, and indicate the fair value hierarchy of the valuation techniques the Company utilized to determine such fair value. In general, fair values determined by Level 1 inputs utilize quoted prices (unadjusted) in active markets for identical assets or liabilities. Fair values determined by Level 2 inputs utilize data points that are observable, such as quoted prices (adjusted), interest rates and yield curves. Fair values determined by Level 3 inputs utilize unobservable data points for the asset or liability, and include situations where there is little, if any, market activity for the asset or liability. The fair value hierarchy level is determined by the lowest level of significant input. Financial assets and liabilities measured at fair value on a recurring basis are summarized as follows, in thousands:


	Description		At			Quoted			Significant			Significant
			December 31,			Prices in			Observable			Unobservable
			2013			Active			Inputs			Inputs
						Markets			(Level 2)			(Level 3)
						(Level 1)
	Cash equivalents		$	32,571		$	32,571		$	—		$	—
	Marketable securities (fixed income):
	Corporate notes			228,462			—			228,462			—
	U.S. Government obligations			56,863			—			56,863			—
	Commercial paper			11,978			—			11,978			—
	Marketable securities (Regulus equity holdings)			45,452			45,452			—			—

	Total		$	375,326		$	78,023		$	297,303		$	—



	Description		At			Quoted			Significant			Significant
			December 31,			Prices in			Observable			Unobservable
			2012			Active			Inputs			Inputs
						Markets			(Level 2)			(Level 3)
						(Level 1)
	Cash equivalents		$	50,213		$	50,213		$	—		$	—
	Marketable securities (fixed income):
	Corporate notes			91,523			—			91,523			—
	U.S. Government obligations			60,661			—			60,661			—
	Commercial paper			22,639			—			22,639			—
	Marketable securities (Regulus equity holdings)			38,748			—			38,748			—

	Total		$	263,784		$	50,213		$	213,571		$	—

	For the year ended December 31, 2013, the Company transferred $45.5 million of marketable securities (equity holdings in Regulus Therapeutics Inc. (“Regulus”)) from Level 2 to Level 1 due to the increased volume in average daily trading on the NASDAQ stock market for these instruments. For the year ended December 31, 2012, there were no transfers between Level 1 and Level 2 financial assets. The carrying amounts reflected in the Company’s consolidated balance sheets for cash, billed and unbilled collaboration receivables, other current assets, accounts payable and accrued expenses approximate fair value due to their short-term maturities.
Investments in Marketable Securities	'
	Investments in Marketable Securities
	The Company invests its excess cash balances in short-term and long-term marketable debt and equity securities. The Company classifies its investments in marketable debt securities as either held-to-maturity or available-for-sale based on facts and circumstances present at the time it purchased the securities. At each balance sheet date presented, the Company classified all of its investments in debt and equity securities as available-for-sale. The Company reports available-for-sale investments at fair value at each balance sheet date and includes any unrealized holding gains and losses (the adjustment to fair value) in accumulated other comprehensive income (loss), a component of stockholders’ equity. Realized gains and losses are determined using the specific identification method and are included in other income. If any adjustment to fair value reflects a decline in the value of the investment, the Company considers all available evidence to evaluate the extent to which the decline is “other than temporary” and, if so, marks the investment to market through a charge to its consolidated statements of comprehensive loss. The Company did not record any impairment charges related to its fixed income marketable securities during the years ended December 31, 2013, 2012 or 2011. During 2011, the Company recorded an impairment charge of $0.6 million related to its former investment in equity securities of Tekmira Pharmaceuticals Corporation (“TPC”), as the decrease in the fair value of this investment was deemed to be other than temporary. The Company’s marketable securities are classified as cash equivalents if the original maturity, from the date of purchase, is 90 days or less, and as marketable securities if the original maturity, from the date of purchase, is in excess of 90 days. The Company’s cash equivalents are composed of money market funds.

	In the fourth quarter of 2012, the Company began accounting for its investment in Regulus as an available-for-sale marketable security. Intraperiod tax allocation rules require the Company to allocate its provision for income taxes between continuing operations and other categories of earnings, such as other comprehensive income. In periods in which the Company has a year-to-date pre-tax loss from continuing operations and pre-tax income in other categories of earnings, such as other comprehensive income, the Company must allocate the tax provision to the other categories of earnings. The Company then records a related tax benefit in continuing operations. The following tables summarize the fair value, accumulated other comprehensive income and intraperiod tax allocation regarding the Company’s investment in Regulus available-for-sale marketable securities at December 31, 2013 and 2012, and for the activity recorded in the year, in thousands:


	Description		At			During Twelve			Balance at
			December 31,			Months Ended			December 31,
			2012			December 31,			2013
						2013
	Carrying value		$	12,449		$	—		$	12,449
	Accumulated other comprehensive income, before tax			26,299			6,704			33,003

	Investment in equity securities of Regulus Therapeutics Inc., as reported		$	38,748		$	6,704		$	45,452

	Accumulated other comprehensive income, before tax		$	26,299		$	6,704		$	33,003
	Intraperiod tax allocation recorded as a benefit from income taxes			(10,572	)		(2,695	)		(13,267	)

	Accumulated other comprehensive income, net of tax		$	15,727		$	4,009		$	19,736

	The Company obtains fair value measurement data for its marketable securities from independent pricing services. The Company performs validation procedures to ensure the reasonableness of this data. This includes meeting with the independent pricing services to understand the methods and data sources used. Additionally, the Company performs its own review of prices received from the independent pricing services by comparing these prices to other sources and confirming those securities are trading in active markets.
	The following tables summarize the Company’s marketable securities, other than its holdings in Regulus noted above, at December 31, 2013 and 2012, in thousands:


			December 31, 2013
			Amortized			Gross			Gross			Fair Value
			Cost			Unrealized			Unrealized
						Gains			Losses
	Commercial paper (Due within 1 year)		$	11,983		$	—		$	(5	)	$	11,978
	Corporate notes (Due within 1 year)			154,175			33			(46	)		154,162
	Corporate notes (Due after 1 year through 2 years)			74,312			23			(35	)		74,300
	U.S. Government obligations (Due within 1 year)			26,553			8			—			26,561
	U.S. Government obligations (Due after 1 year through 2 years)			30,300			2			—			30,302

	Total		$	297,323		$	66		$	(86	)	$	297,303

			December 31, 2012
			Amortized			Gross			Gross			Fair Value
			Cost			Unrealized			Unrealized
						Gains			Losses
	Commercial paper (Due within 1 year)		$	22,650		$	1		$	(12	)	$	22,639
	Corporate notes (Due within 1 year)			41,249			23			(4	)		41,268
	Corporate notes (Due after 1 year through 2 years)			50,322			5			(72	)		50,255
	U.S. Government obligations (Due within 1 year)			7,500			—			—			7,500
	U.S. Government obligations (Due after 1 year through 2 years)			53,168			2			(9	)		53,161

	Total		$	174,889		$	31		$	(97	)	$	174,823

Estimated Liability for Development Costs	'
	Estimated Liability for Development Costs
	The Company records accrued liabilities related to expenses for which service providers have not yet billed the Company with respect to products or services that the Company has received, specifically related to ongoing pre-clinical studies and clinical trials. These costs primarily relate to third-party clinical management costs, laboratory and analysis costs, toxicology studies and investigator fees. The Company has multiple product candidates in concurrent pre-clinical studies and clinical trials at multiple clinical sites throughout the world. In order to ensure that the Company has adequately provided for ongoing pre-clinical and clinical development costs during the period in which the Company incurs such costs, the Company maintains an accrual to cover these expenses. The Company updates the estimate for this accrual on at least a quarterly basis. The assessment of these costs is a subjective process that requires judgment. Upon settlement, these costs may differ materially from the amounts accrued in the Company’s consolidated financial statements. The Company’s historical accrual estimates have not been materially different from the Company’s actual costs.
Revenue Recognition	'
	Revenue Recognition
	The Company has entered into collaboration agreements with leading pharmaceutical and life sciences companies, including Novartis Pharma AG and one of its affiliates (together, “Novartis”), Roche, Takeda, Kyowa Hakko Kirin Co., Ltd. (“Kyowa Hakko Kirin”), Cubist, Monsanto, Genzyme and MDCO. The terms of the Company’s collaboration agreements typically include non-refundable license fees, funding of research and development, payments based upon achievement of clinical and pre-clinical development milestones, regulatory milestones, manufacturing services, sales milestones and royalties on product sales.
	In January 2011, the Company adopted new authoritative guidance on revenue recognition for multiple element arrangements. The guidance, which applied to multiple element arrangements entered into or materially modified on or after January 1, 2011, amended the criteria for separating and allocating consideration in a multiple element arrangement by modifying the fair value requirements for revenue recognition and eliminating the use of the residual method. The fair value of deliverables under the arrangement may be derived using a “best estimate of selling price” if vendor specific objective evidence and third-party evidence is not available. Deliverables under the arrangement could be considered separate units of accounting provided that (i) a delivered item has value to the customer on a standalone basis and (ii) if the arrangement includes a general right of return relative to the delivered item, delivery or performance of the undelivered item is considered probable and substantially in the control of the vendor. The new guidance did not change the criteria for standalone value. As a biotechnology entity with unique and specialized delivered and undelivered performance obligations, the Company has been unable to demonstrate standalone value in its multiple element arrangements. For example, the Company applied the new rules to collaborations executed with Monsanto and Genzyme during 2012, but it was unable to demonstrate standalone value. In addition, the Company has not materially modified any of its multiple element arrangements. As such, the Company has continued to account for license and collaboration agreements under previously issued revenue recognition guidance for multiple element arrangements, as described below.
	Non-refundable license fees are recognized as revenue upon delivery of the license only if the Company has a contractual right to receive such payment, the contract price is fixed or determinable, the collection of the resulting receivable is reasonably assured and the Company has no further performance obligations under the license agreement. Multiple element arrangements, such as license and development arrangements, are analyzed to determine whether the deliverables, which often include a license and performance obligations such as research and steering committee services, can be separated or whether they must be accounted for as a single unit of accounting. The Company recognizes upfront license payments as revenue upon delivery of the license only if the license has standalone value and the fair value of the undelivered performance obligations, typically including research and/or steering committee services, can be determined. If the fair value of the undelivered performance obligations can be determined, such obligations are accounted for separately as such obligations are fulfilled. If the license is considered to either not have standalone value or have standalone value but the fair value of any of the undelivered performance obligations cannot be determined, the arrangement would then be accounted for as a single unit of accounting and the license payments and payments for performance obligations are recognized as revenue over the estimated period of when the performance obligations are performed.

	Whenever the Company determines that an arrangement should be accounted for as a single unit of accounting, the Company determines the period over which the performance obligations will be performed and revenue will be recognized. Revenue is recognized using either a proportional performance or straight-line method. The Company recognizes revenue using the proportional performance method when the level of effort required to complete its performance obligations under an arrangement can be reasonably estimated and such performance obligations are provided on a best-efforts basis. Direct labor hours or full-time equivalents are typically used as the measure of performance. The amount of revenue recognized under the proportional performance method is determined by multiplying the total payments under the contract, excluding royalties and payments contingent upon achievement of milestones, by the ratio of level of effort incurred to date to estimated total level of effort required to complete the Company’s performance obligations under the arrangement. Revenue is limited to the lesser of the cumulative amount of payments received or the cumulative amount of revenue earned, as determined using the proportional performance method, as of the period ending date.
	If the Company cannot reasonably estimate the level of effort to complete its performance obligations under an arrangement, the Company recognizes revenue under the arrangement on a straight-line basis over the period the Company is expected to complete its performance obligations. Revenue is limited to the lesser of the cumulative amount of payments received or the cumulative amount of revenue earned, as determined using the straight-line method, as of the period ending date.
	Significant management judgment is required in determining the level of effort required under an arrangement and the period over which the Company is expected to complete its performance obligations under an arrangement. Steering committee services that are not inconsequential or perfunctory and that are determined to be performance obligations are combined with other research services or performance obligations required under an arrangement, if any, in determining the level of effort required in an arrangement and the period over which the Company expects to complete its aggregate performance obligations.
	Many of the Company’s collaboration agreements entitle it to additional payments upon the achievement of performance-based milestones. These milestones are generally categorized into three types; development milestones which are generally based on the advancement of the Company’s pipeline and initiation of clinical trials, regulatory milestones which are generally based on the submission, filing or approval of regulatory applications such as a new drug application in the United States, and commercialization milestones which are generally based on meeting specific thresholds of sales in certain geographic areas. If the achievement of a milestone is considered probable at the inception of the collaboration, the related milestone payment is included with other collaboration consideration, such as upfront fees and research funding, in the Company’s revenue model. Milestones that are tied to regulatory approval are not considered probable of being achieved until such approval is received. Milestones tied to counter-party performance are not included in the Company’s revenue model until the performance conditions are met.
	The Company performs an assessment to determine whether a substantive milestone exists at the inception of its collaborative arrangements. In evaluating if a milestone is substantive, the Company considers whether uncertainty exists as to the achievement of the milestone event at the inception of the arrangement, the achievement of the milestone involves substantive effort and can only be achieved based in whole or part on the performance or the occurrence of a specific outcome resulting from the Company’s performance, the amount of the milestone payment appears reasonable either in relation to the effort expected to be expended or to the projected enhancement of the value of the delivered items, there is any future performance required to earn the milestone, and the consideration is reasonable relative to all deliverables and payment terms in the arrangement. When a substantive milestone is achieved, the accounting rules permit the Company to recognize revenue related to the milestone payment in its entirety.
	To date, the Company has not recorded any substantive milestones under its collaborations because the Company has not identified any milestones that meet the required criteria listed above. The Company has deferred recognition of payments for achievement of non-substantive milestones and recognized revenue over the estimated period of performance applicable to each collaborative arrangement. As these milestones are achieved, the Company will recognize as revenue a portion of the milestone payment, which is equal to the percentage of the performance period completed when the milestone is achieved, multiplied by the amount of the milestone payment, upon achievement of such milestone. The Company will recognize the remaining portion of the milestone payment over the remaining performance period under the proportional performance method or on a straight-line basis.
	For revenue generating arrangements where the Company, as a vendor, provides consideration to a licensor or collaborator, as a customer, the Company applies the accounting standard that governs such transactions. This standard addresses the accounting for revenue arrangements where both the vendor and the customer make cash payments to each other for services and/or products. A payment to a customer is presumed to be a reduction of the selling price unless the Company receives an identifiable benefit for the payment and it can reasonably estimate the fair value of the benefit received. Payments to a customer that are deemed a reduction of selling price are recorded first as a reduction of revenue, to the extent of both cumulative revenue recorded to date and probable future revenues, which include any unamortized deferred revenue balances, under all arrangements with such customer, and then as an expense. Payments that are not deemed to be a reduction of selling price are recorded as an expense.
	The Company evaluates its collaborative agreements for proper classification in its consolidated statements of comprehensive loss based on the nature of the underlying activity. Transactions between collaborators recorded in the Company’s consolidated statements of comprehensive loss are recorded on either a gross or net basis, depending on the characteristics of the collaborative relationship. The Company generally reflects amounts due under its collaborative agreements related to cost-sharing of development activities as a reduction of research and development expense.
	Amounts received prior to satisfying the above revenue recognition criteria are recorded as deferred revenue in the accompanying consolidated balance sheets. Although the Company follows detailed guidelines in measuring revenue, certain judgments affect the application of its revenue policy. For example, in connection with the Company’s existing collaboration agreements, the Company has recorded on its balance sheet short-term and long-term deferred revenue based on its best estimate of when such revenue will be recognized. Short-term deferred revenue consists of amounts that are expected to be recognized as revenue in the next 12 months. Amounts that the Company expects will not be recognized within the next 12 months are classified as long-term deferred revenue. However, this estimate is based on the Company’s current operating plan and, if its operating plan should change in the future, the Company may recognize a different amount of deferred revenue over the next 12-month period.
	The estimate of deferred revenue also reflects management’s estimate of the periods of the Company’s involvement in certain of its collaborations. The Company’s performance obligations under these collaborations consist of participation on steering committees and the performance of other research and development services. In certain instances, the timing of satisfying these obligations can be difficult to estimate. Accordingly, the Company’s estimates may change in the future. Such changes to estimates would result in a change in revenue recognition amounts. If these estimates and judgments change over the course of these agreements, it may affect the timing and amount of revenue that the Company recognizes and records in future periods. At December 31, 2013, the Company had short-term and long-term deferred revenue of $32.7 million and $93.4 million, respectively, related to its collaborations.
Income Taxes	'
	Income Taxes
	The Company uses the asset and liability method of accounting for income taxes. Under the asset and liability method, deferred tax assets and liabilities reflect the impact of temporary differences between amounts of assets and liabilities for financial reporting purposes and such amounts as measured under enacted tax laws. A valuation allowance is required to offset any net deferred tax assets if, based upon the available evidence, it is more likely than not that some or all of the deferred tax asset will not be realized.
	The Company accounts for uncertain tax positions using a “more-likely-than-not” threshold for recognizing and resolving uncertain tax positions. The evaluation of uncertain tax positions is based on factors that include, but are not limited to, changes in tax law, the measurement of tax positions taken or expected to be taken in tax returns, the effective settlement of matters subject to audit, new audit activity and changes in facts or circumstances related to a tax position. The Company’s policy is to accrue interest and penalties related to unrecognized tax positions in income tax expense. As of December 31, 2013, the Company has not recorded significant interest and penalty expense related to uncertain tax positions.
Research and Development Costs	'
	Research and Development Costs
	The Company expenses research and development costs as incurred. Included in research and development costs are wages, benefits and other operating costs, facilities, supplies, external services, clinical trial and manufacturing costs, and overhead directly related to the Company’s research and development operations, as well as costs to acquire technology licenses.
	The Company has entered into several license agreements for rights to utilize certain technologies. The terms of the licenses may provide for upfront payments, annual maintenance payments, milestone payments based upon certain specified events being achieved and royalties on product sales. The Company charges costs to acquire and maintain licensed technology that has not reached technological feasibility and does not have alternative future use to research and development expense as incurred. During the years ended December 31, 2013, 2012 and 2011, the Company charged to research and development expense costs associated with license fees of $8.0 million, $5.7 million and $1.4 million, respectively.
Accounting for Stock-Based Compensation	'
	Accounting for Stock-Based Compensation
	The Company has stock incentive plans and an employee stock purchase plan under which it grants equity instruments. The Company accounts for all stock-based awards granted to employees at their fair value and generally recognizes compensation expense over the vesting period of the award. Determining the amount of stock-based compensation to be recorded requires the Company to develop estimates of fair values of stock options as of the grant date. The Company calculates the grant date fair values using the Black-Scholes valuation model. The Company’s expected stock price volatility assumption is based on a combination of the historical and implied volatility of the Company’s publicly traded stock.
	For stock-based awards granted to non-employees, the Company generally recognizes compensation expense over the vesting period of the award, which is generally the period during which services are rendered by such non-employees. At the end of each financial reporting period prior to vesting, the Company re-measures the value of these stock-based awards (as calculated using the Black-Scholes option-pricing model) using the then-current fair value of the Company’s common stock. Stock options granted by the Company to non-employees, other than members of the Company’s Board of Directors and Scientific Advisory Board members, generally vest over the service period.
	The fair value of restricted stock awards granted to employees is based upon the quoted closing market price per share on the date of grant, adjusted for assumed forfeitures. Expense is recognized over the vesting period, commencing when the Company determines that it is probable that the awards will vest.
	For performance-based stock awards, expense is first recorded when the Company determines that the achievement of such performance conditions is deemed probable. This determination requires significant judgment by management. At the probable date, the Company records a cumulative expense catch-up, with remaining expense amortized over the remaining service period.
Comprehensive Loss	'
	Comprehensive Loss
	Comprehensive loss is comprised of net loss and certain changes in stockholders’ equity that are excluded from net loss. The Company includes foreign currency translation adjustments in other comprehensive loss for Alnylam Europe AG (“Alnylam Europe”) as the functional currency is not the United States dollar. The Company includes unrealized gains and losses on certain marketable securities in other comprehensive loss.
Net Loss Per Common Share	'
	Net Loss Per Common Share
	The Company computes basic net loss per common share by dividing net loss by the weighted average number of common shares outstanding. The Company computes diluted net loss per common share by dividing net loss by the weighted average number of common shares and dilutive potential common share equivalents then outstanding. Potential common shares consist of shares issuable upon the exercise of stock options (using the treasury stock method), and unvested restricted stock awards. Because the inclusion of potential common shares would be anti-dilutive for all periods presented, diluted net loss per common share is the same as basic net loss per common share.
	The following table sets forth for the periods presented the potential common shares (prior to consideration of the treasury stock method) excluded from the calculation of net loss per common share because their inclusion would be anti-dilutive, in thousands:


			December 31,
			2013			2012			2011
	Options to purchase common stock			8,713			8,932			9,779
	Unvested restricted common stock			500			604			312

				9,213			9,536			10,091

Segment Information	'
	Segment Information
	The Company operates in a single reporting segment, the discovery, development and commercialization of RNAi therapeutics.
Subsequent Events	'
	Subsequent Events
	The Company evaluated all events or transactions that occurred after December 31, 2013 up through the date these consolidated financial statements were issued. During this period, the Company did not have any material recognized subsequent events. However, the Company did have the following nonrecognized subsequent events, which are more fully described in Note 12, “Subsequent Events”:

		•		In January 2014, the Company entered into a stock purchase agreement with Sirna Therapeutics, Inc. (“Sirna”), Merck Sharp & Dohme Corp. (“Merck”), and, for limited purposes, Merck & Co., Inc., pursuant to which the Company will purchase from Merck all of Merck’s right, title and interest in and to all of the outstanding shares of common stock, par value $0.01 per share, of Sirna (the “Sirna Common Stock”). See Note 12.

		•		In January 2014, the Company and Genzyme entered into a new global strategic collaboration agreement to develop and commercialize the Company’s current and future genetic medicine pipeline principally in territories outside of North America and Western Europe, subject to certain broader rights. See Note 12.
Recent Accounting Pronouncements	'
	Recent Accounting Pronouncements
	In February 2013, the Financial Accounting Standards Board (“FASB”) issued amendments to the accounting guidance for presentation of comprehensive income to improve the reporting of reclassifications out of accumulated other comprehensive income. The amendments did not change the current requirements for reporting net income or other comprehensive income, but require an entity to provide information about the amounts reclassified out of accumulated other comprehensive income by component. In addition, an entity is now required to present, either on the face of the statement where the net income is presented or in the notes, significant amounts reclassified out of accumulated other comprehensive income by the respective line items of net income but only if the amount reclassified is required under GAAP to be reclassified to net income in its entirety in the same reporting period. For other amounts that are not required under GAAP to be reclassified in their entirety to net income, an entity is required to cross-reference to other disclosures required under GAAP that provide additional detail about these amounts. For public companies, these amendments were effective prospectively for reporting periods beginning after December 15, 2012. The Company adopted this guidance on January 1, 2013. Other than a change in presentation, the adoption of this guidance did not have a material impact on the Company’s consolidated financial statements.

	In July 2013, the FASB issued new accounting guidance specific to income taxes. The new guidance requires an entity to present an unrecognized tax benefit and a net operating loss carryforward, a similar tax loss, or a tax credit carryforward on a net basis as part of a deferred tax asset, unless the unrecognized tax benefit is not available to reduce the deferred tax asset component or would not be utilized for that purpose, then a liability would be recognized. The updated accounting guidance is effective for fiscal years beginning after December 15, 2013. The Company does not expect the adoption of this guidance to have a material impact on the Company’s consolidated financial statements.

Summary_of_Significant_Account2

Summary of Significant Accounting Policies (Tables)	12 Months Ended
Summary of Significant Accounting Policies (Tables)	Dec. 31, 2013
Schedules of Concentration of Risk by Risk Factor	'
	The following table summarizes customers that represent greater than 10% of the Company’s net revenues from collaborators, for the periods indicated:


			Year Ended
			December 31,
			2013			2012			2011
	Takeda			47	%		33	%		27	%
	Cubist			21	%		*	%		*	%
	Monsanto			12	%		*	%		*	%
	Roche/Arrowhead			*	%		56	%		68	%
	The following table summarizes customers with amounts due that represent greater than 10% of the Company’s billed and unbilled collaboration receivables balance, at the periods indicated:


			At December 31,
			2013			2012
	Genzyme			94	%		*	%
	U.S. Government			*	%		100	%


	*	Represents 10% or less
Fair Value Measured on Recurring Basis	'
	Financial assets and liabilities measured at fair value on a recurring basis are summarized as follows, in thousands:


	Description		At			Quoted			Significant			Significant
			December 31,			Prices in			Observable			Unobservable
			2013			Active			Inputs			Inputs
						Markets			(Level 2)			(Level 3)
						(Level 1)
	Cash equivalents		$	32,571		$	32,571		$	—		$	—
	Marketable securities (fixed income):
	Corporate notes			228,462			—			228,462			—
	U.S. Government obligations			56,863			—			56,863			—
	Commercial paper			11,978			—			11,978			—
	Marketable securities (Regulus equity holdings)			45,452			45,452			—			—

	Total		$	375,326		$	78,023		$	297,303		$	—



	Description		At			Quoted			Significant			Significant
			December 31,			Prices in			Observable			Unobservable
			2012			Active			Inputs			Inputs
						Markets			(Level 2)			(Level 3)
						(Level 1)
	Cash equivalents		$	50,213		$	50,213		$	—		$	—
	Marketable securities (fixed income):
	Corporate notes			91,523			—			91,523			—
	U.S. Government obligations			60,661			—			60,661			—
	Commercial paper			22,639			—			22,639			—
	Marketable securities (Regulus equity holdings)			38,748			—			38,748			—

	Total		$	263,784		$	50,213		$	213,571		$	—

Summary of Fair Value Accumulated Other Comprehensive Income and Intraperiod Tax Allocation in Available-for-Sale Marketable Securities	'
	The following tables summarize the fair value, accumulated other comprehensive income and intraperiod tax allocation regarding the Company’s investment in Regulus available-for-sale marketable securities at December 31, 2013 and 2012, and for the activity recorded in the year, in thousands:


	Description		At			During Twelve			Balance at
			December 31,			Months Ended			December 31,
			2012			December 31,			2013
						2013
	Carrying value		$	12,449		$	—		$	12,449
	Accumulated other comprehensive income, before tax			26,299			6,704			33,003

	Investment in equity securities of Regulus Therapeutics Inc., as reported		$	38,748		$	6,704		$	45,452

	Accumulated other comprehensive income, before tax		$	26,299		$	6,704		$	33,003
	Intraperiod tax allocation recorded as a benefit from income taxes			(10,572	)		(2,695	)		(13,267	)

	Accumulated other comprehensive income, net of tax		$	15,727		$	4,009		$	19,736

Summary of Company's Marketable Securities	'
	The following tables summarize the Company’s marketable securities, other than its holdings in Regulus noted above, at December 31, 2013 and 2012, in thousands:


			December 31, 2013
			Amortized			Gross			Gross			Fair Value
			Cost			Unrealized			Unrealized
						Gains			Losses
	Commercial paper (Due within 1 year)		$	11,983		$	—		$	(5	)	$	11,978
	Corporate notes (Due within 1 year)			154,175			33			(46	)		154,162
	Corporate notes (Due after 1 year through 2 years)			74,312			23			(35	)		74,300
	U.S. Government obligations (Due within 1 year)			26,553			8			—			26,561
	U.S. Government obligations (Due after 1 year through 2 years)			30,300			2			—			30,302

	Total		$	297,323		$	66		$	(86	)	$	297,303

			December 31, 2012
			Amortized			Gross			Gross			Fair Value
			Cost			Unrealized			Unrealized
						Gains			Losses
	Commercial paper (Due within 1 year)		$	22,650		$	1		$	(12	)	$	22,639
	Corporate notes (Due within 1 year)			41,249			23			(4	)		41,268
	Corporate notes (Due after 1 year through 2 years)			50,322			5			(72	)		50,255
	U.S. Government obligations (Due within 1 year)			7,500			—			—			7,500
	U.S. Government obligations (Due after 1 year through 2 years)			53,168			2			(9	)		53,161

	Total		$	174,889		$	31		$	(97	)	$	174,823

Common Shares Excluded from the Calculation of Net Loss Per Common Share	'
	The following table sets forth for the periods presented the potential common shares (prior to consideration of the treasury stock method) excluded from the calculation of net loss per common share because their inclusion would be anti-dilutive, in thousands:


			December 31,
			2013			2012			2011
	Options to purchase common stock			8,713			8,932			9,779
	Unvested restricted common stock			500			604			312

				9,213			9,536			10,091

Significant_Agreements_Tables

Significant Agreements (Tables)	12 Months Ended
Significant Agreements (Tables)	Dec. 31, 2013
Revenue from Collaborators	'
	The following table summarizes the Company’s total consolidated net revenues from collaborators, for the periods indicated, in thousands:

		Year Ended December 31,
		2013		2012		2011
	Takeda	$	21,973	$	21,973	$	22,248
	Cubist		9,721		2,777		2,467
	Monsanto		5,640		1,954		—
	MDCO		4,604		—		—
	Roche/Arrowhead		—		37,318		55,978
	Other		5,229		2,703		2,064

	Total net revenues from collaborators	$	47,167	$	66,725	$	82,757

Property_and_Equipment_Net_Tab

Property and Equipment, Net (Tables)	12 Months Ended
Property and Equipment, Net (Tables)	Dec. 31, 2013
Property Plant and Equipment	'
	Property and equipment consist of the following at December 31, 2013 and 2012, in thousands:


					December 31,
			Useful Life		2013			2012
	Laboratory equipment			5 years	$	22,729		$	21,201
	Computer equipment and software			3 years		4,261			4,203
	Furniture and fixtures			5 years		1,793			1,793
	Leasehold improvements			*		28,953			19,862
	Construction in progress			—		28			8,209

						57,764			55,268
	Less: accumulated depreciation					(41,316	)		(35,469	)

					$	16,448		$	19,799


	*	Shorter of asset life or lease term

2012_Restructuring_Tables

2012 Restructuring (Tables)

12 Months Ended

Dec. 31, 2013

Restructuring Activities

The following table summarizes the components of the Company’s restructuring expenses recorded in operating expenses and in current liabilities, in thousands:

Original

(Reversals) or

Amounts Paid

Amounts

Charges

Adjustments to

Through

Accrued at

and Amounts

Charges

December 31,

Accrued

2013

Employee severance, benefits and related costs

3,909

(179

)

3,730

—

Commitments_and_Contingencies_

Commitments and Contingencies (Tables)	12 Months Ended
Commitments and Contingencies (Tables)	Dec. 31, 2013
Fixed Cancelable Payments under Existing License Agreements	'
	At December 31, 2013, the Company was committed to make the following fixed, estimated and cancelable payments under existing license agreements, in thousands:


	Year Ending December 31,
	2014	$	7,533
	2015		694
	2016		649
	2017		669
	2018		729
	Thereafter		7,196

	Total	$	17,470

Future Minimum Lease Payments under Non-Cancelable Lease	'
	Future minimum payments under the Company’s non-cancelable leases are approximately as follows, in thousands:


	Year Ending December 31,
	2014	$	6,303
	2015		6,550
	2016		5,192
	2017		364
	2018		—

	Total	$	18,409

Stock_Incentive_Plans_Tables

Stock Incentive Plans (Tables)	12 Months Ended
Stock Incentive Plans (Tables)	Dec. 31, 2013
Valuation Assumptions for Stock Options	'

		2013			2012			2011
	Risk-free interest rate		1.0-2.0	%		0.8-1.0	%		1.2-2.6	%
	Expected dividend yield		—			—			—
	Expected option life		5.6 years			5.6-5.9 years			5.8-5.9 years
	Expected volatility		55-56	%		57	%		55-57	%
Stock Option Activity	'
	The following table summarizes the activity of the Company’s stock option plans:


		Number of			Weighted			Weighted			Aggregate
		Options			Average			Average			Intrinsic
					Exercise			Remaining			Value
					Price			Contractual			(in thousands)
								Term (in years)
	Outstanding, December 31, 2012		8,931,583		$	15.71
	Granted		1,849,104		$	54.23
	Exercised		(2,031,916	)	$	13.96
	Cancelled		(35,376	)	$	21.56

	Outstanding, December 31, 2013		8,713,395		$	24.26			6.5		$	348,864

	Exercisable at December 31, 2013		5,324,421		$	18.21			5		$	245,378
	Vested or expected to vest at December 31, 2013		7,650,775		$	20.06			6.1		$	338,514
Restricted Stock Awards Activity	'
	The following table summarizes the activity of the Company’s restricted stock awards:


		Number of			Weighted
		Awards			Average
					Grant Date
					Fair Value
	Unvested at December 31, 2012		603,760		$	9.37
	Granted		1,966		$	61.03
	Vested		(105,093	)	$	10.58
	Forfeited		(1,121	)	$	10.23

	Unvested at December 31, 2013		499,512		$	10.69

Income_Taxes_Tables

Income Taxes (Tables)	12 Months Ended
Income Taxes (Tables)	Dec. 31, 2013
Components of Loss before Income Tax, Domestic and Foreign	'
	The domestic and foreign components of loss before income taxes are as follows, in thousands:


		2013			2012			2011
	Domestic	$	(81,109	)	$	(116,400	)	$	(57,481	)
	Foreign		(10,811	)		(186	)		(168	)

	Loss before income taxes	$	(91,920	)	$	(116,586	)	$	(57,649	)

Schedule of Deferred Tax Assets and Liabilities	'
	Components of the net deferred tax (liability) asset at December 31, 2013 and 2012 are as follows, in thousands:


		2013			2012
	Deferred tax assets:
	Net operating loss carryforwards	$	124,797		$	102,819
	Research and development credits		23,902			17,443
	AMT credits		788			788
	Foreign tax credits		3,196			3,196
	Capitalized research and development and start-up costs		16,214			16,102
	Deferred revenue		37,273			30,776
	Deferred compensation		21,706			24,804
	Intangible assets		2,210			2,540
	Partnership interest		689			7,118
	Other		4,885			4,173

	Total deferred tax assets		235,660			209,759
	Deferred tax liabilities:
	Intangible assets		(7	)		(38	)
	Unrealized gain on available-for-sale securities		(13,267	)		(10,572	)
	Gain on issuance of stock by Regulus		—			(6,466	)
	Deferred tax asset valuation allowance		(222,393	)		(192,721	)

	Net deferred tax liability	$	(7	)	$	(38	)

Benefit for Income Taxes	'
	The benefit from income taxes for the years ended December 31, 2013, 2012 and 2011 are as follows, in thousands:


		2013			2012			2011
	U.S.:
	Current	$	34		$	52		$	52
	Deferred		(2,695	)		(10,572	)		—

	Total U.S.		(2,661	)		(10,520	)		52

	Foreign:
	Current		—			—			—
	Deferred		(34	)		(52	)		(52	)

	Total Foreign		(34	)		(52	)		(52	)

	Benefit from income taxes	$	(2,695	)	$	(10,572	)	$	—

Effective Income Tax Rate	'
	The Company’s effective income tax rate differs from the statutory federal income tax rate as follows for the years ended December 31, 2013, 2012 and 2011:


		2013			2012			2011
	At U.S. federal statutory rate		35	%		35	%		35	%
	State taxes, net of federal effect		4.3			4.9			4.6
	Stock compensation		0.8			(0.7	)		(3.3	)
	Tax credits		8.5			4.2			3.7
	Orphan drug credit addback		(2.7	)		—			—
	Other permanent items		(0.3	)		(1.6	)		(0.2	)
	Foreign rate differential		(4.1	)		(0.1	)		(0.1	)
	Valuation allowance		(38.5	)		(32.6	)		(39.7	)

	Effective income tax rate		3	%		9.1	%		—	%

Reconciliation of Unrecognized Tax Benefits	'
	A reconciliation of the beginning and ending amount of unrecognized tax benefits is as follows, in thousands:


	Balance at December 31, 2011	$	128
	Subtractions for tax positions related to the prior years		(128	)

	Balance at December 31, 2012		—
	Subtractions for tax positions related to the prior years		—

	Balance at December 31, 2013	$	—

Regulus_Tables

Regulus (Tables)	12 Months Ended
Regulus (Tables)	Dec. 31, 2013
Summary Results of Regulus' Operation	'
	Summary results of Regulus’ statements of comprehensive loss for the nine months ended September 30, 2012 and the year ended December 31, 2011 are presented in the tables below, in thousands:


		Nine months ended			Year ended
		September 30,			December 31,
		2012			2011
	Statements of Comprehensive Loss Data:
	Net revenues	$	9,462		$	13,789
	Operating expenses		17,733			20,926

	Loss from operations		(8,271	)		(7,137	)
	Other (expense) income		(2,289	)		(259	)
	Income tax benefit (expense)		28			(206	)

	Net loss	$	(10,532	)	$	(7,602	)

Quarterly_Financial_Data_Table

Quarterly Financial Data (Tables)	12 Months Ended
Quarterly Financial Data (Tables)	Dec. 31, 2013
Schedule of Quarterly Financial Information	'
	The following information has been derived from unaudited consolidated financial statements that, in the opinion of management, include all recurring adjustments necessary for a fair statement of such information.


		Three Months Ended
		March 31,			June 30,			September 30,			December 31,
		2013			2013			2013			2013
		(In thousands, except per share data)
	Revenues	$	18,642		$	8,687		$	8,991		$	10,847
	Operating expenses		28,446			29,999			41,225			40,439
	Net loss		(9,013	)		(18,169	)		(29,686	)		(32,357	)
	Net loss per common share — basic and diluted	$	(0.15	)	$	(0.29	)	$	(0.48	)	$	(0.51	)
	Weighted average common shares — basic and diluted		59,173			61,661			62,416			62,909


		Three Months Ended
		March 31,			June 30,			September 30,			December 31,
		2012			2012			2012			2012
		(In thousands, except per share data)
	Revenues	$	20,587		$	20,884		$	16,759		$	8,495
	Operating expenses		31,480			32,951			34,906			96,844
	Net loss		(11,368	)		(12,956	)		(19,502	)		(62,188	)
	Net loss per common share — basic and diluted	$	(0.25	)	$	(0.25	)	$	(0.38	)	$	(1.20	)
	Weighted average common shares — basic and diluted		46,210			51,280			51,542			51,821

Customers_that_Represent_Great

Customers that Represent Greater than Ten Percent of Net Revenues from Research Collaborators (Detail) (Revenue from Rights Concentration Risk)	12 Months Ended
	Dec. 31, 2013		Dec. 31, 2012		Dec. 31, 2011
Takeda	'		'		'
Concentration Risk [Line Items]	'		'		'
Concentration risk percentage	47.00%		33.00%		27.00%
Cubist	'		'		'
Concentration Risk [Line Items]	'		'		'
Concentration risk percentage	21.00%		'	[1]	'	[1]
Monsanto	'		'		'
Concentration Risk [Line Items]	'		'		'
Concentration risk percentage	12.00%		'	[1]	'	[1]
Roche/Arrowhead	'		'		'
Concentration Risk [Line Items]	'		'		'
Concentration risk percentage	'	[1]	56.00%		68.00%

[1]	Represents 10% or less

Customers_that_Represent_Great1

Customers that Represent Greater than Ten Percent of Billed and Unbilled Collaboration Receivables (Detail) (Accounts Receivable)	12 Months Ended
	Dec. 31, 2013		Dec. 31, 2012
Genzyme	'		'
Concentration Risk [Line Items]	'		'
Concentration risk percentage	94.00%		'	[1]
Government contract	'		'
Concentration Risk [Line Items]	'		'
Concentration risk percentage	'	[1]	100.00%

[1]	Represents 10% or less

Fair_Value_Measured_on_Recurri

Fair Value Measured on Recurring Basis (Detail) (Recurring, USD $)	Dec. 31, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]	'	'
Cash equivalents	$32,571	$50,213
Total	375,326	263,784
Corporate notes	'	'
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]	'	'
Available for sale securities, Fair value disclosure	228,462	91,523
U.S. Government obligations	'	'
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]	'	'
Available for sale securities, Fair value disclosure	56,863	60,661
Commercial paper	'	'
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]	'	'
Available for sale securities, Fair value disclosure	11,978	22,639
Equity Securities	'	'
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]	'	'
Available for sale securities, Fair value disclosure	45,452	38,748
Quoted Prices in Active Markets (Level 1)	'	'
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]	'	'
Cash equivalents	32,571	50,213
Total	78,023	50,213
Quoted Prices in Active Markets (Level 1) \| Equity Securities	'	'
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]	'	'
Available for sale securities, Fair value disclosure	45,452	'
Significant Observable Inputs (Level 2)	'	'
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]	'	'
Total	297,303	213,571
Significant Observable Inputs (Level 2) \| Corporate notes	'	'
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]	'	'
Available for sale securities, Fair value disclosure	228,462	91,523
Significant Observable Inputs (Level 2) \| U.S. Government obligations	'	'
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]	'	'
Available for sale securities, Fair value disclosure	56,863	60,661
Significant Observable Inputs (Level 2) \| Commercial paper	'	'
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]	'	'
Available for sale securities, Fair value disclosure	11,978	22,639
Significant Observable Inputs (Level 2) \| Equity Securities	'	'
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]	'	'
Available for sale securities, Fair value disclosure	'	$38,748

Summary_of_Significant_Account3

Summary of Significant Accounting Policies - Additional Information (Detail) (USD $)	12 Months Ended				12 Months Ended
	Dec. 31, 2013	Dec. 31, 2011	Dec. 31, 2012	Jan. 10, 2014	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
	Segment			Subsequent Event	Research and Development Expense	Research and Development Expense	Research and Development Expense
				Sirna Therapeutics
Significant Accounting Policies [Line Items]	'	'	'	'	'	'	'
Marketable securities transferred from Level 2 to Level 1	$45,500,000	'	$0	'	'	'	'
Other than temporary impairment on equity securities	'	595,000	'	'	'	'	'
Marketable securities classified as cash equivalents, original maturity	'90 days	'	'	'	'	'	'
Policy for marketable securities	'90 days	'	'	'	'	'	'
Deferred revenue	32,696,000	'	31,417,000	'	'	'	'
Deferred revenue, net of current portion	93,394,000	'	100,874,000	'	'	'	'
License fee	'	'	'	'	$8,000,000	$5,700,000	$1,400,000
Number of operating segments	1	'	'	'	'	'	'
Common stock, par value	$0.01	'	$0.01	$0.01	'	'	'

Summary_of_Fair_Value_Accumula

Summary of Fair Value Accumulated Other Comprehensive Income and Intraperiod Tax Allocation in Available-for-Sale Marketable Securities (Detail) (USD $)	3 Months Ended	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2012	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Schedule of Available-for-sale Securities [Line Items]	'	'	'	'
Investment in equity securities of Regulus Therapeutics Inc., as reported	$38,748	$45,452	$38,748	'
Intraperiod tax allocation recorded as a benefit from income taxes	-10,572	-13,267	-10,572	'
Accumulated other comprehensive income, net of tax	15,727	'	15,727	'
Intraperiod tax allocation recorded as a benefit from income taxes	-10,572	'	-10,572	'
Accumulated other comprehensive income, net of tax	'	4,055	15,827	-879
Regulus Therapeutics Inc	'	'	'	'
Schedule of Available-for-sale Securities [Line Items]	'	'	'	'
Carrying value	12,449	12,449	12,449	'
Accumulated other comprehensive income, before tax	26,299	33,003	26,299	'
Investment in equity securities of Regulus Therapeutics Inc., as reported	38,748	45,452	38,748	'
Accumulated other comprehensive income, before tax	26,299	33,003	26,299	'
Intraperiod tax allocation recorded as a benefit from income taxes	-10,572	-13,267	-10,572	'
Accumulated other comprehensive income, net of tax	15,727	19,736	15,727	'
Accumulated other comprehensive income, before tax	'	6,704	'	'
Investment in equity securities of Regulus Therapeutics Inc., as reported	'	6,704	'	'
Accumulated other comprehensive income, before tax	'	6,704	'	'
Intraperiod tax allocation recorded as a benefit from income taxes	'	-2,695	'	'
Accumulated other comprehensive income, net of tax	'	$4,009	'	'

Summary_of_Companys_Marketable

Summary of Company's Marketable Securities (Detail) (USD $)	Dec. 31, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012
Schedule of Available-for-sale Securities [Line Items]	'	'
Amortized Cost	$297,323	$174,889
Gross Unrealized Gains	66	31
Gross Unrealized Losses	-86	-97
Fair Value	297,303	174,823
Commercial paper (Due within 1 year)	'	'
Schedule of Available-for-sale Securities [Line Items]	'	'
Amortized Cost	11,983	22,650
Gross Unrealized Gains	'	1
Gross Unrealized Losses	-5	-12
Fair Value	11,978	22,639
Corporate notes (Due within 1 year)	'	'
Schedule of Available-for-sale Securities [Line Items]	'	'
Amortized Cost	154,175	41,249
Gross Unrealized Gains	33	23
Gross Unrealized Losses	-46	-4
Fair Value	154,162	41,268
Corporate notes (Due after 1 year through 2 years)	'	'
Schedule of Available-for-sale Securities [Line Items]	'	'
Amortized Cost	74,312	50,322
Gross Unrealized Gains	23	5
Gross Unrealized Losses	-35	-72
Fair Value	74,300	50,255
U.S. Government obligations (Due within 1 year)	'	'
Schedule of Available-for-sale Securities [Line Items]	'	'
Amortized Cost	26,553	7,500
Gross Unrealized Gains	8	'
Fair Value	26,561	7,500
U.S. Government obligations (Due after 1 year through 2 years)	'	'
Schedule of Available-for-sale Securities [Line Items]	'	'
Amortized Cost	30,300	53,168
Gross Unrealized Gains	2	2
Gross Unrealized Losses	'	-9
Fair Value	$30,302	$53,161

Potential_Common_Shares_Common

Potential Common Shares Common Shares Excluded from Calculation of Net Loss Per Common Share (Detail)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'	'
Anti-dilutive securities excluded from computation of earnings	9,213	9,536	10,091
Options to Purchase Common Stock	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'	'
Anti-dilutive securities excluded from computation of earnings	8,713	8,932	9,779
Unvested Restricted Common Stock	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'	'
Anti-dilutive securities excluded from computation of earnings	500	604	312

Revenue_from_Collaborators_Det

Revenue from Collaborators (Detail) (USD $)	3 Months Ended								12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Sep. 30, 2013	Jun. 30, 2013	Mar. 31, 2013	Dec. 31, 2012	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'	'	'	'	'	'	'	'
Total net revenues from collaborators	$10,847	$8,991	$8,687	$18,642	$8,495	$16,759	$20,884	$20,587	$47,167	$66,725	$82,757
Takeda	'	'	'	'	'	'	'	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'	'	'	'	'	'	'	'
Total net revenues from collaborators	'	'	'	'	'	'	'	'	21,973	21,973	22,248
Cubist	'	'	'	'	'	'	'	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'	'	'	'	'	'	'	'
Total net revenues from collaborators	'	'	'	'	'	'	'	'	9,721	2,777	2,467
Monsanto	'	'	'	'	'	'	'	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'	'	'	'	'	'	'	'
Total net revenues from collaborators	'	'	'	'	'	'	'	'	5,640	1,954	'
MDCO	'	'	'	'	'	'	'	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'	'	'	'	'	'	'	'
Total net revenues from collaborators	'	'	'	'	'	'	'	'	4,604	'	'
Roche/Arrowhead	'	'	'	'	'	'	'	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'	'	'	'	'	'	'	'
Total net revenues from collaborators	'	'	'	'	'	'	'	'	'	37,318	55,978
Other	'	'	'	'	'	'	'	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'	'	'	'	'	'	'	'
Total net revenues from collaborators	'	'	'	'	'	'	'	'	$5,229	$2,703	$2,064

Significant_Agreements_Additio

Significant Agreements - Additional Information (Detail) (USD $)

12 Months Ended

6 Months Ended

1 Months Ended

3 Months Ended

1 Months Ended

12 Months Ended

1 Months Ended

12 Months Ended

1 Months Ended

12 Months Ended

1 Months Ended

6 Months Ended

12 Months Ended

6 Months Ended

12 Months Ended

1 Months Ended

12 Months Ended

1 Months Ended

In Millions, unless otherwise specified

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Dec. 31, 2013

Jul. 31, 2007

Oct. 31, 2012

Dec. 31, 2013

Feb. 28, 2013

Dec. 31, 2013

Jan. 31, 2009

Dec. 31, 2013

Aug. 31, 2013

Dec. 31, 2012

Aug. 31, 2012

Dec. 31, 2013

Mar. 31, 2011

Mar. 31, 2010

Oct. 31, 2008

Jun. 30, 2008

Dec. 31, 2013

Jul. 31, 2007

Dec. 31, 2013

Mar. 31, 2004

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Mar. 31, 2004

Research and Development Expense

Minimum

Maximum

Cubist Alliance

Roche/Arrowhead

Product Alliances

Platform Alliances

Discovery and Development Alliances

Genzyme

MDCO

Cubist Alliance

Joint Technology Transfer Committee

Joint Delivery Collaboration Committee

Cubist Alliance

Monsanto Alliance

Takeda

Roche/Arrowhead

Arrowhead

Isis

Phase Two Clinical Trial ALN-TTR

Phase Three Clinical Trial

Loss Of Patent Rights

Alnylam Europe Purchase Agreement

Common Stock Purchase Agreement

Research and Development Expense

Up Front Payment

Milestone Payments

Research and Development Expense

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

Upfront fee received

$20

$273.50

$22.50

$25

$20

$29.20

$100

$0.50

Next potential milestone payment

2.5

Deferred revenue

33.5

20.5

29.2

25.6

30.8

Maximum number of potential future milestones

180

171

100

Potential future payment for the achievement of specified development milestones

17.5

Potential future payment for the achievement of specified regulatory milestones

62.5

Potential future payment for the achievement of specified commercialization milestones

100

105

Revenue recognizing period

'5 years

Percentage of sharing in development cost

50.00%

Life of development and manufacturing services

'8 years

Upfront payment recognition period

'8 years

Revenue recognized upon termination of collaboration

9.7

Period of exclusivity in the collaboration

'10 years

Milestone payment earned

1.5

Estimated range of expiration for fundamental patents

'2016

'2025

Period for services under contract

'5 years

Future payment of liquidated damages

Milestones considered probable at inception of collaborations

2.5

Granted period of royalty bearing license

'5 years

Aggregate upfront and near term payments

331

150

Profit sharing agreement ratio

50.00%

Number of licensed products

Additional number of licensed products

Milestone fees to company upon achievement of specified technology transfer milestones

Payments for additional therapeutic areas

License and collaborations agreements, prior written notice period before termination

'180 days

Maximum life of collaboration committee

'7 years

Number of therapeutic areas

License and collaborations agreements, expiration period

'10 years

Upfront fees relating to purchase agreements

42.5

Deferred revenue determined at contract execution

278.2

License fee

5.7

1.4

0.7

2.5

3.4

Potential future payment upon the occurrence of achievement of specified development and regulatory milestones

$3.40

Property_Plant_and_Equipment_D

Property Plant and Equipment (Detail) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013		Dec. 31, 2012
Property, Plant and Equipment [Line Items]	'		'
Furniture and fixtures	$1,793		$1,793
Leasehold improvements	28,953		19,862
Construction in progress	28		8,209
Property Plant And Equipment Gross	57,764		55,268
Less: accumulated depreciation	-41,316		-35,469
Property Plant And Equipment Net	16,448		19,799
Laboratory equipment	'		'
Property, Plant and Equipment [Line Items]	'		'
Property, and equipment, useful life	'5 years		'
Property and equipment other, gross	22,729		21,201
Computer equipment and software	'		'
Property, Plant and Equipment [Line Items]	'		'
Property, and equipment, useful life	'3 years		'
Property and equipment other, gross	$4,261		$4,203
Furniture and Fixtures	'		'
Property, Plant and Equipment [Line Items]	'		'
Property, and equipment, useful life	'5 years		'
Leasehold improvements	'		'
Property, Plant and Equipment [Line Items]	'		'
Property, and equipment, useful life	'	[1]	'
Construction in progress	'		'
Property, Plant and Equipment [Line Items]	'		'
Property, and equipment, useful life	'		'

[1]	Shorter of asset life or lease term

Property_and_Equipment_Net_Add

Property and Equipment Net- Additional Information (Detail) (USD $)	12 Months Ended
In Millions, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Property, Plant and Equipment [Line Items]	'	'	'
Depreciation expense	$6.10	$4.60	$5

Two_Thousand_Twelve_Restructur

Two Thousand Twelve Restructuring - Additional Information (Detail) (USD $)	1 Months Ended	3 Months Ended
In Millions, unless otherwise specified	Jan. 31, 2012	Mar. 31, 2012
	Employee	Mar. 31, 2012
Restructuring Cost and Reserve [Line Items]	'	'
Percentage of workforce reduced by company	33.00%	'
Number of employees remaining	115	'
Restructuring-related costs	'	$3.90

Restructuring_Activities_Detai

Restructuring Activities (Detail) (USD $)	3 Months Ended	12 Months Ended
In Thousands, unless otherwise specified	Mar. 31, 2012	Dec. 31, 2013
		Current liabilities
		Employee severance, benefits and related costs
Restructuring Cost and Reserve [Line Items]	'	'
Original Charges and Amounts Accrued	$3,900	$3,909
(Reversals) or Adjustments to Charges	'	-179
Amounts Paid Through December 31, 2013	'	3,730
Amounts Accrued at December 31, 2013	'	'

Commitments_and_Contingencies_1

Commitments and Contingencies - Additional Information (Detail) (USD $)

3 Months Ended

12 Months Ended

3 Months Ended

12 Months Ended

Dec. 31, 2013

Sep. 30, 2013

Jun. 30, 2013

Mar. 31, 2013

Dec. 31, 2012

Sep. 30, 2012

Jun. 30, 2012

Mar. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2008

sqft

Tekmira Restructured Cross-License Agreement

Tekmira Restructured Cross-License Manufacturing Contracts and Service Agreement

Tekmira Restructured Cross-License Buy-Down

Sanofi

Third Party

Bmr Fresh Pond Research Park Llc

Third Street Lease

sqft

Loss Contingencies [Line Items]

Future purchase commitments

$62,700,000

Future purchase commitments expected to be incurred in 2014

33,600,000

Future purchase commitments expected to be incurred past 2014

29,100,000

Area of office and laboratory space held under operating lease

129,000

15,000

Lease expiration date

'2016-09

Number 0f lease extension options

Lease extension period

'5 years

Area of premises subleased

34,014

18,000

Lease expiration date

30-Sep-16

31-Aug-17

Lease incentive received

200,000

1,800,000

7,300,000

Rent expense

4,900,000

6,400,000

6,500,000

Operating expenses

40,439,000

41,225,000

29,999,000

28,446,000

96,844,000

34,906,000

32,951,000

31,480,000

140,109,000

196,181,000

137,575,000

65,000,000

One time settlement payment

65,000,000

30,000,000

35,000,000

Contingent milestone payments

10,000,000

Future milestone payments

5,000,000

Milestone paid

$5,000,000

Future_Fixed_Cancelable_Paymen

Future Fixed Cancelable Payments under Existing License Agreements (Detail) (USD $)	Dec. 31, 2013
In Thousands, unless otherwise specified	Dec. 31, 2013
Licenses Agreements [Line Items]	'
2014	$7,533
2015	694
2016	649
2017	669
2018	729
Thereafter	7,196
Total	$17,470

Future_Minimum_Lease_Payments_

Future Minimum Lease Payments under Non-Cancelable Lease (Detail) (USD $)	Dec. 31, 2013
In Thousands, unless otherwise specified	Dec. 31, 2013
Schedule of Operating Leases [Line Items]	'
2014	$6,303
2015	6,550
2016	5,192
2017	364
2018	'
Total	$18,409

Stockholders_Equity_Additional

Stockholders Equity - Additional Information (Detail) (USD $)	1 Months Ended		12 Months Ended		1 Months Ended
	Jan. 31, 2013	Feb. 29, 2012	Dec. 31, 2013	Dec. 31, 2012	Jul. 31, 2005	Jul. 13, 2005
	Jan. 31, 2013	Feb. 29, 2012	Dec. 31, 2013	Dec. 31, 2012	Rights	Rights
Stockholders Equity [Line Items]	'	'	'	'	'	'
Preferred stock, shares authorized	'	'	5,000,000	5,000,000	'	'
Preferred stock, par value	'	'	$0.01	$0.01	'	'
Preferred stock, shares outstanding	'	'	'	'	'	'
Right to buy Series A Junior Preferred stock declared as dividend	'	'	'	'	'	0.001
Date on which rights expire	'	'	'	'	'	13-Jul-15
Acquisition of outstanding common stock that trigger exercise of right	'	'	'	'	50.00%	'
Tender or exchange offer for outstanding common stock that trigger exercise of right	'	'	'	'	20.00%	'
Cash purchase price of Series A Junior Preferred stock	'	'	'	'	'	80
Common stocks issued through underwritten public offering	9,200,000	8,625,000	'	'	'	'
Underwritten public offering amount per share	$20.13	$10.75	'	'	'	'
Net proceeds from public issue, after deducting expenses	$173,600,000	$86,800,000	$173,572,000	$86,800,000	'	'
Underwriting discounts and commissions and other estimated offering expenses	$11,600,000	$5,900,000	'	'	'	'

Stock_Incentive_Plans_Addition

Stock Incentive Plans - Additional Information (Detail) (USD $)

12 Months Ended

1 Months Ended

12 Months Ended

1 Months Ended

12 Months Ended

1 Months Ended

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Dec. 31, 2013

Jun. 30, 2009

Jun. 30, 2013

Jun. 30, 2009

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Jun. 30, 2010

Dec. 31, 2004

Oct. 31, 2010

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Jan. 31, 2012

31-May-11

Dec. 31, 2013

Employee Stock Option

Additional Equity Awards

Stock Incentive Plan 2009

Employee Stock Option And Employee Stock Purchase Plan

Employee Stock Purchase Plan

Unvested Restricted Common Stock

Performance Based Restricted Stock Awards

Stock Incentive Plan 2004

Board of Directors

Chairperson of Audit Committee

Chairperson of Science and Technology Committee

Current Employees

Initial Appointment

On Date Of Annual Meeting Of Shareholders

Stock Options Additional Annual Grant

Share-based Compensation Arrangement by Share-based Payment Award [Line Items]

Stock awards, shares authorized

2,200,000

5,900,000

715,789

315,789

12,366,485

Stock incentive plan, shares authorized for non-employee directors

30,000

15,000

10,000

15,000

Stock incentive plan, non-employee directors required service period

'6 months

Stock incentive plan, non-employee directors award vest on each anniversary of grant date

33.33%

Stock incentive plan, shares available for future grant

11,369,175

8,713,395

2,426,811

228,969

Equity awards, term

'10 years

'5 years

Option vesting percentage on the first anniversary of grant date

25.00%

Option vesting percentage at the end of each successive three-month period

6.25%

Stock-based compensation expense

$20,703,000

$12,360,000

$16,676,000

$14,100,000

$9,000,000

$14,800,000

$300,000

$200,000

$300,000

Non-employee stock-based compensation expenses

3,200,000

1,000,000

400,000

Equity awards granted

113,370

1,966

508,928

229,806

Fair value of equity awards granted

1,400,000

5,300,000

2,300,000

Stock awards vesting period

'3 years

'2 years

Restricted stock expense

3,400,000

2,400,000

1,500,000

Expected annual forfeiture rate

8.20%

Unearned compensation expense related to stock options

31,800,000

Weighted-average recognition period

'3 years

'1 month

Weighted average fair value of stock options granted

$26.33

$8.68

$7.68

Aggregate intrinsic value of stock option exercised

57,900,000

4,800,000

40,000

Total grant date fair value of restricted stock awards vested during period

1,100,000

1,500,000

500,000

Unrecognized compensation expense related to non-vested award

$300,000

Employee stock purchase plan, offering period

'6 months

Employee stock purchase plan, purchase price as a percentage of common stock closing price

85.00%

Employee stock purchase plan, shares issued

45,141

73,590

79,038

Weighted average fair value awards granted

$11.49

$2.82

$3.46

$61.03

Weighted-average stock-price volatility

57.00%

55.00%

Expected option life

'5 years 7 months 6 days

'6 months

Risk-free interest rate

0.10%

Valuation_Assumptions_for_Stoc

Valuation Assumptions for Stock Options (Detail)	12 Months Ended
Valuation Assumptions for Stock Options (Detail)	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'
Risk-free interest rate, minimum	1.00%	0.80%	1.20%
Risk-free interest rate, maximum	2.00%	1.00%	2.60%
Expected dividend yield	'	'	'
Expected option life	'5 years 7 months 6 days	'	'
Expected volatility	'	57.00%	'
Expected volatility, minimum	55.00%	'	55.00%
Expected volatility, maximum	56.00%	'	57.00%
Minimum	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'
Expected option life	'	'5 years 7 months 6 days	'5 years 9 months 18 days
Maximum	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'
Expected option life	'	'5 years 10 months 24 days	'5 years 10 months 24 days

Stock_Option_Activity_Detail

Stock Option Activity (Detail) (USD $)	12 Months Ended
In Thousands, except Share data, unless otherwise specified	Dec. 31, 2013
Number of Options	'
Outstanding, beginning balance	8,931,583
Granted	1,849,104
Exercised	-2,031,916
Cancelled	-35,376
Outstanding, ending balance	8,713,395
Exercisable at December 31, 2013	5,324,421
Vested or expected to vest at December 31, 2013	7,650,775
Weighted Average Exercise Price	'
Outstanding, beginning balance	$15.71
Granted	$54.23
Exercised	$13.96
Cancelled	$21.56
Outstanding, ending balance	$24.26
Exercisable at December 31, 2013	$18.21
Vested or expected to vest at December 31, 2013	$20.06
Weighted Average Remaining Contractual Term	'
Outstanding, December 31, 2013	'6 years 6 months
Exercisable at December 31, 2013	'5 years
Vested or expected to vest at December 31, 2013	'6 years 1 month 6 days
Aggregate Intrinsic Value	'
Outstanding, December 31, 2013	$348,864
Exercisable at December 31, 2013	245,378
Vested or expected to vest at December 31, 2013	$338,514

Restricted_Stock_Awards_Detail

Restricted Stock Awards (Detail) (Unvested Restricted Common Stock, USD $)	1 Months Ended	12 Months Ended
	Oct. 31, 2010	Dec. 31, 2013
Unvested Restricted Common Stock	'	'
Number of awards	'	'
Unvested at beginning of year	'	603,760
Granted	113,370	1,966
Vested	'	-105,093
Forfeited	'	-1,121
Unvested at end of year	'	499,512
Weighted Average Grant Date Fair Value	'	'
Unvested at beginning of year	'	$9.37
Granted	'	$61.03
Vested	'	$10.58
Forfeited	'	$10.23
Unvested at end of year	'	$10.69

Components_of_Loss_before_Inco

Components of Loss before Income Tax, Domestic and Foreign (Detail) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Schedule of Income Before Income Tax [Line Items]	'	'	'
Domestic	($81,109)	($116,400)	($57,481)
Foreign	-10,811	-186	-168
Loss before income taxes	($91,920)	($116,586)	($57,649)

Deferred_Tax_Assets_and_Liabil

Deferred Tax Assets and Liabilities (Detail) (USD $)	Dec. 31, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012
Deferred tax assets:	'	'
Net operating loss carryforwards	$124,797	$102,819
Research and development credits	23,902	17,443
AMT credits	788	788
Foreign tax credits	3,196	3,196
Capitalized research and development and start-up costs	16,214	16,102
Deferred revenue	37,273	30,776
Deferred compensation	21,706	24,804
Intangible assets	2,210	2,540
Partnership interest	689	7,118
Other	4,885	4,173
Total deferred tax assets	235,660	209,759
Deferred tax liabilities:	'	'
Intangible assets	-7	-38
Unrealized gain on available-for-sale securities	-13,267	-10,572
Gain on issuance of stock by Regulus	'	-6,466
Deferred tax asset valuation allowance	-222,393	-192,721
Net deferred tax liability	($7)	($38)

Provision_for_Income_Taxes_Det

Provision for Income Taxes (Detail) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Schedule Of Income Taxes [Line Items]	'	'	'
Current	$34	$52	$52
Deferred	-2,695	-10,572	'
Total U.S.	-2,661	-10,520	52
Current	'	'	'
Deferred	-34	-52	-52
Total Foreign	-34	-52	-52
Benefit from income taxes	($2,695)	($10,572)	$0

Effective_Income_Tax_Rate_Deta

Effective Income Tax Rate (Detail)	12 Months Ended
Effective Income Tax Rate (Detail)	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Reconciliation of Provision of Income Taxes [Line Items]	'	'	'
At U.S. federal statutory rate	35.00%	35.00%	35.00%
State taxes, net of federal effect	4.30%	4.90%	4.60%
Stock compensation	0.80%	-0.70%	-3.30%
Tax credits	8.50%	4.20%	3.70%
Orphan drug credit addback	-2.70%	'	'
Other permanent items	-0.30%	-1.60%	-0.20%
Foreign rate differential	-4.10%	-0.10%	-0.10%
Valuation allowance	-38.50%	-32.60%	-39.70%
Effective income tax rate	3.00%	9.10%	'

Income_Taxes_Additional_Inform

Income Taxes - Additional Information (Detail) (USD $)	12 Months Ended
Income Taxes - Additional Information (Detail) (USD $)	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Income Taxes [Line Items]	'	'	'
Increase in valuation allowance due to increase in operating losses and tax credit carryforwards	$29,700,000	$38,300,000	$23,000,000
Benefit from (provision for) income taxes	-2,695,000	-10,572,000	0
Net operating loss carryforwards expiration year	'2033	'	'
Research and development tax credit	'	'	'
Income Taxes [Line Items]	'	'	'
Excess tax benefit from exercise of stock options	500,000	'	'
Tax credit carryforwards expiration year	'2033	'	'
Alternative minimum tax	'	'	'
Income Taxes [Line Items]	'	'	'
Tax credit carryforwards	800,000	'	'
Net operating loss carryforwards	'	'	'
Income Taxes [Line Items]	'	'	'
Excess tax benefit from exercise of stock options	26,600,000	'	'
Federal	'	'	'
Income Taxes [Line Items]	'	'	'
Net operating loss carryforward	372,400,000	'	'
Federal \| Research and development tax credit	'	'	'
Income Taxes [Line Items]	'	'	'
Tax credit carryforwards	20,800,000	'	'
State and local jurisdiction	'	'	'
Income Taxes [Line Items]	'	'	'
Net operating loss carryforward	441,600,000	'	'
State and local jurisdiction \| Research and development tax credit	'	'	'
Income Taxes [Line Items]	'	'	'
Tax credit carryforwards	6,800,000	'	'
Foreign tax authority	'	'	'
Income Taxes [Line Items]	'	'	'
Tax credit carryforwards	$3,200,000	'	'
Tax credit carryforwards expiration year	'2017	'	'

Reconciliation_of_Unrecognized

Reconciliation of Unrecognized Tax Benefits (Detail) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012
Schedule of Unrecognized Tax Benefits [Line Items]	'	'
Beginning balance	'	$128
Subtractions for tax positions related to the prior years	'	-128
Ending balance	'	'

Regulus_Additional_Information

Regulus - Additional Information (Detail) (USD $)	1 Months Ended	3 Months Ended	12 Months Ended			12 Months Ended		1 Months Ended
	Mar. 31, 2009	Dec. 31, 2012	Dec. 31, 2012	Dec. 31, 2013	Sep. 30, 2012	Dec. 31, 2013	Dec. 31, 2012	Mar. 31, 2009
	Mar. 31, 2009	Dec. 31, 2012	Dec. 31, 2012	Dec. 31, 2013	Sep. 30, 2012	Regulus Therapeutics Inc	Regulus Therapeutics Inc	Isis
Schedule Of Equity Method Investments Joint Ventures [Line Items]	'	'	'	'	'	'	'	'
Equity method investments	$10,000,000	'	'	'	'	'	'	$10,000,000
Company ownership percentage	'	'	'	'	44.00%	'	'	'
Company ownership percentage	'	17.00%	'	'	'	'	'	'
Investment in equity securities of Regulus Therapeutics Inc	'	38,700,000	38,700,000	'	'	'	0	'
Gain loss on equity investment	'	16,084,000	16,084,000	'	'	'	16,084,000	'
Increase in carrying value	'	'	'	'	'	12,449,000	12,449,000	'
Unrealized gain in other comprehensive income	'	15,727,000	15,727,000	'	'	19,736,000	15,727,000	'
Net of an intraperiod tax benefit	'	-10,572,000	-10,572,000	'	'	-2,695,000	'	'
Prepaid expenses and other current assets	'	$2,641,000	$2,641,000	$3,910,000	'	'	$600,000	'

Summary_Results_of_Regulus_Ope

Summary Results of Regulus Operation (Detail) (USD $)	9 Months Ended	12 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2012	Dec. 31, 2011
Statements of Comprehensive Loss Data:	'	'
Net revenues	$9,462	$13,789
Operating expenses	17,733	20,926
Loss from operations	-8,271	-7,137
Other (expense) income	-2,289	-259
Income tax benefit (expense)	28	-206
Net loss	($10,532)	($7,602)

Quarterly_Financial_Data_Detai

Quarterly Financial Data (Detail) (USD $)	3 Months Ended								12 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Dec. 31, 2013	Sep. 30, 2013	Jun. 30, 2013	Mar. 31, 2013	Dec. 31, 2012	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Quarterly Financial Data [Line Items]	'	'	'	'	'	'	'	'	'	'	'
Revenues	$10,847	$8,991	$8,687	$18,642	$8,495	$16,759	$20,884	$20,587	$47,167	$66,725	$82,757
Operating expenses	40,439	41,225	29,999	28,446	96,844	34,906	32,951	31,480	140,109	196,181	137,575
Net loss	($32,357)	($29,686)	($18,169)	($9,013)	($62,188)	($19,502)	($12,956)	($11,368)	($89,225)	($106,014)	($57,649)
Net loss per common share - basic and diluted	($0.51)	($0.48)	($0.29)	($0.15)	($1.20)	($0.38)	($0.25)	($0.25)	($1.45)	($2.11)	($1.36)
Weighted average common shares - basic and diluted	62,909	62,416	61,661	59,173	51,821	51,542	51,280	46,210	61,551	50,286	42,410

Quarterly_Financial_Data_Addit

Quarterly Financial Data - Additional Information (Detail) (USD $)	3 Months Ended	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2012	Dec. 31, 2012
Quarterly Financial Information [Line Items]	'	'
Increase in operating expenses	$65,000	$65,000
Gain from other income	16,084	16,084
Income tax benefit from initial public offering	($10,572)	($10,572)

Subsequent_Events_Additional_I

Subsequent Events - Additional Information (Detail) (USD $)

Dec. 31, 2013

Dec. 31, 2012

Jan. 11, 2014

Jan. 10, 2014

In Millions, except Share data, unless otherwise specified

Subsequent Event

Genzyme

Sirna Therapeutics

Minimum

Maximum

Phase Three Clinical Trial

Regional and Co-developed/Co-promoted Collaboration Product

Global Collaboration Product

Regional Collaboration Product

Co-developed/ Co-promoted Collaboration Product

Additional

Intellectual Property

Clinical Development and Regulatory Milestone

Commercial Milestones

Subsequent Event [Line Items]

Business acquisition cash consideration

$25

Business acquisition issuable common stock, shares

2,520,044

Common stock, par value

$0.01

Business acquisition issuable common stock

150

Business acquisition consideration upon achievement of milestones

105

Lock up period

'6 months

Subsequent lock up period stock holding percentage

50.00%

Maximum number of potential future milestones

200

Next potential milestone payment

Percentage of sharing in development cost

100.00%

20.00%

50.00%

Number of shares under agreement to sell stock

8,766,338

Stock price under agreement to sell stock

$700

Stock price per share

$0.01

Approximate percentage of ownership interest

12.00%

Agreement to acquire outstanding shares of common stock percentage

5.00%

30.00%

Voting percentage

20.00%

Minimum percentage of ownership interest terminate

7.50%

Percentage of ownership interest

30.00%