Cubist Pharmaceuticals (CBST) Inactive 10-K25 Feb 142013 FY Annual reportFinancial data

Company Profile

Document_and_Entity_Informatio

Document and Entity Information (USD $)	12 Months Ended
In Billions, except Share data, unless otherwise specified	Dec. 31, 2013	Feb. 14, 2014	Jun. 28, 2013
Document and Entity Information	'	'	'
Entity Registrant Name	'CUBIST PHARMACEUTICALS INC	'	'
Entity Central Index Key	'0000912183	'	'
Document Type	'10-K	'	'
Document Period End Date	31-Dec-13	'	'
Amendment Flag	'false	'	'
Current Fiscal Year End Date	'--12-31	'	'
Entity Well-known Seasoned Issuer	'Yes	'	'
Entity Voluntary Filers	'No	'	'
Entity Current Reporting Status	'Yes	'	'
Entity Filer Category	'Large Accelerated Filer	'	'
Entity Public Float	'	'	$3.20
Entity Common Stock, Shares Outstanding	'	74,798,250	'
Document Fiscal Year Focus	'2013	'	'
Document Fiscal Period Focus	'FY	'	'

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	$91,058	$104,041
Short-term investments	487,500	872,188
Accounts receivable, net	123,155	93,467
Inventory	57,663	41,947
Deferred tax assets, net	52,108	14,190
Prepaid expenses and other current assets	58,285	31,217
Total current assets	869,769	1,157,050
Property and equipment, net	177,544	166,465
In-process research and development	896,400	272,700
Goodwill	383,018	114,130
Other intangible assets, net	721,066	152,830
Long-term investments	'	3,167
Other assets	98,024	66,043
Total assets	3,145,821	1,932,385
Current liabilities:	'	'
Accounts payable	31,877	45,603
Accrued liabilities	245,078	163,633
Short-term deferred revenue	6,411	6,784
Short-term contingent consideration	20,428	38,998
Other current liabilities	7,034	3,500
Total current liabilities	310,828	258,518
Long-term deferred revenue	31,010	34,091
Long-term deferred tax liabilities, net	357,802	103,081
Long-term contingent consideration	202,894	150,215
Long-term debt, net	817,830	367,811
Other long-term liabilities	31,726	27,921
Total liabilities	1,752,090	941,637
Commitments and contingencies (Notes C, D, K, M and O)	'	'
Stockholders' equity:	'	'
Preferred stock, non-cumulative; convertible, $.001 par value; authorized 5,000,000 shares; no shares issued and outstanding	'	'
Common stock, $.001 par value; authorized 150,000,000 shares; 74,428,087 and 64,713,695 shares issued and outstanding as of December 31, 2013 and 2012, respectively	74	65
Additional paid-in capital	1,362,240	940,969
Accumulated other comprehensive income (loss)	215	-59
Retained earnings	31,202	49,773
Total stockholders' equity	1,393,731	990,748
Total liabilities and stockholders' equity	$3,145,821	$1,932,385

CONSOLIDATED_BALANCE_SHEETS_Pa

CONSOLIDATED BALANCE SHEETS (Parenthetical) (USD $)	Dec. 31, 2013	Dec. 31, 2012
CONSOLIDATED BALANCE SHEETS	'	'
Preferred stock, non-cumulative; convertible, par value (in dollars per share)	$0.00	$0.00
Preferred stock, non-cumulative; convertible, authorized shares	5,000,000	5,000,000
Preferred stock, non-cumulative; convertible, shares issued	0	0
Preferred stock, non-cumulative; convertible, shares outstanding	0	0
Common stock, par value (in dollars per share)	$0.00	$0.00
Common stock, authorized shares	150,000,000	150,000,000
Common stock, shares issued	74,428,087	64,713,695
Common stock, shares outstanding	74,428,087	64,713,695

CONSOLIDATED_STATEMENTS_OF_INC

CONSOLIDATED STATEMENTS OF INCOME (USD $)	12 Months Ended
In Thousands, except Share data, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Revenues:	'	'	'
U.S. product revenues, net	$971,196	$849,371	$701,367
International product revenues	61,237	50,454	36,658
Service revenues	12,287	23,249	6,725
Other revenues	9,722	3,285	9,222
Total revenues, net	1,054,442	926,359	753,972
Costs and expenses:	'	'	'
Cost of product revenues	260,310	230,057	172,864
Research and development	477,740	277,729	184,533
Impairment charges	55,300	38,700	'
Contingent consideration	-47,577	-29,021	91,537
Selling, general and administrative	257,940	171,788	163,228
Restructuring charges	24,319	'	9,279
Total costs and expenses	1,028,032	689,253	621,441
Operating income	26,410	237,106	132,531
Other income (expense), net:	'	'	'
Interest income	2,438	3,076	2,670
Interest expense	-37,602	-32,991	-31,415
Other income (expense)	-34,890	-7,595	1,003
Total other income (expense), net	-70,054	-37,510	-27,742
(Loss) income before income taxes	-43,644	199,596	104,789
(Benefit) provision for income taxes	-25,073	45,521	71,766
Net (loss) income	($18,571)	$154,075	$33,023
Basic net (loss) income per common share (in dollars per share)	($0.27)	$2.42	$0.54
Diluted net (loss) income per common share (in dollars per share)	($0.27)	$2.10	$0.52
Shares used in calculating:	'	'	'
Basic net (loss) income per common share (in shares)	68,160,798	63,766,209	60,839,128
Diluted net (loss) income per common share (in shares)	68,160,798	81,444,658	62,937,141

CONSOLIDATED_STATEMENTS_OF_COM

CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME	'	'	'
Net (loss) income	($18,571)	$154,075	$33,023
Other comprehensive income (loss):	'	'	'
Unrealized gains (losses) on available-for-sale securities	197	126	-256
Foreign currency translation adjustment	77	'	'
Total other comprehensive income (loss)	274	126	-256
Comprehensive (loss) income	($18,297)	$154,201	$32,767

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) income	($18,571)	$154,075	$33,023
Adjustments to reconcile net (loss) income to net cash provided by operating activities:	'	'	'
Loss on extinguishment of convertible debt, including write-off of debt issuance costs	12,592	4,280	'
Depreciation and amortization	43,194	33,279	12,508
Amortization and accretion of investments	10,748	9,103	7,463
Amortization of debt discount and debt issuance costs, excluding write-off of debt issuance costs	23,381	18,924	20,275
Premium paid for convertible subordinated debt repurchase	'	-39,672	'
Deferred income taxes	-38,984	-32,942	8,717
Stock-based compensation	32,357	25,702	19,368
Contingent consideration	-47,577	-29,021	91,537
Payment of contingent consideration	-24,254	-17,408	-23,209
Impairment charges	55,300	38,700	'
Other non-cash	-2,554	15,304	6,703
Changes in assets and liabilities, net of effects from acquisitions:	'	'	'
Accounts receivable	-19,309	-5,667	-21,970
Inventory	-11,758	-11,531	-9,999
Prepaid expenses and other current assets	-14,964	5,483	-10,536
Other assets	207	3,558	-4,425
Accounts payable and accrued liabilities	17,702	36,764	51,341
Deferred revenue and other liabilities	-1,101	6,719	19,573
Total adjustments	34,980	61,575	167,346
Net cash provided by operating activities	16,409	215,650	200,369
Cash flows from investing activities:	'	'	'
Acquisition of business, net of acquired cash	-1,211,000	'	-200,659
Purchases of property and equipment	-15,509	-18,129	-100,068
Purchases of investments	-980,264	-1,529,281	-1,406,763
Proceeds from maturities of investments	1,439,148	1,314,993	1,267,945
Payment for purchase option	-20,000	'	'
Net cash used in investing activities	-787,625	-232,417	-439,545
Cash flows from financing activities:	'	'	'
Payment of contingent consideration	-15,746	-12,592	-16,791
Issuance of common stock	39,066	36,127	61,555
Excess tax benefit on stock-based awards	17,711	10,787	18,076
Extinguishment of convertible debt	'	-109,218	'
Proceeds from issuance of convertible debt	800,000	'	'
Payment of debt issuance costs	-25,156	-1,914	'
Proceeds from issuance of warrants	121,675	'	'
Purchase of convertible bond hedge	-179,390	'	'
Net cash provided by (used in) financing activities	758,160	-76,810	62,840
Net decrease in cash and cash equivalents	-13,056	-93,577	-176,336
Effect of changes in foreign exchange rates on cash balances	73	'	985
Cash and cash equivalents at beginning of year	104,041	197,618	372,969
Cash and cash equivalents at end of year	91,058	104,041	197,618
Cash paid during the year for:	'	'	'
Interest, net of amounts capitalized	8,485	12,441	11,318
Income taxes	20,350	49,685	41,770
Non-cash investing and financing activities:	'	'	'
Purchases of property and equipment	($5,242)	($4,354)	($919)

CONSOLIDATED_STATEMENTS_OF_CHA

CONSOLIDATED STATEMENTS OF CHANGES IN STOCKHOLDERS' EQUITY (USD $)	Total	Common Stock	Additional Paid-in Capital	Accumulated Other Comprehensive Income (Loss)	(Accumulated Deficit) / Retained Earnings
In Thousands, except Share data, unless otherwise specified	Total	Common Stock	Additional Paid-in Capital	Accumulated Other Comprehensive Income (Loss)	(Accumulated Deficit) / Retained Earnings
Balance at Dec. 31, 2010	$663,423	$59	$800,618	$71	($137,325)
Balance (in shares) at Dec. 31, 2010	'	59,344,957	'	'	'
Changes in Stockholders' Equity	'	'	'	'	'
Comprehensive income (loss)	32,767	'	'	-256	33,023
Exercise of stock options and vesting of restricted stock units	57,591	3	57,588	'	'
Exercise of stock options and vesting of restricted stock units (in shares)	'	2,951,672	'	'	'
Shares issued in connection with employee stock purchase plan and 401(k) plan	8,554	1	8,553	'	'
Shares issued in connection with employee stock purchase plan and 401(k) plan (in shares)	'	340,826	'	'	'
Tax benefit on stock-based awards	18,076	'	18,076	'	'
Stock-based compensation	19,446	'	19,446	'	'
Stock-based compensation (in shares)	'	3,447	'	'	'
Balance at Dec. 31, 2011	799,857	63	904,281	-185	-104,302
Balance (in shares) at Dec. 31, 2011	'	62,640,902	'	'	'
Changes in Stockholders' Equity	'	'	'	'	'
Comprehensive income (loss)	154,201	'	'	126	154,075
Equity component of convertible debt issuance, net of tax and issuance costs	-40,343	'	-40,343	'	'
Exercise of stock options and vesting of restricted stock units	32,526	2	32,524	'	'
Exercise of stock options and vesting of restricted stock units (in shares)	'	1,857,578	'	'	'
Shares issued in connection with employee stock purchase plan and 401(k) plan	7,923	'	7,923	'	'
Shares issued in connection with employee stock purchase plan and 401(k) plan (in shares)	'	211,925	'	'	'
Tax benefit on stock-based awards	10,787	'	10,787	'	'
Stock-based compensation	25,797	'	25,797	'	'
Stock-based compensation (in shares)	'	3,290	'	'	'
Balance at Dec. 31, 2012	990,748	65	940,969	-59	49,773
Balance (in shares) at Dec. 31, 2012	'	64,713,695	'	'	'
Changes in Stockholders' Equity	'	'	'	'	'
Comprehensive income (loss)	-18,297	'	'	274	-18,571
Sale of warrants	121,675	'	121,675	'	'
Purchase of convertible bond hedge, net of tax	-113,379	'	-113,379	'	'
Reacquisition of equity component of convertible debt upon conversion, net of tax	-277,491	'	-277,491	'	'
Issuance of common stock upon conversion of convertible debt	483,219	8	483,211	'	'
Issuance of common stock upon conversion of convertible debt (in shares)	'	7,580,923	'	'	'
Equity component of convertible debt issuance, net of tax and issuance costs	113,053	'	113,053	'	'
Exercise of stock options and vesting of restricted stock units	36,696	1	36,695	'	'
Exercise of stock options and vesting of restricted stock units (in shares)	'	1,974,118	'	'	'
Shares issued in connection with employee stock purchase plan and 401(k) plan	7,298	'	7,298	'	'
Shares issued in connection with employee stock purchase plan and 401(k) plan (in shares)	'	159,351	'	'	'
Tax benefit on stock-based awards	17,711	'	17,711	'	'
Stock-based compensation	32,498	'	32,498	'	'
Balance at Dec. 31, 2013	$1,393,731	$74	$1,362,240	$215	$31,202
Balance (in shares) at Dec. 31, 2013	'	74,428,087	'	'	'

NATURE_OF_BUSINESS

NATURE OF BUSINESS	12 Months Ended
NATURE OF BUSINESS	Dec. 31, 2013
NATURE OF BUSINESS	'
NATURE OF BUSINESS	'

	A. NATURE OF BUSINESS

	Cubist Pharmaceuticals, Inc. ("Cubist" or "the Company") is a biopharmaceutical company headquartered in Lexington, Massachusetts, focused on the research, development and commercialization of novel therapies to treat serious medical conditions in acutely-ill patients who are hospitalized or are being treated in other acute care settings. Cubist has three marketed products, CUBICIN® (daptomycin for injection), DIFICID® (fidaxomicin) and ENTEREG® (alvimopan). In addition, Cubist has four late-stage product candidates: tedizolid phosphate, ceftolozane/tazobactam, surotomycin and bevenopran.

	CUBICIN is a once-daily, bactericidal, intravenous antibiotic with activity against methicillin-resistant Staphylococcus aureus (S. aureus), or MRSA. CUBICIN is approved in the United States, or U.S., European Union, or EU, Japan and various other countries for the treatment of certain Gram-positive bacteria and for certain bloodstream infections. DIFICID is approved in the U.S. for the treatment of Clostridium difficile-associated diarrhea, or CDAD, and in Europe (where it has the trade name DIFICLIR®), Australia, Canada and other countries for the treatment of Clostridium difficile-infection, or CDI. ENTEREG is approved in the U.S. to accelerate upper and lower gastrointestinal, or GI, recovery following surgeries that include partial bowel resections with primary anastomosis. ENTEREG is not approved for marketing outside of the U.S.

	On October 24, 2013, Cubist acquired Optimer Pharmaceuticals, Inc., or Optimer, and with it, obtained rights to the marketed product, DIFICID. On September 11, 2013, Cubist acquired Trius Therapeutics, Inc., or Trius, and with it, obtained rights to the late-stage product candidate, tedizolid phosphate. See Note D., "Business Combinations and Acquisitions," for additional information.

	Cubist is subject to risks common to companies in the pharmaceutical industry including, but not limited to, risks related to the development by Cubist or its competitors of research and development stage products, the ability to market products or services, the Company's ability to attract and retain key personnel, the market acceptance of its products, the size of the market for its products, the Company's dependence on key suppliers, the ability to manufacture and supply sufficient quantities of its products and product candidates to meet commercial and clinical demand, the protection, enforcement and maintenance of the Company's patents and other proprietary technology, including in connection with the notice letters Cubist received from Strides, Inc., on behalf of Agila Specialties Private Limited, collectively Strides, and Hospira, Inc., or Hospira, in connection with which Strides and Hospira are seeking approval to market generic versions of CUBICIN, the Company's ability to obtain additional financing and the Company's compliance with governmental and other regulations. See Note M., "Commitments and Contingencies," for additional information.

ACCOUNTING_POLICIES

ACCOUNTING POLICIES	12 Months Ended
ACCOUNTING POLICIES	Dec. 31, 2013
ACCOUNTING POLICIES	'
ACCOUNTING POLICIES	'

	B. ACCOUNTING POLICIES

	Basis of Presentation and Consolidation

	The accompanying consolidated financial statements have been prepared under accounting principles generally accepted in the U.S., or GAAP and include the accounts of Cubist and its wholly-owned subsidiaries. All intercompany balances and transactions have been eliminated in consolidation. The assets acquired and liabilities assumed in connection with the Company's acquisitions of Optimer and Trius were recorded at their fair values as of October 24, 2013, and September 11, 2013, respectively, the dates of acquisition. The operating results of Optimer and Trius have been consolidated with those of Cubist from the dates of acquisition. See Note D., "Business Combinations and Acquisitions," for additional information.

	Use of Estimates

	The preparation of financial statements in conformity with GAAP requires extensive use of estimates and assumptions that affect the reported amounts of assets, liabilities, revenues and expenses, and related disclosures. The most significant assumptions are employed in estimates used in determining values of: inventory; investments; acquisition-date fair value and subsequent fair value estimates used to assess impairment of long-lived assets, including goodwill, in-process research and development, or IPR&D, and other intangible assets; accrued clinical research costs; contingent consideration; income taxes; stock-based compensation; product rebate, chargeback and return accruals; as well as in estimates used in accounting for contingencies and revenue recognition. Actual results could differ from these estimates.

	Fair Value Measurements

	The accounting standard for fair value measurements defines fair value, establishes a framework for measuring fair value in accordance with GAAP, and requires detailed disclosures about fair value measurements. Under this standard, 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 valuation techniques are based on observable and unobservable inputs. Observable inputs reflect readily obtainable data from independent sources, while unobservable inputs reflect certain market assumptions. This standard classifies these inputs into the following hierarchy:

	Level 1 Inputs—Quoted prices for identical instruments in active markets.

	Level 2 Inputs—Quoted prices for similar instruments in active markets; quoted prices for identical or similar instruments in markets that are not active; and model-derived valuations whose inputs are observable or whose significant value drivers are observable.

	Level 3 Inputs—Instruments with primarily unobservable value drivers.

	The fair value hierarchy level is determined by asset class based on the lowest level of significant input. In periods of market inactivity, the observability of prices and inputs may be reduced for certain instruments. This condition could cause an instrument to be reclassified between levels. During the year ended December 31, 2013, there were no transfers between levels.

	The carrying amounts of Cubist's cash and cash equivalents, accounts receivable, net, accounts payable and accrued expenses approximate their fair value due to the short-term nature of these amounts. Short-term and long-term investments primarily consist of available-for-sale securities as of December 31, 2013 and 2012, and are carried at fair value.

	Cash and Cash Equivalents

	Cash and cash equivalents consist of short-term, interest-bearing instruments with original maturities of 90 days or less at the date of purchase. These may include money market instruments, bank deposits, corporate and municipal notes, U.S. Treasury securities and federal agency securities.

	Investments

	Investments with original maturities of greater than 90 days and remaining maturities of less than one year are classified as short-term investments. Investments with remaining maturities of greater than one year from the balance sheet date are classified as long-term investments. Short-term and long-term investments may include bank deposits, corporate and municipal notes, U.S. Treasury securities and federal agency securities. See Note E., "Investments," for additional information.

	Unrealized gains and temporary losses on investments are included in accumulated other comprehensive income (loss) as a separate component of stockholders' equity. Realized gains and losses, dividends and declines in value judged to be other-than-temporary credit losses are included in other income (expense) within the consolidated statements of income. Any premium or discount arising at purchase is amortized and/or accreted to interest income within the consolidated statements of income.

	Concentration of Risk

	Financial instruments, which potentially subject the Company to concentrations of credit risk, consist principally of cash and cash equivalents, investments and accounts receivable. The Company's cash and cash equivalents are held with several major financial institutions. The Company's investments are restricted, in accordance with its investment policy, to a concentration limit per institution.

	Cubist's accounts receivable, net at December 31, 2013 and 2012, represent amounts due to the Company from customers, including AmerisourceBergen Drug Corporation, Cardinal Health, Inc. and McKesson Corporation. Cubist performs ongoing credit evaluations of its customers, including key wholesalers and distributors, and generally does not require collateral. For the year ended December 31, 2013, Cubist did not have any significant write-offs of accounts receivable and its days sales outstanding has not significantly changed since December 31, 2012.


			Percentage of
			Total Accounts
			Receivable
			Balance as of
			December 31,
			2013			2012
	AmerisourceBergen Drug Corporation			18	%		22	%
	Cardinal Health, Inc.			17	%		18	%
	McKesson Corporation			18	%		20	%





			Percentage of Total
			Net Revenues for
			the Years Ended
			December 31,
			2013			2012			2011
	AmerisourceBergen Drug Corporation			19	%		20	%		21	%
	Cardinal Health, Inc.			17	%		18	%		21	%
McKesson Corporation			18	%		18	%		17	%

The Company depends on a single-source supplier of the active pharmaceutical ingredient, or API, in CUBICIN, and two suppliers to provide fill-finish services related to the manufacture of CUBICIN. If any of the Company's suppliers were to limit or terminate production, or otherwise fail to meet the quality or delivery requirements needed to supply CUBICIN at levels to meet market demand, the Company could experience a loss of revenue, which could materially and adversely impact its results of operations.

Inventory

Inventory is stated at the lower of cost or market on a first-in, first-out (FIFO) basis. The Company analyzes its inventory levels on a quarterly basis and writes down inventory that is expected to expire prior to being sold, inventory in excess of expected sales requirements and inventory that fails to meet commercial sale specifications, with a corresponding charge to cost of product revenues. The Company disposes of its expired inventory. Inventory that is in excess of the amount expected to be sold within one year is classified as long-term inventory and is included in other assets within the consolidated balance sheets.

The Company capitalizes inventory produced for commercial sales, including inventory produced for potential sales of a product candidate when it considers the probability of a product candidate's regulatory approval to be high and expects the future economic benefit from sales of the product to be realized. Inventory capitalization is assessed on a product-by-product basis, and begins either on or after the date the New Drug Application, or NDA, is accepted for filing by the U.S. Food and Drug Administration, or FDA, or an international equivalent. Determining whether or not to continue to record the commercial supply costs related to a product candidate as research and development expenses or to capitalize these costs as inventory involves significant judgment. The Company will assess the costs capitalized prior to regulatory approval each quarter for indicators of impairment, such as reduced likelihood of approval.

Property and Equipment, Net

Property and equipment are recorded at cost and are depreciated when placed into service using the straight-line method, based on their estimated useful lives as follows:


Asset Description		Estimated Useful Life
		(in years)
Land			Indefinite
Building			40
Building enhancements			Not to exceed 20
Furniture and fixtures			5 - 10
Laboratory equipment			5
Computer hardware and software			3

Costs for capital assets not yet placed into service have been capitalized as construction-in-progress and will be depreciated in accordance with the above guidelines once placed into service. Costs for repairs and maintenance are expensed as incurred, while major betterments are capitalized. The Company capitalizes interest cost incurred on funds used to construct property and equipment. The capitalized interest is recorded as part of the asset to which it relates and is depreciated over the asset's estimated useful life. When assets are retired or otherwise disposed of, the assets and related allowances for depreciation or amortization are eliminated from the consolidated balance sheets and any resulting gain or loss is reflected in the consolidated statements of income.

Intangible Assets

IPR&D

IPR&D acquired in a business combination is capitalized on the Company's consolidated balance sheets at its acquisition-date fair value. Until the underlying project is completed, these assets are accounted for as indefinite-lived intangible assets and are subject to impairment testing. Once the project is completed, the carrying value of the IPR&D is amortized over the estimated useful life of the asset. Post-acquisition research and development expenses related to the IPR&D projects are expensed as incurred.

The projected discounted cash flow models used to estimate the fair values of the Company's IPR&D reflect significant assumptions regarding the estimates a market participant would make in order to evaluate a drug development asset, including: (i) probability of successfully completing clinical trials and obtaining regulatory approval; (ii) market size, market growth projections, and market share; (iii) estimates regarding the timing of and the expected costs to advance Cubist's clinical programs to commercialization; (iv) estimates of future cash flows from potential product sales; and (v) a discount rate.

The accounting standard for testing indefinite-lived intangible assets for impairment permits a company to first assess the qualitative factors to determine whether the existence of events and circumstances indicates that it is more likely than not that the indefinite-lived intangible asset is impaired. The more-likely-than-not threshold is defined as having a likelihood of more than 50%. If, after assessing the totality of events or circumstances, a company concludes it is more likely than not that the fair value of the indefinite-lived intangible asset exceeds its carrying value, then the company is not required to take further action. A company also has the option to bypass the qualitative assessment for any indefinite-lived intangible asset in any period and proceed directly to performing the quantitative impairment test and may resume performing the qualitative assessment in any subsequent period.

IPR&D is tested for impairment on an annual basis or more frequently if impairment indicators are present. If IPR&D becomes impaired or is abandoned, the carrying value of the IPR&D is written down to its revised fair value with the related impairment charge recognized in the period in which the impairment occurs. If the carrying value of the asset becomes impaired as the result of unfavorable data from any ongoing or future clinical trial, changes in assumptions that negatively impact projected cash flows, or because of any other information regarding the prospects of successfully developing or commercializing the Company's programs, Cubist could incur significant charges in the period in which the impairment occurs. The valuation techniques utilized in performing quantitative impairment tests incorporate significant assumptions and judgments to estimate the fair value. The use of different valuation techniques or assumptions could result in materially different fair value estimates. The Company recorded impairment charges of $35.3 million and $38.7 million during the years ended December 31, 2013 and 2012, respectively, to write down its bevenopran IPR&D asset to its revised fair value. See Note I., "Goodwill, IPR&D and Other Intangible Assets, Net," and Note F., "Fair Value Measurements," for additional information. Cubist did not recognize any impairment charges related to IPR&D during the year ended December 31, 2011.

Goodwill

Goodwill relates to amounts that arose in connection with the acquisitions of Optimer and Trius in 2013, as well as Adolor Corporation, or Adolor, in 2011, and Calixa Therapeutics Inc., or Calixa, in 2009. Goodwill represents the excess of the purchase price over the fair value of the net assets acquired when accounted for using the acquisition method of accounting for business combinations. Goodwill is not amortized but is evaluated for impairment within the Company's single reporting unit on an annual basis, during the fourth quarter, or more frequently if an event occurs or circumstances change that would more-likely-than-not reduce the fair value of the Company's reporting unit below its carrying amount. Cubist performed step one of the two-step goodwill impairment test by assessing the fair value of its reporting unit as compared to its carrying value, including goodwill. The Company determined that the carrying value of its single reporting unit did not exceed its fair value, and therefore, goodwill was not impaired as of December 31, 2013. The Company did not recognize any impairment charges related to goodwill during the years ended December 31, 2013, 2012 and 2011.

Other Intangible Assets

Other intangible assets consist of patents, acquired intellectual property, acquired technology rights, manufacturing rights, contract intangibles, and other intangibles with finite lives. The Company amortizes its intangible assets using the straight-line method over their estimated economic lives, which range from nine to 14 years. The fair values of patents obtained through an acquisition transaction are capitalized and amortized over the lesser of the patent's remaining legal life or its useful life. Costs to obtain, maintain and defend the Company's patents are expensed as incurred. Cubist evaluates the potential impairment of other intangible assets if events or changes in circumstances indicate that the carrying amount of the assets may not be fully recoverable or that the useful lives of these assets are no longer appropriate. The impairment test is based on a comparison of the undiscounted cash flows expected to be generated from the use of the asset group and its eventual disposition to the carrying value of the asset group. If impairment is indicated, the asset is written down by the amount by which the carrying value of the asset exceeds the related fair value of the asset. Cubist did not recognize an impairment charge related to other intangible assets during the years ended December 31, 2013, 2012 and 2011.

Revenue Recognition

The Company's principal sources of revenue during the reporting period were: (i) product sales of CUBICIN, DIFICID and ENTEREG in the U.S.; (ii) revenues derived from sales of CUBICIN and DIFICID by Cubist's international distribution partners; (iii) license fees and milestone payments that are derived from collaboration, license and commercialization agreements with other biopharmaceutical companies; and (iv) prior to Cubist's acquisition of Optimer, service revenues derived from Cubist's co-promotion agreement with Optimer for the promotion and support of DIFICID in the U.S., which was terminated on October 24, 2013, as a result of Cubist's acquisition of Optimer. In all instances, revenue is recognized only when the price is fixed or determinable, persuasive evidence of an arrangement exists, delivery has occurred or services have been rendered, and collectibility of the resulting receivable is reasonably assured.

Multiple-Element Arrangements

Cubist accounts for revenue arrangements with multiple elements entered into or materially modified after January 1, 2011, by separating and allocating consideration according to the relative selling price of each deliverable. The selling price 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 will be separate units of accounting, provided (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 Company's control.

Cubist's other license and collaboration agreements continue to be accounted for under previously-issued revenue recognition guidance for multiple-element arrangements. Under this guidance, the Company recognizes non-refundable upfront license payments as revenue upon receipt if the license has standalone value and the fair value of the undelivered obligations, if any, can be determined. If the license is considered to have standalone value but the fair value of any of the undelivered items cannot be determined, the license payments are recognized as revenue over the period of Cubist's performance for such undelivered items or services. License fees with ongoing involvement or performance obligations are recorded as deferred revenue once received, and generally are recognized ratably over the period of such performance obligation only after both the license period has commenced and the technology has been delivered by Cubist.

U.S. Product Revenues, net

All revenues from product sales are recorded net of applicable provisions for returns, chargebacks, discounts, wholesaler management fees, government and commercial rebates, and other applicable allowances in the same period the related sales are recorded.

Gross U.S. product revenues were offset by provisions for the years ended December 31, 2013, 2012 and 2011, as follows:


		For the Years Ended December 31,
		2013			2012			2011
		(in thousands)
Gross U.S. product revenues		$	1,116,870		$	977,874		$	802,457
Provisions offsetting U.S. product revenues
Contractual adjustments			(61,448	)		(55,331	)		(45,093	)
Governmental rebates			(84,226	)		(73,172	)		(55,997	)


Total provisions, net offsetting U.S. product revenues			(145,674	)		(128,503	)		(101,090	)


U.S. product revenues, net		$	971,196		$	849,371		$	701,367





Certain product sales qualify for rebates or discounts from standard list pricing due to government sponsored programs or other contractual agreements. Contractual adjustments include provisions for returns, pricing and early payment discounts extended to the Company's external customers, as well as wholesaler distribution fees, volume-based rebates and other commercial rebates. The Company allows customers to return product within a specified period prior to and subsequent to the product's expiration date and in the event of certain circumstances, such as a product recall. The estimate of the provision for returns is analyzed quarterly and is based upon many factors, including historical experience of actual returns, analysis of the level of inventory in the distribution channel, if any, and reorder rates of end users. In certain circumstances, for example, in the event of a product recall or similar circumstance outside of the customers' control, Cubist may issue the customer replacement product for product returned. In these limited circumstances, expected costs of the replacement product are recognized within cost of product revenues, whereas expected refunds or credits granted to the customer are recognized as revenue deductions at full sales value within provisions for product returns.

Governmental rebates represent estimated amounts for government-mandated rebates and discounts relating to federal and state programs, such as Medicaid, the Veterans' Administration and Department of Defense programs, the Medicare Part D Coverage Gap Discount Program and certain other qualifying federal and state government programs. Estimates and assumptions for reserves are analyzed quarterly. Reserves for government and commercial rebates and chargebacks represent the Company's estimates of outstanding claims for end-user rebate-eligible sales that have occurred, but for which related claim submissions have not been received. The estimates are based on an analysis of customer sales mix data, prior claims history and third-party studies to determine which sales may flow through to a rebate- or chargeback-eligible customer.

Effective March 23, 2010, the Patient Protection and Affordable Care Act, as amended by the Health Care and Education reconciliation Act of 2010, or the Affordable Care Act, extended Medicaid rebates to drug volume issued to Medicaid patients whose drug coverage is managed by managed care organizations, or MCOs, under individual agreements with states. The Company accrues for the expected liability at the time it records the sale; however, the time lag between sale and payment of Medicaid program rebates and Medicare coverage gap discount program rebates can be lengthy. In addition, the Company continues to experience delays in billing by certain state authorities under the MCO plans. As a result, in any particular period, Medicaid and Medicare rebate adjustments may incorporate revisions of accruals for several periods.

Reserves for returns, discounts, chargebacks, wholesaler management fees and doubtful accounts are offset against accounts receivable and were $16.0 million and $9.2 million at December 31, 2013 and 2012, respectively. Reserves for governmental and commercial rebates are included in accrued liabilities and were $18.6 million and $20.6 million at December 31, 2013 and 2012, respectively. The Company reversed $18.0 million of revenue reserves during the year ended December 31, 2013, which includes $10.0 million related to Medicaid program rebate reserves that had been accrued since the enactment of the Affordable Care Act. The change in estimate for Medicaid rebates was based on receipt of claims information from certain state governments and other additional data during 2013, as a result of lower than estimated usage of CUBICIN by MCOs.

International Product Revenues

The Company's principal sources of international product revenues during the period were sales of CUBICIN and DIFICID to international distribution partners. Sales with international distribution partners are based upon contractually predetermined transfer price arrangements. Once Cubist's distribution partner sells the product to a third party, Cubist may also be owed an additional payment or royalty. Certain agreements with the Company's distribution partners contain multiple elements in which Cubist has continuing performance obligations. In such arrangements in which the Company determined that the undelivered elements in each arrangement did not have objective evidence of fair value, payments from distribution partners are recorded as deferred revenue. The Company amortizes deferred revenue to international product revenue over the remaining performance obligation. Total deferred revenue related to international product revenues was $20.5 million and $20.4 million at December 31, 2013 and 2012, respectively.

Service Revenues

Service revenues for the years ended December 31, 2013, 2012 and 2011, were $12.3 million, $23.2 million and $6.7 million, respectively. Service revenues represent the ratable recognition of the quarterly service fee earned in accordance with the co-promotion agreement with Optimer, which the Company entered into in April 2011 and terminated in October 2013, as described in Note D., "Business Combinations and Acquisitions." In addition, service revenues during the year ended December 31, 2012, include $8.5 million related to a bonus payment received from Optimer for the achievement of an annual sales target and Cubist's portion of Optimer's gross profits on net sales of DIFICID in the U.S. that exceeded the annual sales target for the first sales year, as stipulated in the co-promotion agreement.

Other Revenues

Other revenues include revenue related to upfront license payments, license fees and milestone payments received through Cubist's license, collaboration and commercialization agreements. Milestone payments received in accordance with these agreements and in which there are continuing performance obligations are recognized under accounting guidance for milestone payments. Consideration for an event that meets the definition of a milestone in accordance with the accounting guidance for the milestone method of revenue recognition is recognized as revenue in its entirety in the period in which the milestone is achieved only if all of the following conditions are met, and therefore, the milestone is considered substantive: (i) the milestone is commensurate with either Cubist's performance to achieve the milestone or the enhancement of the value of the delivered item as a result of a specific outcome resulting from the Company's performance to achieve the milestone; (ii) the consideration relates solely to past performance; and (iii) the amount of the milestone consideration is reasonable relative to all of the deliverables and payment terms, including other potential milestone consideration, within the arrangement. Otherwise, the milestone payments are not considered to be substantive and are, therefore, recognized as revenue as Cubist completes its remaining performance obligations. Total deferred revenue related to other revenues was $16.9 million and $20.5 million at December 31, 2013 and 2012, respectively.

Research and Development

Research and development costs, including upfront fees and milestones paid to collaborators who are performing research and development activities under contractual agreement with the Company, are expensed as incurred if no planned alternative future use exists for the technology and if the payment is not payment for future services. The Company defers and capitalizes its nonrefundable advance payments that are for research and development activities until the related goods are delivered or the related services are performed. When the Company is reimbursed by a collaboration partner for work the Company performs, it records the costs incurred as research and development expenses and the related reimbursement as a reduction to research and development expenses in its consolidated statement of income. Research and development expenses primarily consist of employee-related expenses, clinical and non-clinical activities performed by contract research organizations, or CROs, lab services, purchases of drug product materials, manufacturing development costs, general overhead and facilities, and upfront and milestone payments related to the licensing or purchase of research and development assets that did not qualify as business combinations.

Stock-Based Compensation

The Company expenses the fair value of employee stock-based compensation using the straight-line recognition method over the employees' service periods, which are generally the vesting period of the equity award. Compensation expense is measured using the fair value of the award at the grant date, adjusted for estimated forfeitures. In order to determine the fair value of each option award on the grant date, the Company uses the Black-Scholes option-pricing model. Inherent in this model are assumptions related to expected stock price volatility, estimated option life, risk-free interest rate and dividend yield. Cubist's expected stock price volatility assumption is based on the historical volatility of the Company's stock price, which is obtained from public data sources. In prior years, the Company also utilized peer group data to derive its expected stock price volatility. Expected stock price volatility is determined based on the instrument's expected term. The expected life represents the weighted average period of time that stock-based awards are expected to be outstanding giving consideration to vesting schedules, historical exercise patterns and post-vesting cancellations for terminated employees that have been exhibited historically, adjusted for specific factors that may influence future exercise patterns. The risk-free interest rate is a less subjective assumption as it is based on factual data derived from public sources. Cubist uses a dividend yield of zero as it has never paid cash dividends and has no intention of paying cash dividends in the foreseeable future.

The Company estimates forfeitures of awards based on its historical experience of pre-vesting cancellations for terminated employees. Its estimated forfeiture rate is applied to all equity awards, which includes option awards and restricted stock units. The Company believes that its estimates are based on outcomes that are reasonably likely to occur. To the extent actual forfeitures differ from its estimates, such amounts will be recorded as a cumulative adjustment in the period the estimates are revised. See Note L., "Employee Stock Benefit Plans," for additional information.

Income Taxes

Cubist accounts for income taxes under the asset and liability method. Under this method, deferred tax assets and liabilities are recognized for the estimated future tax consequences attributable to differences between the financial statement carrying amounts of existing assets and liabilities and their respective tax bases. Deferred tax assets and liabilities are measured using enacted rates in effect for the year in which those temporary differences are expected to be recovered or settled. A deferred tax asset is established for the expected future benefit of net operating loss, or NOL, and credit carryforwards. A valuation allowance against net deferred tax assets is required if, based upon available evidence, it is more-likely-than-not that some or all of the deferred tax assets will not be realized.

The Company recognizes the tax benefit from an uncertain tax position only if it is more-likely-than-not that the tax position will be sustained upon examination by the taxing authorities, based on the technical merits of the tax position. 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; and changes in facts or circumstances related to a tax position. Any changes to these estimates, based on the actual results obtained and/or a change in assumptions, could impact the Company's income tax provision in future periods. Interest and penalty charges, if any, related to unrecognized tax benefits would be classified as a provision for income tax in the consolidated statements of income. See Note O., "Income Taxes," for additional information.

Basic and Diluted Net (Loss) Income Per Common Share

Basic net (loss) income per common share has been computed by dividing net (loss) income by the weighted average number of shares outstanding during the period. Diluted net (loss) income per share has been computed by dividing diluted net (loss) income by the diluted number of shares outstanding during the period. Except where the result would be antidilutive to income from continuing operations, diluted net (loss) income per share has been computed assuming the conversion of convertible obligations and the elimination of the interest expense related to the Company's 2.25% convertible subordinated notes due June 2013, or 2013 Notes, 2.50% convertible senior notes due 2017, or 2017 Notes, 1.125% convertible senior notes due 2018, or 2018 Notes, 1.875% convertible senior notes due 2020, or 2020 Notes, the exercise of stock options, the exercise of warrants issued in connection with the convertible bond hedge transactions discussed below, and the vesting of restricted stock units, or RSUs, as well as their related income tax effects. In 2012, Cubist retired the remainder of its 2013 Notes.

In September 2013, in connection with the issuance of the 2018 Notes and 2020 Notes, the Company entered into convertible bond hedge transactions, or convertible bond hedges. The convertible bond hedges are not considered for purposes of calculating the number of diluted shares outstanding, as their effect would be antidilutive. The convertible bond hedges are generally expected, but not guaranteed, to reduce the potential dilution and/or offset the cash payments Cubist is required to make upon conversion of the 2018 Notes and 2020 Notes. See Note K., "Debt," for additional information.

The following table sets forth the computation of basic and diluted net (loss) income per common share:


		For the Years Ended December 31,
		2013			2012			2011
		(in thousands, except share and per share data)
Basic net (loss) income		$	(18,571	)	$	154,075		$	33,023
Effect of dilutive securities:
Interest on 2017 Notes, net of tax			—			7,088			—
Debt issuance costs related to 2017 Notes, net of tax			—			936			—
Debt discount amortization related to 2017 Notes, net of tax			—			8,705			—


Diluted net (loss) income		$	(18,571	)	$	170,804		$	33,023




Shares used in calculating basic net (loss) income per common share			68,160,798			63,766,209			60,839,128
Effect of dilutive securities:
Options to purchase shares of common stock and RSUs			—			2,254,294			2,098,013
2017 Notes payable convertible into shares of common stock			—			15,424,155			—


Shares used in calculating diluted net (loss) income per common share			68,160,798			81,444,658			62,937,141




Basic net (loss) income per share		$	(0.27	)	$	2.42		$	0.54
Diluted net (loss) income per share		$	(0.27	)	$	2.1		$	0.52

Potential shares of common stock excluded from the calculation of diluted net (loss) income per share as their inclusion would have been antidilutive, were:


		For the Years Ended December 31,
		2013			2012			2011
Options to purchase shares of common stock and RSUs			8,360,441			2,449,796			1,962,363
Warrants			9,705,442			—			—
2020 Notes convertible into shares of common stock			5,459,311			—			—
2018 Notes convertible into shares of common stock			4,246,131			—			—
2017 Notes convertible into shares of common stock			7,842,943			—			15,424,155
2013 Notes convertible into shares of common stock			—			1,962,273			3,549,377

Accumulated Other Comprehensive Income

In February 2013, the Financial Accounting Standards Board, or FASB, issued amended accounting guidance for reporting accumulated other comprehensive income. The amendments require a company to provide information about the amounts reclassified out of accumulated other comprehensive income by component. In addition, a company is required to present, either on the face of the statement where 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. The Company adopted this guidance on January 1, 2013. The Company had de minimis realized gains or losses from sales of its available-for-sale securities and did not reclassify any amounts out of accumulated other comprehensive income during the year ended December 31, 2013.

Subsequent Events

Cubist considers events or transactions that have occurred after the balance sheet date of December 31, 2013, but prior to the filing of the financial statements with the Securities and Exchange Commission, or SEC, to provide additional evidence relative to certain estimates or to identify matters that require additional recognition or disclosure. Subsequent events have been evaluated through the filing of the financial statements accompanying this Annual Report on Form 10-K.

Recent Accounting Pronouncements

In July 2013, the FASB issued an accounting standards update clarifying the presentation of an unrecognized tax benefit when an NOL carryforward, a similar tax loss, or a tax credit carryforward exists. The updated guidance requires the netting of unrecognized tax benefits against a deferred tax asset for a loss or other carryforward when settlement of the liability for an unrecognized tax benefit in this manner is available. The update is effective prospectively for reporting periods beginning after December 15, 2013, and early adoption and retrospective adoption are permitted. The adoption of this guidance is not expected to have an impact on the Company's consolidated financial statements.

BUSINESS_AGREEMENTS

BUSINESS AGREEMENTS	12 Months Ended
BUSINESS AGREEMENTS	Dec. 31, 2013
BUSINESS AGREEMENTS	'
BUSINESS AGREEMENTS	'

	C. BUSINESS AGREEMENTS

	CUBICIN Agreements

	Novartis AG

	In October 2003, Cubist entered into a license agreement and a manufacturing and supply agreement with Chiron Healthcare Ireland Ltd., or Chiron, for the development and commercialization of CUBICIN in Europe, Australia, New Zealand, India and certain Central American, South American and Middle Eastern countries. After the acquisition of Chiron by Novartis AG, or Novartis, in 2006, the license agreement and manufacturing and supply agreement were assigned to a subsidiary of Novartis. During each of the years ended December 31, 2013 and 2011, the Company received a $5.0 million sales milestone payment as a result of Novartis achieving a predetermined level of aggregate sales to third parties. Cubist recognized these sales milestones as other revenue upon achievement. Under the license agreement, Cubist is eligible to receive from Novartis' subsidiary additional remaining milestone payments of up to $15.0 million upon Novartis achieving certain sales milestones. Under the manufacturing and supply agreement, Novartis' subsidiary pays Cubist a transfer price for CUBICIN, and under the license agreement, Novartis' subsidiary pays Cubist royalty payments, net of the transfer price, based on Novartis' sales of CUBICIN. Unless terminated earlier, in accordance with its terms, the license agreement expires on the later of: (a) expiration of the last-to-expire of the CUBICIN patents owned by Cubist or jointly-owned by Cubist and Novartis' subsidiary; (b) the date on which there no longer exists a claim of a pending CUBICIN patent application owned by Cubist or jointly-owned by Cubist and Novartis' subsidiary; and (c) the earlier of: (i) generic daptomycin sales reaching a specified percentage of the total market share for all daptomycin sales in Novartis' territory, and (ii) June 30, 2020.

	Eli Lilly & Co.

	Cubist licensed the exclusive worldwide rights to develop, manufacture and market daptomycin, the active ingredient in CUBICIN from Eli Lilly & Co., or Eli Lilly, pursuant to an amended and restated October 2000 license agreement. Cubist is required to pay royalties to Eli Lilly on worldwide sales of CUBICIN. In July 2003 and March 2005, Cubist entered into amendments to the restated license agreement and issued to Eli Lilly an aggregate 2,599,792 shares of common stock valued at an aggregate of $28.0 million in consideration for single-digit reductions in the royalty rates payable to Eli Lilly. In September 2003, Cubist issued 38,922 shares of common stock valued at $0.5 million as a milestone payment to Eli Lilly upon Cubist receiving FDA approval for the commercial sale of CUBICIN. The aggregate payments of $28.5 million were recorded as intangible assets within the consolidated balance sheets and are being amortized through 2016, which was the estimated remaining life of the license agreement with Eli Lilly on the dates of the transactions. The amortization of these intangible assets is included in cost of product revenues within the consolidated statements of income.

	As of December 31, 2013, in addition to the milestone payments made in stock, Cubist has made payments to Eli Lilly of approximately $588.6 million for royalties on sales of CUBICIN, which were paid in cash. Unless terminated earlier in accordance with its terms, Cubist's license agreement with Eli Lilly expires on the later of: (a) the expiration of the last-to-expire of the patents assigned or licensed under the agreement; and (b) the end of the tenth year from the date of first sale of CUBICIN in any of the U.S., Canada, Japan, the United Kingdom, or UK, Germany, France, Italy, Spain, Switzerland, Netherlands or Belgium in which know-how royalties are due under the agreement.

	DIFICID Agreements

	Astellas Pharma Europe Ltd.

	In connection with the Company's acquisition of Optimer in October 2013, Cubist acquired a collaboration and license agreement and a supply agreement, which were entered into by Optimer and Astellas Pharma Europe Ltd., or Astellas Europe, in February 2011. Under the terms of the collaboration and license agreement, Astellas Europe was granted an exclusive, royalty-bearing license to develop and commercialize fidaxomicin, the active ingredient in DIFICID, in Europe and certain other countries, or the Astellas Territory. Cubist is the exclusive supplier of fidaxomicin for Astellas Europe's development and commercialization activities in the Astellas Territory, for which supply Astellas Europe is obligated to pay Cubist an amount equal to cost plus an agreed upon margin.

	In March 2011, Astellas Europe paid Optimer an upfront fee of $69.2 million under the terms of the agreement. In June 2012, Astellas Europe paid Optimer 50.0 million euros, which consisted of a regulatory approval milestone payment of 40.0 million euros and a milestone payment for the first commercial launch of DIFICLIR in an Astellas Territory of 10.0 million euros. Cubist is eligible to receive additional remaining milestone payments totaling up to 65.0 million euros if certain sales milestones are achieved. In addition, Cubist is entitled to receive escalating double-digit royalties ranging from the high teens to low twenties on net sales of fidaxomicin products in the Astellas Territory, which royalties are subject to reduction in certain, limited circumstances. The agreements expire on a product-by-product and country-by-country basis when a generic product accounts for a specified market share of the applicable fidaxomicin product in the applicable country.

	Par Pharmaceutical, Inc.

	In connection with the Company's acquisition of Optimer, Cubist is obligated, under the terms of a January 2007 buy-back agreement entered into by Optimer and Par Pharmaceutical, Inc., or Par, to pay Par a single-digit royalty on net sales of fidaxomicin by: (i) Cubist, its affiliates or licensees in the U.S., Canada and Israel and (ii) Cubist and its affiliates in all countries outside the U.S., Canada and Israel. Cubist is also obligated to pay Par a royalty on net revenues received by Cubist in connection with licensing or granting rights to commercialize fidaxomicin to a third party in any country outside of the U.S., Canada and Israel. Cubist is obligated to pay the net sales royalties on a country-by-country basis for seven years following the applicable commercial launch in each such country and is obligated to pay the net revenues royalties for seven years following the first commercial launch in any such country.

	Optimer Pharmaceuticals, Inc.

	In April 2011, the Company entered into a co-promotion agreement with Optimer, pursuant to which Optimer engaged Cubist as its exclusive partner for the promotion of DIFICID in the U.S. Optimer and Cubist co-promoted DIFICID from July 2011 until October 2013, at which point the agreement was terminated in connection with the completion of the Company's acquisition of Optimer. See Note D., "Business Combinations and Acquisitions," for additional information.

	ENTEREG Agreements

	Glaxo Group Limited, Eli Lilly & Co., Shire, U.S. Inc.

	In December 2011, Cubist acquired Adolor and with it, rights to Adolor's commercialized product, ENTEREG. Cubist assumed obligations to pay single-digit royalties on net sales of ENTEREG to Shire U.S. Inc., or Shire, Eli Lilly and Glaxo Group Limited, or Glaxo, as a result of its acquisition of Adolor. The option and license agreement with Shire, as successor-in-interest to Roberts Laboratories Inc., and the license agreement with Eli Lilly remain in effect through the last-to-expire of the licensed Eli Lilly patents.

	In connection with the acquisition, Cubist also assumed the obligation to pay to Glaxo: i) $25.0 million payable in annual installments through 2017, of which $2.5 million was paid by Adolor prior to Cubist's acquisition of Adolor, and $6.5 million has been paid by Cubist to Glaxo as of December 31, 2013; and ii) a one-time milestone of $15.0 million upon achievement of a predetermined level of sales in the U.S. in a given year. The agreement with Glaxo expires on the date of the last commercial sale of ENTEREG in the U.S. See Note F., "Fair Value Measurements," for additional information.

	Tedizolid Phosphate Agreements

	Bayer Pharma AG

	In connection with the Company's acquisition of Trius in September 2013, Cubist acquired a July 2011 collaboration and license agreement between Trius and Bayer Pharma AG, or Bayer. Under the terms of the agreement, Bayer was granted exclusive rights to develop and commercialize tedizolid phosphate in China, Japan and substantially all other countries in Asia, excluding North and South Korea, Africa, Latin America and the Middle East, or the Bayer Licensed Territory. Trius retained full development and commercialization rights outside the Bayer Licensed Territory, including the U.S., Canada and the EU, but excluding North and South Korea, where Dong-A ST Co., Ltd., or Dong-A, retained its rights. In exchange for development and commercialization rights in the Bayer Licensed Territory, Bayer made an upfront, non-refundable payment of $25.0 million to Trius, prior to Cubist's acquisition of Trius, and agreed to support approximately 25% of the future development costs of tedizolid phosphate required for global approval for treatment of acute bacterial skin and skin structure infections, or ABSSSI, and hospital-acquired bacterial pneumonia, or HABP, or ventilator-associated bacterial pneumonia, or VABP, subject to certain adjustments and limitations. In addition, Bayer agreed to support 100% of the future development costs required for local approval in the Bayer Licensed Territory. Cubist is also eligible to receive remaining payments of up to $55.0 million under the agreement upon the achievement of certain development, regulatory, and sales milestones and double-digit royalties on net sales of tedizolid phosphate in the Bayer Licensed Territory.

	Dong-A ST Co., Ltd.

	In connection with the Company's acquisition of Trius in September 2013, Cubist acquired rights to tedizolid phosphate. Trius licensed exclusive worldwide rights, excluding North and South Korea, to develop, manufacture and market tedizolid phosphate from Dong-A under a January 2007 license agreement. As a result of acquiring Trius, Cubist assumed obligations under the license agreement to pay Dong-A remaining milestone payments of up to $11.5 million if certain development and regulatory approval milestones are achieved. As of December 31, 2013, the Company has an obligation to make remaining milestone payments to Dong-A of up to $8.5 million. In addition, Cubist is obligated to pay Dong-A tiered single-digit royalties on worldwide net sales of tedizolid phosphate on a country-by-country basis, excluding North and South Korea, until the later of: (i) 12 years after the date of the first commercial sale of tedizolid phosphate in such country; and (ii) the expiration of the last-to-expire patent covering tedizolid phosphate in such country. The license agreement terminates upon the expiration of all of the royalty obligations under the agreement.

	Ceftolozane/tazobactam Agreements

	Astellas Pharma Inc.

	Cubist's development and commercialization rights to ceftolozane under Calixa's original November 2007 agreement with Astellas Pharma Inc., or Astellas, covered all territories of the world except certain Asia-Pacific and Middle Eastern territories. The agreement was amended in September 2010 to allow Cubist to develop ceftolozane/tazobactam and other products that incorporate ceftolozane in all territories of the world.

	In March 2013, the license agreement with Astellas was amended to expand the territory for which Cubist holds the rights to manufacture, market and sell any eventual products that incorporate ceftolozane, including ceftolozane/tazobactam, to include the Asia-Pacific and Middle East territories that Astellas had retained under the original agreement. As a result of this amendment, Cubist owns all worldwide rights to ceftolozane/tazobactam, subject to ongoing milestone and royalty obligations to Astellas. As consideration for these expanded rights, Cubist made a one-time payment of $25.0 million to Astellas in March 2013, which was recorded within research and development expense within the consolidated statements of income for the year ended December 31, 2013, as the acquisition of these rights was not accounted for as a business combination and the asset has no alternative future use.

	The Company has an obligation to make remaining milestone payments to Astellas that could total up to $40.0 million if certain specified development, regulatory and sales milestones are achieved. If the licensed products are successfully developed and commercialized, Cubist will be required to pay Astellas tiered single-digit royalties on net sales of such products. Unless terminated earlier in accordance with the agreement, the agreement expires on a country-by-country basis when the Company stops developing or selling licensed products in such country.

	Other

	In April 2011, the Company entered into a settlement and license agreement, or settlement agreement, with Teva Parenteral Medicines Inc., or Teva, and its affiliates to resolve the Company's patent infringement litigation with respect to CUBICIN that Cubist filed in response to Teva's notification that it had submitted an Abbreviated New Drug Application, or ANDA, to the FDA seeking approval to market a generic version of CUBICIN. The settlement agreement provides for a full settlement and release by both Cubist and Teva of all claims that were or could have been asserted in the patent infringement litigation and all resulting damages or other remedies. Under the settlement agreement, the Company granted Teva a non-exclusive, royalty-free license to sell a generic daptomycin for injection product in the U.S. beginning on the later of: (i) December 24, 2017; and (ii) if Cubist's daptomycin for injection product receives pediatric exclusivity, June 24, 2018. The license Cubist granted to Teva would become effective prior to the later of these two dates if the patents that were the subject of the patent litigation with Teva are held invalid, unenforceable or not infringed with respect to a third party's generic version of daptomycin for injection, if a third party sells a generic version of daptomycin for injection under a license or other authorization from Cubist, or if there are no longer any unexpired patents listed in the FDA's list of "Approved Drug Products with Therapeutic Equivalence Evaluations," or the Orange Book, as applying to Cubist's NDA covering CUBICIN. Teva may also sell the generic daptomycin for injection supplied by Cubist at an earlier date upon certain specified types of "at risk" launches of a generic daptomycin for injection product by a third party.

The settlement agreement also provides that, for the period that the Company's license to Teva is in effect, Teva will purchase its U.S. requirements of daptomycin for injection exclusively from Cubist. The Company is required to use commercially reasonable efforts to satisfy Teva's requirements. The supply terms provide that the Company will receive payments from Teva for product supplied by Cubist reflecting two components: one based on the cost of product revenues plus a margin, and the other based on a specified percentage of gross margin (referred to as net profit in the supply terms) from Teva's sales of daptomycin supplied by Cubist. The supply terms also provide for a forecasting and ordering mechanism, and that Teva will determine the price at which any such generic daptomycin for injection product will be resold and the trademark and name under which it is sold, which may not be confusingly similar to Cubist's trademarks. In addition, under the supply terms, Teva may instead supply on its own or from a third party and sell its generic daptomycin for injection product in the event of specified Cubist supply failures or if the arrangement is terminated due to Cubist's uncured breach or bankruptcy.

The settlement agreement will remain in effect until the expiration of the term of the license granted by the Company to Teva and the expiration of a non-exclusive, royalty-free license granted by Teva to the Company under any Teva U.S. patent rights that Teva has the right to license and that may be applicable to CUBICIN and the daptomycin for injection product to be supplied by the Company to Teva.

BUSINESS_COMBINATIONS_AND_ACQU

BUSINESS COMBINATIONS AND ACQUISITIONS	12 Months Ended
BUSINESS COMBINATIONS AND ACQUISITIONS	Dec. 31, 2013
BUSINESS COMBINATIONS AND ACQUISITIONS	'
BUSINESS COMBINATIONS AND ACQUISITIONS	'

	D. BUSINESS COMBINATIONS AND ACQUISITIONS

	Acquisition of Optimer Pharmaceuticals, Inc.

	On October 24, 2013, Cubist completed its acquisition of Optimer, a publicly-held biopharmaceutical company, upon which Optimer became a wholly-owned subsidiary of Cubist. The transaction provided Cubist with an existing commercialized product, DIFICID.

	Under the terms of the merger agreement, Cubist purchased 100% of the issued and outstanding shares of Optimer common stock for: (i) $10.75 per share in cash plus (ii) one transferable contingent value right, or CVR, per share, which entitles the holder to receive an additional cash payment of up to $5.00 per CVR upon achievement of certain sales milestones for a maximum, undiscounted potential CVR payout of $253.9 million. The CVRs are registered for trading on the NASDAQ Global Select Market under the symbol "CBSTZ" and contingent consideration is recorded as a liability and measured at fair value based upon the market price of the CVR on the day of valuation. See Note F., "Fair Value Measurements," for additional information.

	The acquisition-date fair value of the consideration transferred is as follows:


			Total
			Acquisition-
			Date
			Fair Value
			(in thousands)
	Cash transferred		$	569,452
	Contingent consideration (CVRs)			115,634


	Total consideration transferred		$	685,086





	Prior to the acquisition, Cubist had a $25.0 million equity interest in Optimer in the form of non-voting senior preferred stock resulting from an interim financing arrangement. Cash transferred in the table above is comprised of $544.5 million in acquisition date payments and the $25.0 million of non-voting preferred stock. In addition, the acquisition-date fair value of total consideration transferred above excludes approximately $7.2 million of cash payments made to settle nonvested equity awards of Optimer pursuant to the merger agreement, which was recognized as stock-based compensation expense in the postcombination period ended December 31, 2013. The total $7.2 million charge was comprised of $1.8 million of research and development expense and $5.4 million of selling, general and administrative expense.

	The transaction was accounted for as a business combination under the acquisition method of accounting. Accordingly, the tangible and identifiable intangible assets acquired and liabilities assumed were recorded at fair value as of the date of acquisition, with the remaining purchase price recorded as goodwill.

	The following table summarizes the estimated fair values of the assets acquired and liabilities assumed at the date of acquisition:


			October 24,
			2013
			(in thousands)
	Cash		$	31,466
	Investments			42,067
	Inventory			32,000
	DIFICID intangible asset			561,000
	Contract intangible asset			36,000
	Deferred tax assets			116,199
	Goodwill			108,631
	Other assets acquired			15,942


	Total assets acquired			943,305


	Deferred tax liabilities			(224,110	)
	Other liabilities assumed			(34,109	)


	Total liabilities assumed			(258,219	)


	Total net assets acquired		$	685,086





The purchase price allocation has been prepared on a preliminary basis and is subject to change as additional information becomes available concerning the fair value and tax basis of the assets acquired and liabilities assumed. Any adjustments to the purchase price allocation will be made as soon as practicable but no later than one year from October 24, 2013, the acquisition date.

The fair value of the DIFICID intangible asset was determined using an income approach, including a discount rate of 14.5% applied to the projected cash flows. The Company believes the assumptions are representative of those a market participant would use in estimating fair value. The DIFICID intangible asset will be amortized to cost of product revenues over its expected useful life of approximately 14 years. The fair value of the contract intangible asset relates to a collaborative research and license agreement with Cempra, Inc., or Cempra, under which Cubist may receive certain milestone payments if certain macrolide and ketolide antibiotic product candidates are developed by Cempra and may receive royalty payments based on a percentage of any net sales of licensed products. The fair value of the contract intangible asset was determined using an income approach, including a discount rate of 16.0% applied to the projected cash flows. The Company believes the assumptions are representative of those a market participant would use in estimating fair value. The contract intangible asset will be amortized to research and development expense over its expected life of approximately 11 years.

The deferred tax assets of $116.2 million are primarily related to federal NOL carryforwards and federal research tax credits. See Note O., "Income Taxes," for additional information. The deferred tax liability of $224.1 million primarily relates to the temporary differences associated with the DIFICID intangible asset, which is not deductible for tax purposes.

Goodwill is calculated as the difference between the acquisition-date fair value of the consideration transferred and the fair values of the assets acquired and liabilities assumed, and is not expected to be deductible for income tax purposes. Goodwill is recorded as an indefinite-lived asset and is not amortized but tested for impairment on an annual basis or when indications of impairment exist.

The operating results of Optimer for the period from October 24, 2013, to December 31, 2013, including revenues and an operating loss of $14.7 million and $11.0 million, respectively, have been included in the Company's consolidated financial statements as of and for the year ended December 31, 2013. The Company incurred a total of $12.4 million in transaction costs in connection with the acquisition, which were included in selling, general and administrative expenses within the consolidated statements of income for the year ended December 31, 2013.

The following supplemental unaudited pro forma information presents Cubist's financial results as if the acquisition of Optimer had occurred on January 1, 2012 (in thousands):


		For the Years Ended
		December 31,
		2013			2012
		(unaudited)
Total revenues, net		$	1,101,824		$	1,004,641
Net (loss) income		$	(91,973	)	$	26,100

The above unaudited pro forma information was determined based on the historical GAAP results of Cubist and Optimer. The unaudited pro forma consolidated results are not necessarily indicative of what the Company's consolidated results of operations actually would have been if the acquisition was completed on January 1, 2012. The unaudited pro forma consolidated net (loss) income includes pro forma adjustments relating to the following significant recurring and non-recurring items directly attributable to the business combination:



(i)
elimination of $34.3 million of transaction costs for both Cubist and Optimer from the year ended December 31, 2013, and inclusion of these transaction costs in the year ended December 31, 2012;

(ii)
elimination of $7.2 million of stock-based compensation expense related to the acceleration of vesting of previously unvested Optimer awards in connection with the acquisition from the year ended December 31, 2013, and inclusion of this charge in the year ended December 31, 2012;

(iii)
additional amortization of the DIFICID and contract intangible assets acquired of $35.6 million and $44.0 million for the years ended December 31, 2013 and 2012, respectively;

(iv)
elimination of $21.6 million of expense related to restructuring charges from the year ended December 31, 2013, and inclusion of these restructuring charges in the year ended December 31, 2012;

(v)
elimination of intercompany revenues related to Cubist's co-promotion of DIFICID of $12.3 million and $23.2 million for the years ended December 31, 2013 and 2012, respectively;

(vi)
additional interest expense related to the 2018 Notes and 2020 Notes, which were used to fund the acquisition, of $29.7 million and $41.5 million for the years ended December 31, 2013 and 2012, respectively; and

(vii)
the tax effect of the unaudited pro forma consolidated net income and adjustments for the year ended December 31, 2013 and 2012.

Acquisition of Trius Therapeutics, Inc.

On September 11, 2013, Cubist completed its acquisition of Trius, a publicly-held biopharmaceutical company, upon which Trius became a wholly-owned subsidiary of Cubist. The transaction provided Cubist with an existing late-stage product candidate, tedizolid phosphate.

Under the terms of the merger agreement, Cubist purchased 100% of the issued and outstanding shares of Trius common stock for: (i) $13.50 per share in cash plus (ii) one non-transferable CVR per share, which entitles the holder to receive an additional cash payment of up to $2.00 per CVR upon achievement of certain sales milestones for a maximum, undiscounted potential CVR payout of $108.4 million. The CVRs may not be sold, assigned, transferred, pledged, encumbered or disposed of, subject to limited exceptions. Contingent consideration is recorded as a liability and measured at fair value based on significant unobservable inputs. See Note F., "Fair Value Measurements," for additional information.

The acquisition-date fair value of the consideration transferred is as follows:


		Total
		Acquisition-
		Date Fair
		Value
		(in thousands)
Cash transferred, including transaction costs		$	695,710
Contingent consideration (CVRs)			4,603


Total consideration transferred		$	700,313





Cubist paid $13.7 million in transaction costs on behalf of Trius, which are included as cash transferred in total consideration transferred in the table above. The acquisition-date fair value of total consideration transferred above excludes approximately $22.7 million of primarily cash payments made to settle nonvested equity awards of Trius pursuant to the merger agreement, which was recognized as stock-based compensation expense in the postcombination period ended December 31, 2013. The total $22.7 million charge was comprised of $11.0 million of research and development expense and $11.7 million of selling, general and administrative expense.

The transaction was accounted for as a business combination under the acquisition method of accounting. Accordingly, the tangible and identifiable intangible assets acquired and liabilities assumed were recorded at fair value as of the date of acquisition, with the remaining purchase price recorded as goodwill.

The following table summarizes the estimated fair values of the assets acquired and liabilities assumed at the date of acquisition :


		September 11,
		2013
		(in thousands)
Cash		$	22,697
Investments			39,513
IPR&D			659,000
Deferred tax assets			92,567
Goodwill			160,257
Other assets acquired			5,522


Total assets acquired			979,556


Deferred tax liabilities			(248,884	)
Other liabilities assumed			(30,359	)


Total liabilities assumed			(279,243	)


Total net assets acquired		$	700,313





The purchase price allocation was prepared on a preliminary basis and is subject to change as additional information becomes available concerning the fair value and tax basis of the assets acquired and liabilities assumed. During 2013, the Company recorded measurement period adjustments that resulted in an immaterial change to the purchase price allocation. The purchase price allocation is subject to change as additional information becomes available. Any additional adjustments to the purchase price allocation will be made as soon as practicable but no later than one year from September 11, 2013, the acquisition date.

The fair value of the acquired IPR&D asset relates to tedizolid phosphate. The fair value was determined using an income approach, including a discount rate of 9.5%, applied to the probability-adjusted cash flows. The Company believes the assumptions are representative of those a market participant would use in estimating fair value.

The deferred tax assets of $92.6 million primarily relate to federal NOL carryforwards, capitalized research and development costs and federal research tax credits. See Note O., "Income Taxes," for additional information. The deferred tax liabilities of $248.9 million primarily relate to the temporary differences associated with acquired IPR&D, which is not deductible for tax purposes.

Goodwill is calculated as the difference between the acquisition-date fair value of the consideration transferred and the fair values of the assets acquired and liabilities assumed, and is not expected to be deductible for income tax purposes. Goodwill is recorded as an indefinite-lived asset and is not amortized but tested for impairment on an annual basis or when indications of impairment exist.

The operating results of Trius for the period from September 12, 2013, to December 31, 2013, including revenues and an operating loss of $2.0 million and $23.4 million, respectively, have been included in the Company's consolidated financial statements as of and for the year ended December 31, 2013. The Company incurred a total of $10.2 million in transaction costs in connection with the acquisition, excluding costs paid on behalf of Trius. These transaction costs were included in selling, general and administrative expenses within the consolidated statements of income for the year ended December 31, 2013.

The following supplemental unaudited pro forma information presents Cubist's financial results as if the acquisition of Trius had occurred on January 1, 2012 (in thousands):


		For the Years Ended
		December 31,
		2013			2012
		(unaudited)
Total revenues, net		$	1,054,442		$	938,460
Net (loss) income		$	(28,312	)	$	75,594

The above unaudited pro forma information was determined based on the historical GAAP results of Cubist and Trius. The unaudited pro forma consolidated results are not necessarily indicative of what the Company's consolidated results of operations actually would have been if the acquisition was completed on January 1, 2012. The unaudited pro forma consolidated net (loss) income includes pro forma adjustments relating to the following significant non-recurring items directly attributable to the business combination:



(i)
elimination of $24.9 million of transaction costs for both Cubist and Trius from the year ended December 31, 2013, and inclusion of these costs in the year ended December 31, 2012;

(ii)
elimination of $22.7 million of stock-based compensation expense related to the acceleration of vesting of previously unvested Trius awards in connection with the acquisition from the year ended December 31, 2013, and inclusion of this charge in the year ended December 31, 2012;

(iii)
elimination of $9.4 million of expense related to Trius severance and retention agreements from the year ended December 31, 2013, and inclusion of these charges in the year ended December 31, 2012;

(iv)
the tax effect of the unaudited pro forma consolidated net income and adjustments for the year ended December 31, 2013 and 2012; and

(v)
reclassification of certain Trius revenues related to research and development expense reimbursement to research and development expense of $4.1 million and $15.1 million for the year ended December 31, 2013 and 2012, respectively, in accordance with Cubist accounting policy.

Acquisition of Adolor Corporation

On December 12, 2011, Cubist acquired 100% of the outstanding shares of common stock of Adolor for cash consideration of $220.8 million and contingent consideration with an acquisition-date fair value of $110.2 million. Adolor's assets included an existing commercialized product, ENTEREG, and rights to an additional clinical-stage product candidate, bevenopran.

The transaction was accounted for as a business combination under the acquisition method of accounting. Accordingly, the tangible and identifiable intangible assets acquired and liabilities assumed were recorded at fair value, with the remaining purchase price recorded as goodwill.

Of the identifiable intangible assets acquired through the Company's acquisition of Adolor, $117.4 million related to the IPR&D asset, bevenopran. The fair value as of December 31, 2013, is approximately $43.4 million as a result of impairment charges recognized since the date of acquisition. See Note I., "Goodwill, IPR&D and Other Intangible Assets, Net," for additional information. The Company also recorded $163.3 million of finite-lived intangible assets related to the rights to ENTEREG, which is amortized to cost of product revenues over its expected useful life.

The Company incurred a total of $8.1 million in transaction costs in connection with the acquisition, which were included in selling, general and administrative expenses within the consolidated statements of income for the year ended December 31, 2011. The operating results of Adolor for the period from December 12, 2011, to December 31, 2011, including revenues of $2.6 million, have been included in the Company's consolidated financial statements for the year ended December 31, 2011.

The following supplemental unaudited pro forma information presents Cubist's financial results as if the acquisition of Adolor had occurred on January 1, 2010 (in thousands):


		For the Year
		Ended
		December 31, 2011
		(unaudited)
Total revenues, net		$	809,416
Net income		$	29,147

The above unaudited pro forma information was determined based on the historical GAAP results of Cubist and Adolor. The unaudited pro forma consolidated results are not necessarily indicative of what the Company's consolidated results of operations actually would have been if the acquisition was completed on January 1, 2010. The unaudited pro forma consolidated net income includes pro forma adjustments relating to the following significant recurring and non-recurring items directly attributable to the business combination:



(i)
inclusion of $20.2 million of additional cost of product revenues related to the amortization of the ENTEREG intangible asset and the fair value step-up of ENTEREG inventory sold during the years ended December 31, 2011;

(ii)
elimination of $13.1 million of transaction costs for both Cubist and Adolor and $9.3 million of restructuring charges for the year ended December 31, 2011, which are directly attributable to the transaction; and

(iii)
the tax effect of the unaudited pro forma consolidated net income and adjustments for the year ended December 31, 2011.

INVESTMENTS

INVESTMENTS	12 Months Ended
INVESTMENTS	Dec. 31, 2013
INVESTMENTS	'
INVESTMENTS	'

	E. INVESTMENTS

	Marketable Securities

	The following table summarizes the amortized cost and estimated fair value of the Company's marketable securities, which are considered to be available-for-sale investments and were included in short-term and long-term investments on the consolidated balance sheets:


		Amortized		Unrealized		Unrealized			Fair
		Cost		Gains		Losses			Value
		(in thousands)
	Balance at December 31, 2013:
	Bank deposits	$	40,000	$	—	$	—		$	40,000
	U.S. Treasury securities		67,648		6		(4	)		67,650
	Corporate and municipal notes		362,561		173		(36	)		362,698


	Total	$	470,209	$	179	$	(40	)	$	470,348




	Balance at December 31, 2012:
	Bank deposits	$	61,000	$	—	$	—		$	61,000
	U.S. Treasury securities		114,041		4		(3	)		114,042
	Corporate and municipal notes		640,234		158		(215	)		640,177


	Total	$	815,275	$	162	$	(218	)	$	815,219





	The following table contains information regarding the range of contractual maturities of the Company's investments:


		December 31,
		2013				2012
		Amortized		Fair		Amortized			Fair
		Cost		Value		Cost			Value
		(in thousands)
	Within 1 year	$	470,209	$	470,348	$	812,104		$	812,052
	1 - 2 years		—		—		3,171			3,167


	Total	$	470,209	$	470,348	$	815,275		$	815,219





	Certain short-term debt securities with original maturities of less than 90 days are included in cash and cash equivalents on the consolidated balance sheets and are not included in the tables above. In addition, certificates of deposit of $17.2 million and $60.1 million as of December 31, 2013 and 2012, respectively, were included within short-term investments in the consolidated balance sheets but are excluded from the tables above as they were not deemed to be securities. See Note B., "Accounting Policies," for additional information.

	Adynxx Option Agreement

	In February 2013, Cubist entered into an option agreement with Adynxx, Inc., or Adynxx. Under the agreement, Cubist made a $20.0 million payment to Adynxx, which was non-refundable except in limited circumstances, and obtained an exclusive option to acquire 100% of the outstanding shares of Adynxx. The option was exercisable any time prior to 60 days following Cubist's receipt of the data from a Phase 2 clinical trial for Adynxx's lead product candidate, AYX1, subject to extension in certain limited circumstances. After the Company's receipt of the AYX1 Phase 2 data in December 2013, management decided to not exercise the option and as a result recorded a $20.0 million impairment charge for the year ended December 31, 2013, representing the write-off of the non-refundable option payment.

FAIR_VALUE_MEASUREMENTS

FAIR VALUE MEASUREMENTS	12 Months Ended
FAIR VALUE MEASUREMENTS	Dec. 31, 2013
FAIR VALUE MEASUREMENTS	'
FAIR VALUE MEASUREMENTS	'

	F. FAIR VALUE MEASUREMENTS

	Recurring Fair Value Measurements

	The following tables set forth the Company's assets and liabilities that were accounted for at fair value on a recurring basis as of December 31, 2013 and 2012:


			December 31, 2013
			Fair Value Measurements Using
			Level 1			Level 2			Level 3			Total
			(in thousands)
	Assets
	Cash and cash equivalents:(1)
	Money market funds		$	146		$	—		$	—		$	146
	Short-term investments:(2)
	Bank deposits			—			40,000			—			40,000
	U.S. Treasury securities			67,650			—			—			67,650
	Corporate and municipal notes			—			362,698			—			362,698


	Total assets		$	67,796		$	402,698		$	—		$	470,494




	Liabilities
	Contingent consideration—Optimer CVRs		$	68,561		$	—		$	—		$	68,561
	Contingent consideration—other			—			—			154,761			154,761


	Total liabilities		$	68,561		$	—		$	154,761		$	223,322









			December 31, 2012
			Fair Value Measurements Using
			Level 1			Level 2			Level 3			Total
			(in thousands)
	Assets
	Cash and cash equivalents:(1)
	Corporate and municipal notes		$	—		$	18,422		$	—		$	18,422
	Short-term and long-term investments:(2)
	Bank deposits			—			61,000			—			61,000
	U.S. Treasury securities			114,042			—			—			114,042
	Corporate and municipal notes			—			640,177			—			640,177


	Total assets		$	114,042		$	719,599		$	—		$	833,641




	Liabilities
	Contingent consideration—other		$	—		$	—		$	189,213		$	189,213


Total liabilities		$	—		$	—		$	189,213		$	189,213






-1
Excludes $90.9 million and $85.6 million of cash as of December 31, 2013 and 2012, respectively.

-2
Excludes certificates of deposit of $17.2 million and $60.1 million recorded at cost as of December 31, 2013 and 2012, respectively.

Marketable Securities

The Company classifies its money market funds and U.S. Treasury securities as Level 1 assets under the fair value hierarchy as these assets have been valued using quoted market prices in active markets without any valuation adjustment. The Company classifies its bank deposits and corporate and municipal notes as Level 2 assets under the fair value hierarchy, as these assets have been valued using information obtained through a third-party pricing service at each balance sheet date, using observable market inputs that may include trade information, broker or dealer quotes, bids, offers, or a combination of these data sources.

Contingent Consideration

Level 1

In connection with the acquisition of Optimer, Cubist issued one transferable CVR for each outstanding share of Optimer's common stock. The CVRs are registered for trading on the NASDAQ Global Select Market under the symbol "CBSTZ". The fair value of the liability relating to the amount payable by the Company to the holders of the CVRs, upon the achievement of certain sales milestones for DIFICID and other specified products, was $68.6 million as of December 31, 2013. The fair value of the liability is based upon the market price of the security, which is traded in an active market, and is therefore considered a Level 1 liability within the fair value hierarchy. Changes in the fair value of the liability related to changes in the market price of the security are recognized within the consolidated statements of income. The undiscounted amount of contingent consideration that Cubist could pay to the holders of the Optimer CVRs ranges from zero to $253.9 million.

Level 3

In connection with the acquisitions of Trius, Adolor, and Calixa, Cubist recorded contingent consideration pertaining to the amounts potentially payable to the former stockholders of each company. Such contingent consideration is measured at fair value and is based on significant inputs not observable in the market, which represent Level 3 inputs within the fair value hierarchy. The valuation of contingent consideration uses assumptions the Company believes would be made by a market participant. The Company assesses these estimates on an ongoing basis as additional data impacting the assumptions is obtained. Changes in the fair value of contingent consideration related to updated assumptions and estimates are recognized within the consolidated statements of income.

Contingent consideration may change significantly as development progresses and additional data is obtained, affecting the Company's assumptions regarding probabilities of successful achievement of related milestones used to estimate the fair value of the liability and the timing in which they are expected to be achieved. In evaluating the fair value information, considerable judgment is required to interpret the market data used to develop the estimates. The estimates of fair value may not be indicative of the amounts that could be realized in a current market exchange. Accordingly, the use of different market assumptions and/or different valuation techniques could result in materially different fair value estimates.

The following table provides quantitative information associated with the fair value measurement of the Company's contingent consideration using Level 3 inputs:


		Contingent Consideration
		Trius		Adolor		Calixa
Fair value as of December 31, 2013: (in thousands)		$5,012		$44,161		$105,588
Valuation technique		Probability-adjusted		Probability-adjusted		Probability-adjusted
Valuation technique		discounted cash flow		discounted cash flow		discounted cash flow
Unobservable input
Probabilities of success—range		4.0% - 6.5%		25.0% - 30.0%		40.0% - 86.0%
(weighted average)		-5.80%		-27.00%		-65.00%
Periods in which milestones are projected to be achieved		2016		2018 - 2022		2014 - 2018
Discount rate		8.00%		5.3% / 13.0%		5.30%

The significant unobservable inputs used in the fair value measurement of Cubist's contingent consideration are the probabilities of successful achievement of development, regulatory and sales milestones, the period in which these milestones are expected to be achieved and a discount rate. Significant increases or decreases in any of the probabilities of success would result in a significantly higher or lower fair value measurement, respectively. Significant increases or decreases in the discount rate and/or the period in which milestones will be achieved would result in a significantly lower or higher fair value measurement, respectively.

Trius Therapeutics, Inc.—The fair value of contingent consideration relating to amounts payable by the Company to the former stockholders of Trius, upon the achievement of certain sales milestones of tedizolid phosphate and other specified products was estimated to be $5.0 million as of December 31, 2013. The undiscounted amount of contingent consideration that Cubist could pay to the former stockholders of Trius under the merger agreement ranges from zero to $108.4 million. Tedizolid phosphate is in development for the potential treatment of certain serious Gram-positive bacterial infections, including those caused by MRSA.

Adolor Corporation—The fair value of contingent consideration relating to amounts payable by the Company to the former stockholders of Adolor upon the achievement of certain regulatory milestones, sales milestones or a combination of both, with respect to bevenopran, was estimated to be $44.2 million and $77.0 million as of December 31, 2013 and 2012, respectively. The change in the fair value of the contingent consideration liability during the year ended December 31, 2013, of $32.8 million is primarily the result of reduced probabilities of pursuing the program, and the Company's decision to stop the Phase 3 efficacy trials in light of the FDA's planned 2014 Advisory Committee meeting to discuss the potential for elevated cardiovascular events related to mu-opioid antagonists and the enrollment challenges associated with the current design of these Phase 3 efficacy trials. The aggregate, undiscounted amount of contingent consideration that Cubist could pay to the former stockholders of Adolor under the merger agreement ranges from zero to $233.8 million. Bevenopran is in development for the potential treatment of opioid-induced constipation in patients with chronic, non-cancer pain.

Calixa Therapeutics Inc.—The fair value of contingent consideration relating to amounts payable by the Company to the former stockholders of Calixa, upon the achievement of certain development, regulatory and sales milestones with respect to ceftolozane/tazobactam, was estimated to be $105.6 million and $112.2 million as of December 31, 2013 and 2012, respectively. The change in fair value for the year ended December 31, 2013, is primarily due to a $40.0 million milestone payment made in August 2013 as a result of first patient enrollment in the Company's ceftolozane/tazobactam open-label study in patients with VABP and an increase in certain probabilities of success assumptions within the Company's valuation model due to ceftolozane/tazobactam meeting its primary endpoints of statistical non-inferiority compared to levofloxacin for complicated urinary tract infections, or cUTI, and meropenem for complicated intra-abdominal infections, or cIAI. The aggregate, remaining, undiscounted amount of contingent consideration that Cubist could pay to the former stockholders of Calixa under the merger agreement ranges from zero to $180.0 million. Ceftolozane/tazobactam is being developed as a potential treatment for cUTI, cIAI, HABP and VABP.

Changes in the fair value of contingent consideration based upon Level 3 inputs, were as follows:



		Contingent
		Consideration
		(in thousands)
Balance at December 31, 2011		$	248,234
Contingent consideration income			(29,021	)
Contingent consideration milestone payment			(30,000	)


Balance at December 31, 2012			189,213
Contingent consideration liability recorded upon acquisition			4,879
Contingent consideration expense			669
Milestone payment			(40,000	)


Balance at December 31, 2013		$	154,761





Other Fair Value Measurements

Debt

The Company estimates the fair value of its 2020 Notes, 2018 Notes and 2017 Notes, or collectively, the Convertible Senior Notes, by using a quoted market rate in an inactive market, which is classified as a Level 2 input. The estimated fair values of the Convertible Senior Notes were as follows:


		December 31,
		2013			2012
		(in thousands)
2020 Notes		$	516,843		$	—
2018 Notes			403,473			—
2017 Notes			550,317			699,750


Total estimated fair value of Convertible Senior Notes		$	1,470,633		$	699,750





See Note K., "Debt," for additional information.

Payable to Glaxo

In connection with the Company's acquisition of Adolor in December 2011, Cubist assumed the obligation to pay Glaxo annual payments totaling $22.5 million as a result of Adolor's termination of its collaboration agreement with Glaxo in September 2011. The payable to Glaxo was recorded at its estimated fair value at the time of acquisition and was allocated between current and non-current liabilities within the consolidated balance sheets based on the contractual payment dates. The fair value estimate utilizes a discount rate, which is classified as a Level 3 input. The Company has made total payments of $6.5 million to Glaxo. As of December 31, 2013, the carrying value of the remaining four annual payments to Glaxo of $16.0 million approximates its fair value. Imputed interest on the payable to Glaxo is recorded as interest expense within the consolidated statements of income.

Non-Recurring Fair Value Measurements

Certain assets such as IPR&D are measured at fair value on a non-recurring basis in periods subsequent to initial recognition. During 2013, the Company recorded an impairment charge of $35.3 million to write down the bevenopran IPR&D asset to its revised fair value, which was recorded as impairment charges within its consolidated statements of income for the year ended December 31, 2013. The fair value was derived from assumptions that are representative of those a market participant would use in estimating fair value. See Note I., "Goodwill, IPR&D and Other Intangible Assets, Net," for additional information.

The non-recurring Level 3 fair value measurement of the impairment analysis performed in the fourth quarter of 2013 included the following significant unobservable inputs:


		Fair Value as of			Valuation Technique		Unobservable Input		Percentage
		December 31,
		2013
		(in thousands)
IPR&D asset (bevenopran)		$	43,400		Income approach -		Discount rate			13	%
					Probability-adjusted
					discounted cash flow

INVENTORY

INVENTORY	12 Months Ended
INVENTORY	Dec. 31, 2013
INVENTORY	'
INVENTORY	'

	G. INVENTORY

	Inventory consisted of the following:


		December 31,
		2013		2012
		(in thousands)
	Raw materials	$	17,904	$	9,132
	Work-in-process		8,104		8,485
	Finished goods		31,655		24,330


	Inventory		57,663		41,947
	Included in other assets:
	Raw materials		57,284		34,091
	Work-in-process		1,882		1,733
	Finished goods		—		1,669


	Total	$	116,829	$	79,440





	Inventory included in other assets within the consolidated balance sheets as of December 31, 2013 and 2012, represents the amount of DIFICID and ENTEREG inventory held that is in excess of the amount expected to be sold within one year. In connection with the acquisitions of Optimer and Adolor, Cubist recorded the acquired DIFICID and ENTEREG inventory at a preliminary fair value, which required a step-up adjustment to recognize the inventory at its expected net realizable value. See Note D., "Business Combinations and Acquisitions," for additional information.

	DIFICID finished goods have a shelf-life of three years from the date of manufacture. The Company expects to sell the DIFICID finished goods prior to expiration. The Company recorded an inventory fair value step-up on acquired DIFICID API, which will be recorded to cost of product revenues within the consolidated statements of income in the period in which the inventory is sold. The DIFICID API, which is classified as raw materials, has a shelf-life of three years from the date of manufacture. The Company expects to process substantially all of the DIFICID API into finished goods over a period of approximately three years based on the Company's long-range sales projections of DIFICID.

	ENTEREG finished goods have a shelf-life of three years from the date of manufacture. The Company expects to sell the ENTEREG finished goods prior to expiration, with the corresponding inventory step-up recorded to cost of product revenues within the consolidated statements of income in the period in which the inventory is sold. The ENTEREG API, which is classified as raw materials, has a shelf-life of five years from the date of manufacture, but can be reprocessed at an immaterial cost to the Company with no expected reduction in potency, thereby extending its shelf-life as needed. The Company expects to consume substantially all of the ENTEREG API over a period of approximately seven years based on the Company's long-range sales projections of ENTEREG.

PROPERTY_AND_EQUIPMENT_NET

PROPERTY AND EQUIPMENT, NET	12 Months Ended
PROPERTY AND EQUIPMENT, NET	Dec. 31, 2013
PROPERTY AND EQUIPMENT, NET	'
PROPERTY AND EQUIPMENT, NET	'

	H. PROPERTY AND EQUIPMENT, NET

	Property and equipment, net consisted of the following at:


		December 31,
		2013			2012
		(in thousands)
	Land and buildings	$	172,199		$	166,659
	Laboratory equipment		48,997			35,961
	Furniture and fixtures		4,923			3,351
	Computer hardware and software		28,126			20,903
	Construction-in-progress		1,256			3,120


			255,501			229,994
	Less: accumulated depreciation		(77,957	)		(63,529	)


	Property and equipment, net	$	177,544		$	166,465





	Depreciation expense was $14.4 million, $12.4 million and $9.0 million in 2013, 2012 and 2011, respectively.

GOODWILL_IPR_AND_D_AND_OTHER_I

GOODWILL, IPR AND D AND OTHER INTANGIBLE ASSETS, NET	12 Months Ended
GOODWILL, IPR AND D AND OTHER INTANGIBLE ASSETS, NET	Dec. 31, 2013
GOODWILL, IPR&D AND OTHER INTANGIBLE ASSETS, NET	'
GOODWILL, IPR&D AND OTHER INTANGIBLE ASSETS, NET	'

	I. GOODWILL, IPR&D AND OTHER INTANGIBLE ASSETS, NET

	Goodwill

	The Company's goodwill balance as of December 31, 2013, changed from the goodwill balance as of December 31, 2012 as follows:


			Goodwill
			(in thousands)
	Beginning balance as of December 31, 2012		$	114,130
	Goodwill acquired			268,888


	Ending balance as of December 31, 2013		$	383,018





	Goodwill of $268.9 million was recognized in connection with the acquisition of Trius in September 2013 and Optimer in October 2013. See Note D., "Business Combinations and Acquisitions," for additional information. As of December 31, 2013, there were no accumulated impairment losses. Goodwill has been assigned to the Company's single reporting unit, which is the single operating segment by which the chief decision maker manages the Company. See Note P., "Segment Information," for additional information.

	IPR&D

	The carrying value of the Company's IPR&D assets consisted of the following at:


			December 31,
			2013			2012
			(in thousands)
	Development and potential commercialization of:
	Tedizolid phosphate		$	659,000		$	—
	Bevenopran			43,400			78,700
	Ceftolozane/tazobactam for HABP and VABP			174,000			174,000
	Ceftolozane/tazobactam for cUTI and cIAI			20,000			20,000


	Total IPR&D		$	896,400		$	272,700





	An IPR&D asset for tedizolid phosphate of $659.0 million was recognized in connection with the acquisition of Trius in September 2013. See Note D., "Business Combinations and Acquisitions," for additional information.

	During the fourth quarters of 2013 and 2012, the Company updated the fair value estimates of the bevenopran IPR&D asset as a result of internal decisions and in conjunction with the Company's annual impairment tests. During the fourth quarter of 2013, the Company revised the fair value estimates of its bevenopran IPR&D asset to incorporate reduced probabilities of pursuing the program and its decision to stop the bevenopran Phase 3 efficacy trials in light of the FDA's planned 2014 Advisory Committee meeting to discuss the potential for elevated cardiovascular events related to mu-opioid antagonists and the enrollment challenges associated with the current design of these Phase 3 efficacy trials. Accordingly, in the year ended December 31, 2013, the Company recorded an impairment charge of $35.3 million to write down its bevenopran IPR&D asset to its revised fair value of $43.4 million. In 2012, the fair value estimate reflected a decision to deprioritize efforts to develop bevenopran for the EU market, resulting in the recognition of a $38.7 million impairment charge in the year ended December 31, 2012.

	Development of tedizolid phosphate, ceftolozane/tazobactam and bevenopran requires various levels of internal and external testing, clinical trials and approvals from the FDA or comparable foreign regulatory authorities before any of these product candidates could be commercialized for various indications in the U.S. or other territories. Drug development involves a high degree of risk, and most products that make it into clinical development do not receive marketing approval. Numerous risks and uncertainties can delay or stop clinical development of a pharmaceutical product prior to the receipt of marketing approval, including, but not limited to: results from clinical trials that do not support continuing development, issues related to manufacturing or intellectual property protection, and other events or circumstances that cause unanticipated delays, technical problems or other difficulties. Given these risks and uncertainties, there can be no assurance that the development of the above mentioned development programs for any of the indications will be successfully completed. If the programs are not successful, in whole or in part, or are not completed in a timely manner, the Company may not realize the expected financial benefits from such programs, which could have a material adverse effect on the Company's results of operations.

	Other Intangible Assets

	Other intangible assets, net, consisted of the following finite-lived assets:


			December 31,
			2013			2012
			(in thousands)
	Patents		$	2,627		$	2,627
	Acquired technology rights			788,800			191,800


	Other intangible assets, gross			791,427			194,427
	Less: accumulated amortization—patents			(2,493	)		(2,431	)
accumulated amortization—acquired technology rights			(67,868	)		(39,166	)


Other intangible assets, net		$	721,066		$	152,830





The Company recorded $597.0 million of intangible assets in connection with its acquisition of Optimer in October 2013, which is included within acquired technology rights and is comprised of gross asset values of $561.0 million and $36.0 million for the DIFICID and contract intangible assets acquired, respectively. See Note D., "Business Combinations and Acquisitions," for additional information. In addition, other intangible assets includes the ENTEREG intangible asset acquired in connection with the acquisition of Adolor in 2011. The ENTEREG intangible asset is being amortized using the straight-line method over approximately nine years. Amortization expense was $28.8 million, $20.9 million and $3.5 million in 2013, 2012 and 2011, respectively, and is primarily included within cost of product revenues.

The estimated aggregate remaining amortization of other intangible assets as of December 31, 2013, for each of the five succeeding years is as follows:


		(in thousands)
2014		$	64,741
2015			64,741
2016			63,460
2017			62,221
2018			62,221
2019 and thereafter			403,682


Total		$	721,066

ACCRUED_LIABILITIES

ACCRUED LIABILITIES	12 Months Ended
ACCRUED LIABILITIES	Dec. 31, 2013
ACCRUED LIABILITIES	'
ACCRUED LIABILITIES	'

	J. ACCRUED LIABILITIES

	Accrued liabilities consisted of the following at:


		December 31,
		2013		2012
		(in thousands)
	Accrued royalties	$	83,591	$	72,103
	Accrued bonus		24,540		13,971
	Accrued Medicaid, Medicare and commercial rebates		18,595		20,565
	Accrued clinical trials		44,830		29,143
	Accrued benefits and incentive compensation		18,183		8,603
	Accrued restructuring		19,753		933
	Other accrued costs		35,586		18,315


	Accrued liabilities	$	245,078	$	163,633

DEBT

DEBT	12 Months Ended
DEBT	Dec. 31, 2013
DEBT	'
DEBT	'

	K. DEBT

	Convertible Senior Notes

	Long-term debt, net is comprised of the Company's Convertible Senior Notes, as follows:


			December 31,
			2013			2012
			(in thousands)
	2020 Convertible Senior Notes
	Principal amount outstanding		$	450,000		$	—
	Unamortized discount			(111,015	)		—


	Net carrying amount			338,985			—


	2018 Convertible Senior Notes
	Principal amount outstanding			350,000			—
	Unamortized discount			(65,733	)		—


	Net carrying amount			284,267			—


	2017 Convertible Senior Notes
	Principal amount outstanding			228,822			450,000
	Unamortized discount			(34,244	)		(82,189	)


	Net carrying amount			194,578			367,811


	Total Convertible Senior Notes
	Principal amount outstanding			1,028,822			450,000
	Unamortized discount			(210,992	)		(82,189	)


	Net carrying amount		$	817,830		$	367,811





	In accordance with accounting guidance for debt with conversion and other options, Cubist separately accounted for the liability and equity components of the Convertible Senior Notes by allocating the proceeds between the liability component and the embedded conversion option, or equity component, due to Cubist's ability to settle the Convertible Senior Notes in cash, common stock or a combination of cash and common stock, at Cubist's option. The allocation was performed in a manner that reflected the non-convertible debt borrowing rate of Cubist for similar debt. The equity component of the Convertible Senior Notes was recognized as a debt discount and represents the difference between the proceeds from the issuance of the convertible notes and the fair value of the liability of the Convertible Senior Notes on their respective dates of issuance. The debt discount is amortized to interest expense using the effective interest method over the expected life of a similar liability without an equity component.

	2018 Convertible Senior Notes and 2020 Convertible Senior Notes

	In September 2013, Cubist issued $800.0 million aggregate principal amount of convertible senior unsecured notes in two series, with one series consisting of $350.0 million aggregate principal amount of the 2018 Notes, and the other series consisting of $450.0 million aggregate principal amount of the 2020 Notes, resulting in net proceeds to Cubist, after debt issuance costs, of $775.6 million. The 2018 Notes and 2020 Notes are convertible into common stock at an initial conversion rate of 12.1318 shares of common stock per $1,000 principal amount of convertible notes, subject to adjustment upon certain events, which is equivalent to an initial conversion price of approximately $82.43 per share of common stock. Holders of the 2018 Notes and 2020 Notes may convert their notes at any time prior to the close of business on the business day immediately before March 1, 2018 or March 1, 2020, respectively, only under the following circumstances: (i) during any calendar quarter (and only during such calendar quarter), if the last reported sale price of the common stock for at least 20 trading days (whether or not consecutive) during a period of 30 consecutive trading days ending on the last trading day of the immediately preceding calendar quarter is greater than or equal to 130% of the conversion price on each applicable trading day; (ii) during the five business day period after any five consecutive trading day period, or the measurement period, in which the trading price per $1,000 principal amount of notes for each trading day of the measurement period was less than 98% of the product of the last reported sale price of Cubist's common stock and the conversion rate on each such trading day; or (iii) upon the occurrence of specified corporate events. Upon conversion, Cubist may deliver cash, common stock or a combination of cash and common stock, at Cubist's option.

	The 2018 Notes and 2020 Notes will mature on September 1, 2018 and 2020, respectively, unless repurchased or converted in accordance with their terms prior to such date. The 2018 Notes and 2020 Notes bear cash interest at an annual rate of 1.125% and 1.875%, respectively, which is payable on March 1^st and September 1^st of each year, beginning on March 1, 2014. As of December 31, 2013, the "if-converted value" did not exceed the principal amount of the 2018 Notes and 2020 Notes. The fair value of the remaining aggregate principal amount of the outstanding 2018 Notes and 2020 Notes was estimated to be $403.5 million and $516.8 million, respectively, as of December 31, 2013, and was determined using a quoted market rate in an inactive market.

	In connection with the issuance of the 2018 Notes and 2020 Notes, the Company incurred $24.4 million of issuance costs, which primarily consisted of underwriting, legal and other professional fees. The portions of these costs allocated to the equity components totaling $5.6 million were recorded as a reduction to additional paid-in capital. The portions of these costs allocated to the liability components totaling $18.8 million were recorded as assets on the balance sheet. The portions allocated to the liability components are amortized to interest expense using the effective interest method over the expected life of the respective 2018 Notes and 2020 Notes.

	The Company determined the expected life of the debt for the 2018 Notes and 2020 Notes to be equal to the original five-year and seven-year terms of each of the 2018 Notes and 2020 Notes, respectively. The carrying value of the equity component related to the 2018 Notes and 2020 Notes as of December 31, 2013, net of issuance costs and taxes, was $42.6 million and $70.5 million, respectively. The effective interest rates on the liability components of the 2018 Notes and 2020 Notes for the period from the date of issuance through December 31, 2013 were 5.7% and 6.4%, respectively.

	2017 Convertible Senior Notes

	In October 2010, Cubist issued $450.0 million aggregate principal amount of the 2017 Notes, resulting in net proceeds to Cubist, after debt issuance costs, of $436.0 million. The 2017 Notes are convertible into common stock at an initial conversion rate of 34.2759 shares of common stock per $1,000 principal amount of convertible notes, subject to adjustment upon certain events, which is equivalent to an initial conversion price of approximately $29.18 per share of common stock. Holders of the 2017 Notes may convert their notes at any time prior to the close of business on the business day immediately preceding May 1, 2017, only under the following circumstances: (i) during any calendar quarter (and only during such calendar quarter), if the last reported sale price of the common stock for at least 20 trading days (whether or not consecutive) during a period of 30 consecutive trading days ending on the last trading day of the immediately preceding calendar quarter is greater than or equal to 130% of the conversion price on each applicable trading day; (ii) during the five business day period after any five consecutive trading day period, or the measurement period, in which the trading price per $1,000 principal amount of notes for each trading day of the measurement period was less than 98% of the product of the last reported sale price of Cubist's common stock and the conversion rate on each such trading day; or (iii) upon the occurrence of specified corporate events. Upon conversion, Cubist may deliver cash, common stock or a combination of cash and common stock, at Cubist's option.

	The 2017 Notes will mature on November 1, 2017, unless repurchased or converted in accordance with their terms prior to such date. The 2017 Notes bear cash interest at an annual rate of 2.50%, which is payable on May 1^st and November 1^st of each year. As of December 31, 2013, the "if-converted value" exceeded the remaining principal amount of the 2017 Notes by $311.3 million. The fair value of the remaining aggregate principal amount of the outstanding 2017 Notes was estimated to be $550.3 million as of December 31, 2013, and was determined using a quoted market rate in an inactive market.

The Company determined the expected life of the 2017 Notes to be equal to the original seven-year term of each of the 2017 Notes, resulting in an amortization period ending on November 1, 2017. The carrying value of the equity component related to the 2017 Notes as of December 31, 2013 and 2012, net of issuance costs and taxes, was $33.8 million and $66.4 million, respectively. For the years ended December 31, 2013, 2012 and 2011, the effective interest rate on the liability component of the 2017 Notes was 7.0%.

In September 2013, certain holders of $221.2 million of the aggregate principal amount of the 2017 Notes converted their notes at a conversion rate of 34.2759 shares of common stock per $1,000 of principal amount, or approximately $29.18 per share of common stock, into 7,580,923 shares of the Company's common stock. To induce these holders to convert, the Company agreed to make individually-negotiated cash payments to the converting holders of the 2017 Notes in an aggregate amount of $22.0 million as consideration for their agreement to convert their 2017 Notes. No transaction or solicitation fees were incurred as a result of the conversion and privately-negotiated payments. The conversions were accounted for as an extinguishment of the liability and equity components of the 2017 Notes. In accordance with the accounting guidance for induced conversions of convertible debt with a cash conversion feature, the Company recognized an aggregate loss of $34.6 million during the year ended December 31, 2013, comprised of: (i) $22.0 million equal to the amount of the cash inducement payments, which represents the fair value of the consideration transferred in excess of the fair value of consideration issuable in accordance with the original conversion terms and (ii) $12.6 million representing the difference between the net carrying value and the fair value of the liability component of the principal at the time of each conversion. The aggregate loss was recorded to other income (expense) within the consolidated statements of income. The remainder of the consideration transferred was allocated to the reacquisition of the equity component and recorded as a reduction to additional paid-in capital.

Convertible Bond Hedge and Warrant Transactions

To minimize the impact of potential dilution to the Company's common stock upon conversion of the 2018 Notes and 2020 Notes, Cubist entered into convertible bond hedges covering 9,705,442 shares of the Company's common stock. The convertible bond hedges have an exercise price of approximately $82.43 per share and are exercisable when and if the 2018 Notes and 2020 Notes are converted. If upon conversion of the 2018 Notes and 2020 Notes, the price of the Company's common stock is above the exercise price of the convertible bond hedges, the counterparties will deliver shares of the Company's common stock and/or cash with an aggregate value approximately equal to the difference between the price of the Company's common stock at the conversion date and the exercise price, multiplied by the number of shares of the Company's common stock related to the convertible bond hedges being exercised. The convertible bond hedges are separate transactions entered into by the Company and are not part of the terms of the 2018 Notes, 2020 Notes or the warrants, which are discussed below. Holders of the 2018 Notes, 2020 Notes and warrants will not have any rights with respect to the convertible bond hedges. The Company paid $179.4 million for these convertible bond hedges and recorded this amount as a reduction to additional paid-in capital, net of tax.

Concurrently with entering into the convertible bond hedge transactions, Cubist entered into warrant transactions whereby Cubist sold warrants to acquire, subject to customary adjustments, 9,705,442 shares of the Company's common stock with an exercise price of approximately $96.43 per share, also subject to adjustment. The warrants are exercisable over the 80 trading day period beginning on November 30, 2018 or November 30, 2020, as applicable. The warrants will have a dilutive effect to the extent that the market price per share of the Company's common stock, as measured under the terms of the warrant transactions, exceeds the applicable exercise price of the warrants during the measurement period at the maturity of the warrants. The Company received $121.7 million for these warrants and recorded this amount to additional paid-in capital.

2013 Convertible Subordinated Notes

In October 2012, Cubist called for redemption of the remaining $34.5 million aggregate principal amount of its outstanding 2013 Notes and notified holders that all conversions of the 2013 Notes prior to the date of redemption would be settled in cash. Cubist held the right on or after June 20, 2011, to redeem all or a portion of the 2013 Notes at 100% of the principal amount plus accrued and unpaid interest to the date of redemption if the closing price of Cubist's common stock on the date of the redemption notice was greater than 150% of the conversion price for at least 20 trading days (whether or not consecutive) out of 30 consecutive trading days immediately prior to the date Cubist gave notice of the redemption. The 2013 Notes were convertible at any time prior to maturity into common stock at an initial conversion rate of 32.4981 shares of common stock per $1,000 of the 2013 Notes principal, subject to adjustment upon certain events, which is equivalent to an initial conversion price of approximately $30.77 per share of common stock. Cubist could deliver cash or a combination of cash and common stock in lieu of shares of common stock, at Cubist's option. Substantially all holders of the 2013 Notes elected to convert, and in November 2012, the Company retired the 2013 Notes at an average stock price of approximately $42.14 per share, resulting in a cash outflow of $47.2 million.

In June 2012, the Company repurchased, in privately-negotiated transactions, $74.7 million of the principal amount of its 2013 Notes at an average price of approximately $136.07 per $100 par value of debt plus accrued interest and transaction fees, resulting in a cash outflow of $102.6 million. The repurchases in June 2012 and November 2012 resulted in an aggregate loss of $4.4 million during the year ended December 31, 2012, primarily due to the difference between the net carrying value and the fair value of the liability component of the principal at the time of each repurchase. The aggregate loss was recorded to other income (expense) within the consolidated statements of income.

The table below summarizes the interest expense the Company incurred on its Convertible Senior Notes and other interest expense, which includes interest expense for the payable to Glaxo, for the periods presented:


		For the Years Ended
		December 31,
		2013			2012			2011
		(in thousands)
Contractual interest coupon payment		$	13,370		$	12,667		$	13,707
Amortization of discount on debt			20,333			17,244			18,447
Amortization debt issuance costs			3,048			1,971			1,828
Other interest expense			851			1,109			—
Capitalized interest			—			—			(2,567	)


Total interest expense		$	37,602		$	32,991		$	31,415





At December 31, 2013, future payments of principal and interest on existing debt and the payable to Glaxo are due as follows:


		Principal
		(in thousands)
2014		$	3,500
2015			3,500
2016			4,500
2017			233,322
2018			350,000
2019 and thereafter			450,000


Total payments			1,044,822
Less current portion			(3,500	)


Total long-term debt and payable obligations		$	1,041,322





Credit Facility

In November 2012, Cubist entered into a $150.0 million three-year senior secured, syndicated revolving credit facility, or the credit facility, with a group of lenders, including Royal Bank of Canada, or RBC, as administrative agent. In September 2013, the Company entered into an amendment to the credit facility. The credit facility was amended to: (i) permit the 2018 Notes, 2020 Notes and the convertible bond hedge and warrant transactions; (ii) adjust the definition of consolidated adjusted EBITDA to permit specific acquisitions; (iii) modify certain covenants related to investments, restricted payments and indebtedness; (iv) add additional financial covenants including a senior secured leverage ratio and minimum liquidity requirement; (v) increase the maximum permitted level of the Company's total leverage ratio; and (vi) allow for the option to increase the credit facility by up to an additional $150.0 million, subject to pro forma compliance with financial covenants under the credit facility. In addition, the amendment added a new pricing tier based on the Company's total leverage ratio. The credit facility, which includes a sublimit for letters of credit, is for general corporate purposes.

The obligations under the credit facility are guaranteed by the Company's existing and future domestic subsidiaries and are secured by substantially all of the assets of the Company and its subsidiary guarantors. The credit facility contains affirmative and negative covenants that are customary for a senior secured credit agreement. The negative covenants include, among other things, limitations on capital expenditures, asset sales, mergers and acquisitions, indebtedness, liens, dividends, investments and transactions with the Company's affiliates. The credit facility also requires the Company to maintain a maximum leverage ratio and a minimum interest coverage ratio.

Borrowings under the credit facility bear interest at a rate per year equal to, at the Company's option, either: (a) a base rate determined by reference to the highest of (i) the prime rate of RBC; (ii) the federal funds effective rate plus 0.50%; and (iii) a Eurodollar rate determined by reference to the costs of funds for U.S. dollar deposits for an interest period of one month adjusted for certain additional costs, plus 1.00% or (b) a Eurodollar rate determined by reference to the costs of funds for U.S. dollar deposits for the interest period relevant to such borrowing adjusted for certain additional costs, in each case plus an applicable margin. The applicable margin ranges from 2.25% to 3.00% for the Eurodollar rate and 1.25% to 2.00% for the base rate based on the Company's total leverage ratio. There were no outstanding borrowings under the credit facility as of December 31, 2013 or December 31, 2012, and the Company was in compliance with all covenants.

EMPLOYEE_STOCK_BENEFIT_PLANS

EMPLOYEE STOCK BENEFIT PLANS	12 Months Ended
EMPLOYEE STOCK BENEFIT PLANS	Dec. 31, 2013
EMPLOYEE STOCK BENEFIT PLANS	'
EMPLOYEE STOCK BENEFIT PLANS	'

	L. EMPLOYEE STOCK BENEFIT PLANS

	Summary of Stock-Based Compensation Plans

	The 2012 Equity Incentive Plan, or 2012 EIP, is the only existing equity compensation plan from which the Company has been authorized to make equity-based awards to employees, directors and consultants. Under the 2012 EIP, the Company reserved 5,000,000 shares of common stock for grant to employees, officers, directors and consultants in the form of stock options, RSUs, performance-based restricted stock units, or PRSUs, stock grants and stock appreciation rights. In addition, the number of shares of common stock available for grant includes the number of shares of common stock subject to stock options and RSUs granted and outstanding under the 2010 Equity Incentive Plan, the Directors' Equity Incentive Plan and the Amended and Restated 2000 Equity Incentive Plan as of June 7, 2012, which become available for grant upon the forfeiture, cancellation, expiration or termination of those awards after June 7, 2012. At December 31, 2013, there were 2,974,464 shares remaining available for grant under the 2012 EIP.

	Cubist does not currently hold any treasury shares. Upon stock option exercise, the Company issues new shares and delivers them to the participant. In line with its current business plan, Cubist does not intend to repurchase shares in the foreseeable future.

	Summary of Employee Stock Purchase Plan

	Eligible employees may participate in an employee stock purchase plan sponsored by the Company. Under this program, participants purchase Cubist common stock at the end of pre-determined six-month intervals at 85% of the lower of the fair market value at the beginning or end of the period. Shares are purchased through payroll deductions of up to 15% of each participating employee's annual compensation over the course of the six-month period, subject to certain limitations. The current plan allows for the issuance of 1,250,000 shares of common stock to eligible employees. At December 31, 2013, there were 131,369 shares available for future sale to employees under this plan.

	Summary of Stock-Based Compensation Expense

	Stock-based compensation expense recorded in the consolidated statements of income for the periods ended December 31, 2013, 2012 and 2011, respectively, was as follows:


			For the Years Ended December 31,
			2013			2012			2011
			(in thousands)
	Stock-based compensation expense allocation:
	Cost of product revenues		$	525		$	497		$	264
	Research and development			12,249			9,100			6,623
	Selling, general and administrative			19,583			16,105			12,481


	Total stock-based compensation			32,357			25,702			19,368
	Income tax effect			(11,454	)		(9,510	)		(7,449	)


	After-tax effect of stock-based compensation expense		$	20,903		$	16,192		$	11,919





	Stock-based compensation expense for the period ended December 31, 2013, presented above, excludes $7.2 million and $22.7 million of postcombination stock-based compensation expense resulting from the cash settlement of nonvested equity awards of Optimer and Trius, respectively. The total $29.9 million expense was comprised of $12.8 million of research and development expense and $17.1 million of selling, general and administrative expense. See Note D., "Business Combinations and Acquisitions," for additional information.

	Valuation Assumptions

	The following weighted-average assumptions were used to calculate the fair value of each stock-based option award under the Black-Scholes option-pricing model:


			For the Years Ended December 31,
			2013		2012		2011
	Expected stock price volatility		36.20%		39.60%		41.00%
	Risk-free interest rate		0.7% - 1.7%		0.6% - 1.1%		0.9% - 2.4%
	Expected annual dividend yield per share		—		—		—
	Expected life of options		4.5 years		4.6 years		4.6 years

	General Option Information

	A summary of option activity for the period ended December 31, 2013, is as follows:


			Number of			Weighted-			Aggregate			Weighted-
			Shares			Average			Intrinsic Value			Average
						Exercise Price						Contractual
												Life
									(in thousands)			(in years)
	Outstanding as of December 31, 2012			8,025,194		$	27.31		$	333,507
	Granted			1,288,393		$	45.83		$	29,688
Exercised			(1,695,244	)	$	21.73		$	58,051
Canceled			(140,174	)	$	35.91		$	4,620


Outstanding as of December 31, 2013			7,478,169		$	31.61		$	278,661			6.6




Vested and exercisable as of December 31, 2013			4,654,759		$	25.99		$	199,619			5.6
Expected to vest as of December 31, 2013			2,437,787		$	40.87		$	68,247			8.4

The total intrinsic value of options exercised during the years ended December 31, 2013, 2012 and 2011, was $58.1 million, $39.1 million and $42.2 million, respectively. As of December 31, 2013, there was $30.4 million of total unrecognized compensation cost related to nonvested options granted under the Company's stock-based compensation plans. That cost is expected to be recognized over the weighted-average period of 1.2 years. The fair value of shares vested during the years ended December 31, 2013, 2012 and 2011, was approximately $19.1 million, $17.3 million and $14.3 million, respectively.

The weighted average grant-date fair value of options granted during the years ended December 31, 2013, 2012 and 2011, was $14.23, $14.37 and $12.46, respectively. The weighted-average grant-date fair value of options vested as of December 31, 2013, 2012 and 2011, was $10.20, $9.23 and $8.46, respectively.

RSU Information

A summary of RSU activity, including PRSUs, during the year ended December 31, 2013, is as follows:


		Number of			Weighted-			Aggregate
		Shares			Average Grant			Intrinsic Value
					Date Fair Value
								(in thousands)
Nonvested as of December 31, 2012			735,939		$	35.33		$	50,684
Granted			457,820		$	44.75		$	31,530
Vested			(278,874	)	$	32.71		$	19,206
Canceled			(32,613	)	$	37.44		$	2,246


Nonvested as of December 31, 2013			882,272		$	40.97		$	60,762




Expected to vest as of December 31, 2013			584,061		$	40.97		$	40,224

At December 31, 2013, there was $22.7 million of total unrecognized compensation cost related to nonvested RSUs and PRSUs granted under the Company's stock-based compensation plans, which is expected to be recognized over a period of approximately 1.3 years.

COMMITMENTS_AND_CONTINGENCIES

COMMITMENTS AND CONTINGENCIES	12 Months Ended
	Dec. 31, 2013
COMMITMENTS AND CONTINGENCIES	'
COMMITMENTS AND CONTINGENCIES	'

	M. COMMITMENTS AND CONTINGENCIES

	Legal Proceedings

	CUBICIN Patent Infringement Litigation

	In February 2012, the Company received a Paragraph IV Certification Notice Letter from Hospira, notifying Cubist that it had submitted an ANDA to the FDA, seeking approval to market a generic version of CUBICIN. Hospira's notice letter advised that it is seeking FDA approval to market daptomycin for injection, 500 mg/vial, prior to the expiration of U.S. Patent Nos. 6,468,967 and 6,852,689, which expire on September 24, 2019, U.S. Patent No. RE39,071, which expires on June 15, 2016, U.S. Patent No. 8,058,238, which expires on November 28, 2020, and U.S. Patent No. 8,003,673, which expires on September 4, 2028. In May 2012, the Company received a second Paragraph IV Certification Notice Letter from Hospira notifying Cubist that it had submitted to the FDA an amendment to its ANDA. Hospira's second notice letter advised that it is seeking FDA approval to market daptomycin for injection, 500 mg/vial, prior to the expiration of U.S. Patent No. 8,129,342, which expires on November 28, 2020. In August 2012, the Company received a third Paragraph IV Certification Notice Letter from Hospira notifying Cubist that it had submitted to the FDA an NDA, under Section 505(b)(2) of the Federal Food, Drug, and Cosmetic Act seeking approval to market a generic version of CUBICIN. Hospira's third notice letter advised that it is seeking FDA approval to market daptomycin for injection, 350 mg/vial, prior to the expiration of U.S. Patent Nos. 6,468,967, 6,852,689, RE39,071, 8,058,238, 8,003,673 and 8,129,342. Each of these patents is listed in the Orange Book. Each of the notice letters further stated that Hospira is asserting that each claim in the respectively referenced patents is invalid, and/or unenforceable and/or will not be infringed by the commercial manufacture, use or sale of the drug product respectively described by Hospira's ANDA, as amended, and NDA. In March 2012, Cubist filed a patent infringement lawsuit against Hospira in response to its initial ANDA filing. In July 2012, Cubist filed a new complaint against Hospira to allege infringement of U.S. Patent No. 8,129,342 in response to Hospira's amendment to its ANDA. In September 2012, Cubist filed a patent infringement lawsuit against Hospira in response to its NDA filing. The complaints, which were each filed in the U.S. District Court for the District of Delaware, respectively allege infringement of U.S. Patent Nos. 6,468,967; 6,852,689; RE39,071; 8,058,238; and 8,129,342. The complaints seek: (i) an order preventing the effective date of the FDA's approval of Hospira's ANDA and NDA until the expiration of the patents in the respective lawsuits; (ii) an order preventing Hospira from making, using, selling, offering for sale, marketing, distributing or importing Hospira's generic versions of CUBICIN until the expiration of the patents in the respective lawsuits; and (iii) an award of attorney's fees. By statute, the FDA is automatically prohibited from approving Hospira's ANDA for 30 months from Cubist's receipt of Hospira's first Paragraph IV notification letter for such ANDA and from finally approving Hospira's NDA for 30 months from Cubist's receipt of Hospira's first Paragraph IV notification letter for such NDA, as respectively applicable, unless the court enters a judgment finding the patents invalid, unenforceable or not infringed before the expiration of the respective 30-month period or otherwise shortens the respective 30-month period. In July 2013, the court endorsed the parties' stipulation that Hospira's ANDA and NDA products infringed certain claims of each the asserted patents. The trial in these related actions began on February 18, 2014. The Company cannot predict the outcome of these litigations. Any final, unappealable adverse result in these litigations would likely have a material adverse effect on the Company's results of operations and financial condition.

	In August 2013, the Company received a Paragraph IV Certification Notice Letter from Strides, notifying Cubist that Strides had submitted an ANDA to the FDA seeking approval to market a generic version of CUBICIN. Strides' notice letter advised that it is seeking FDA approval to market daptomycin for injection, 500 mg/vial, prior to the expiration of U.S. Patent Nos. 6,468,967; 6,852,689; 8,058,238; 8,129,342; and 8,003,673, which expire on the periods described above and are each listed in the Orange Book. The notice letter further stated that Strides is asserting that each claim in the respectively referenced patents is invalid, and/or unenforceable and/or will not be infringed by the commercial manufacture, use, sale, offer to sell in the U.S., or importation into the U.S. of the drug product described by Strides' ANDA. In response to Strides' ANDA filing, Cubist filed patent infringement lawsuits against Strides in October 2013 in the U.S. District Court for the District of Delaware and the U.S. District Court for the District of New Jersey. Cubist later filed a notice of dismissal of its complaint filed in the District of New Jersey and the case was subsequently terminated. The remaining complaint filed in the District of Delaware alleges infringement of U.S. Patent Nos. 6,468,967; 6,852,689; 8,058,238; and 8,129,342. The complaint seeks: (i) an order preventing the effective date of the FDA's approval of Strides' ANDA until the expiration of the patents in the respective lawsuits; (ii) an order preventing Strides from making, using, selling, offering for sale, marketing, distributing or importing Strides' generic version of CUBICIN until the expiration of the patents in the respective lawsuits; and (iii) an award of attorney's fees. By statute, the FDA is automatically prohibited from approving Strides' ANDA for 30 months from Cubist's receipt of Strides' Paragraph IV notification letter, unless the court enters a judgment finding the patents invalid, unenforceable or not infringed before the expiration of the 30-month period or otherwise shortens the 30-month period. The Company cannot predict the outcome of this matter. Any final, unappealable adverse result in this litigation would likely have a material adverse effect on the Company's results of operations and financial condition.

	Optimer U.S. Governmental Investigations

	Prior to the Company's acquisition of Optimer, Optimer became aware of an attempted share grant by Optimer and certain related matters in 2011, including a potentially improper $0.3 million payment to a research laboratory involving an individual associated with the share grant, that may have violated certain applicable laws, including the U.S. Foreign Corrupt Practices Act. Optimer had engaged external counsel to assist it in an internal investigation to review these matters. In April 2012, Optimer self-reported the results of its preliminary findings to the SEC and the U.S. Department of Justice, and removed the Chairman of its Board of Directors. In February 2013, the independent members of Optimer's Board of Directors determined that additional remedial action should be taken in light of prior compliance, record keeping and conflict-of-interest issues surrounding the potentially improper payment to the research laboratory and certain related matters. On February 26, 2013, Optimer's then-President and Chief Executive Officer and its then-General Counsel and Chief Compliance Officer resigned at the request of the independent members of the Board of Directors.

	Cubist is continuing to cooperate with the investigations by the relevant U.S. authorities in their review of these matters, and Optimer has already taken remedial steps in response to its internal investigation. Nonetheless, these events could result in lawsuits being filed against Cubist or Optimer and certain of Optimer's former employees and directors or certain of the Company's employees. Such persons could also be the subject of criminal or civil enforcement proceedings, and Cubist may be required to indemnify such persons for any costs or losses incurred in connection with such proceedings. Cubist cannot predict the ultimate resolution of these matters, whether Cubist or such persons will be charged with violations of applicable civil or criminal laws or whether the scope of the investigations will be extended to new issues. Cubist also cannot predict what potential penalties or other remedies, if any, the authorities may seek against it, any of its employees, or any of Optimer's former employees and directors, or what the collateral consequences may be of any such government actions. Cubist has not accrued any amounts related to potential penalties or other remedies related to these matters as of December 31, 2013, and cannot estimate a reasonably possible range of loss. In the event any such lawsuit is filed or enforcement proceeding is initiated, Cubist could be subject to a variety of risks and uncertainties that could have material adverse effects on its business, operating results and financial condition.

	Other

	Cubist has minimum volume purchase commitments with third-party contract manufacturers with scheduled payments over the next five years that total $172.9 million at December 31, 2013. Cubist has a manufacturing and supply agreement with ACS Dobfar SpA, or ACSD, under which Cubist has minimum order requirements to purchase API from ACSD.

	Cubist has various operating leases, primarily for buildings, computers and equipment. Rent expense amounted to $1.0 million, $0.7 million, and $2.5 million in fiscal years ended December 31, 2013, 2012, and 2011, respectively. Future minimum payments under these non-cancelable leases as of December 31, 2013 are as follows:


		(in thousands)
	2014	$	2,950
	2015		2,623
	2016		2,687
	2017		2,686
	2018		2,352
	2019 and thereafter		7,116


	Total	$	20,414





	The Company is attempting to sublease portions of certain leased premises in New Jersey and California that were vacated in December 2013, and if successful, future operating lease commitments will be partially offset by proceeds received from the subleases.

	Cubist had other purchase obligations of $8.1 million at December 31, 2013, to be paid over the next five years. Other purchase obligations primarily related to clinical trial payment obligations owed to its CROs and independent clinical investigators related to certain clinical trials of candidates in its product pipeline, as well as amounts owed to its third-party service provider for the purposes of conducting clinical trials on Cubist's behalf related to ceftolozane/tazobactam.

RESTRUCTURING

RESTRUCTURING	12 Months Ended
RESTRUCTURING	Dec. 31, 2013
RESTRUCTURING	'
RESTRUCTURING	'

	N. RESTRUCTURING

	The following table summarizes the activity within the restructuring liability included in accrued liabilities and other long-term liabilities within the consolidated balance sheets:


		Employee-			Lease			Total
		Related			Restructuring
		Severance
		(in thousands)
	Balance at December 31, 2011	$	8,089		$	1,190		$	9,279
	Cash payments made		(7,156	)		(1,190	)		(8,346	)


	Balance at December 31, 2012		933			—			933
	Restructuring expense		19,824			4,495			24,319
	Cash payments made		(1,584	)		—			(1,584	)


	Balance at December 31, 2013	$	19,173		$	4,495		$	23,668





	In connection with Cubist's acquisitions of Trius and Optimer, Cubist committed to a restructuring program in the fourth quarter of 2013, which included severance benefits primarily related to former Optimer employees and restructuring Optimer's lease obligations related to its New Jersey and California facilities. The Company recorded restructuring expense of $24.3 million during the year ended December 31, 2013, of which $19.8 million related to employee severance and $4.5 million related to the lease restructuring costs. The restructuring liability associated with severance benefits is expected to be paid during 2014.

	In connection with Cubist's acquisition of Optimer, the Company vacated certain floors of Optimer's leased premises by December 31, 2013, as it does not intend to occupy or utilize this space for its operations. As a result, the Company recorded a lease restructuring liability which represents the lease obligations associated with the vacated space in both the Optimer New Jersey and California facilities, net of expected sublease income, and accordingly recognized restructuring expense of $4.5 million during the period ended December 31, 2013. The restructuring liability associated with the leases is expected to be paid over the lease terms ending in 2022 and 2018 for the California and New Jersey facilities, respectively. Any future changes to the Company's estimate of the liability will be recorded as additional restructuring expense or income.

	In connection with Cubist's acquisition of Adolor, Cubist committed to a restructuring program in the fourth quarter of 2011, which included severance benefits to former Adolor employees and execution of a lease termination agreement with respect to Adolor's operating lease for its facility in Pennsylvania, as of December 31, 2011. The Company vacated the leased premises in June 2012. The Company incurred restructuring expense of $9.3 million during the fourth quarter of 2011, of which $8.1 million related to employee severance and $1.2 million related to the lease termination. The lease termination payment was made in June 2012, and the remaining severance payments were made through the first half of 2013.

INCOME_TAXES

INCOME TAXES	12 Months Ended
INCOME TAXES	Dec. 31, 2013
INCOME TAXES	'
INCOME TAXES	'

	O. INCOME TAXES

	Income Tax Expense

	The components of federal and state income tax expense (benefit) consist of the following:


			For the Years Ended December 31,
			2013			2012			2011
			(in thousands)
	Current income tax expense
	Federal		$	9,163		$	74,744		$	55,656
	State			4,748			3,719			7,393


	Total current income tax expense			13,911			78,463			63,049


	Deferred income tax (benefit) expense
	Federal			(32,449	)		(15,874	)		10,112
	State			(6,535	)		(17,068	)		(1,395	)


	Total deferred income tax (benefit) expense			(38,984	)		(32,942	)		8,717


	Total current and deferred income tax (benefit) expense		$	(25,073	)	$	45,521		$	71,766





	Effective Tax Rate

	The following table reconciles the federal statutory tax rate to the effective tax rates and the related impact to the (benefit) provision for income taxes for each of the years ended December 31, 2013, 2012 and 2011:


			For the Years Ended December 31,
			2013						2012						2011
			Amount			Tax Rate			Amount			Tax Rate			Amount			Tax Rate
			(in thousands, except for percentages)
	Federal statutory tax rate applied to (loss) income before taxes		$	(15,275	)		35	%	$	69,859			35	%	$	36,676			35	%
	Differential arising from:
	State			(1,161	)		2.7	%		2,247			1.1	%		3,899			3.7	%
	Non-deductible expenses			1,606			(3.7	)%		1,284			0.6	%		1,386			1.3	%
	Current year federal research credit			(6,176	)		14.2	%		—			—	%		(1,763	)		(1.7	)%
	Prior year federal research credits			(4,399	)		10.1	%		—			—	%		—			—	%
	Impact of reserve for uncertain tax positions			(192	)		0.4	%		(10,923	)		(5.5	)%		—			—	%
	Domestic manufacturing deduction			(262	)		0.6	%		(5,820	)		(2.9	)%		—			—	%
	Transaction costs			3,797			(8.7	)%		—			—	%		967			1	%
	Loss on extinguishment of 2017 Notes			8,070			(18.5	)%		—			—	%		—			—	%
	Contingent consideration			(19,147	)		43.9	%		(12,029	)		(6.0	)%		29,881			28.5	%
	Valuation allowance on Adynxx impairment			7,000			(16.0	)%		—			—	%		—			—	%
	Other			1,066			(2.6	)%		903			0.5	%		720			0.7	%


	Total		$	(25,073	)		57.4	%	$	45,521			22.8	%	$	71,766			68.5	%





In the table above, permanent differences that increase the tax benefit for the year ended December 31, 2013, and increase the tax provision for the years ended December 31, 2012 and 2011, are shown as increases to the effective tax rate. Similarly, permanent differences that reduce the tax benefit for the year ended December 31, 2013, and reduce the tax provision for the years ended December 31, 2012 and 2011, are shown as decreases to the effective tax rate.

The difference between the federal rate and the effective tax rate for the year ended December 31, 2013, primarily related to the impact of contingent consideration income, which is not subject to income tax, and the benefit of the 2013 and 2012 federal research credits that were retroactively extended to January 1, 2012, by the American Taxpayer Relief Act of 2012, enacted on January 2, 2013. These benefits were partially offset by non-deductible losses of $23.1 million incurred in connection with the induced conversion of $221.2 million of the principal amount of the 2017 Notes in September 2013, non-deductible transaction costs associated with the acquisitions of Trius and Optimer, and the impairment of the Adynxx investment which is expected to result in a capital loss. The capital loss will only be recognized to the extent that the Company generates future capital gains. Since the Company does not anticipate that it will have future capital gains, a full valuation allowance has been recorded against this deferred tax asset. The difference between the federal rate and the effective tax rate for the year ended December 31, 2012, primarily related to the impact of contingent consideration income recorded in the fourth quarter of 2012, which is not subject to income tax, and an $11.0 million income tax benefit, net, recorded during the second quarter of 2012, as a result of the resolution of uncertain state tax positions. The difference between the federal rate and the effective tax rate for the year ended December 31, 2011, primarily related to the impact of non-deductible contingent consideration.

The Company and its subsidiaries file income tax returns with the U.S. federal government, multiple state and local jurisdictions in the U.S., and foreign jurisdictions. Changes in the effective tax rates from period to period may be significant as they depend on many factors including, but not limited to, changes in circumstances surrounding the need for a valuation allowance, size of the Company's income or loss, changes in the geographical mix of earnings, or non-recurring activities during the period. Contingent consideration will fluctuate as a result of any changes in the fair value assumptions based on any additional data received on the Company's ceftolozane/tazobactam, bevenopran and/or tedizolid phosphate programs. Contingent consideration will also fluctuate based upon the market price of the CVRs issued in connection with the acquisition of Optimer. Any significant contingent consideration expense or income will result in a significantly higher or lower effective tax rate, because contingent consideration expense is largely not deductible for tax purposes and contingent consideration income is not taxable.

Deferred Taxes and Valuation Allowance

The components of the net deferred tax assets and the related valuation allowance are as follows:


		December 31,
		2013			2012
		(in thousands)
Deferred income tax assets:
NOL carryforwards		$	215,155		$	50,043
Deferred revenues			12,539			10,141
Research and development costs			17,461			517
Tax credit carryforwards			30,815			9,357
Stock-based compensation			21,136			18,485
Capital loss carryforward			10,472			11,118
Investment impairment			7,341			—
Other			15,721			8,868


Total deferred tax assets		$	330,640		$	108,529
Deferred income tax liabilities:
Prepaid expenses		$	(2,066	)	$	(2,669	)
Debt discount			(12,220	)		(29,919	)
IPR&D			(327,272	)		(100,104	)
Other intangible assets			(226,408	)		(32,880	)
Inventory			(13,871	)		(14,539	)
Depreciation			(9,036	)		(3,968	)


Total deferred tax liabilities			(590,873	)		(184,079	)


Total deferred tax assets and liabilities			(260,233	)		(75,550	)
Valuation allowance			(45,461	)		(13,341	)


Net deferred tax liabilities		$	(305,694	)	$	(88,891	)





At December 31, 2013, the Company had federal, foreign and state NOL carryforwards of $551.7 million, $15.8 million and $318.5 million, respectively. These NOLs expire between 2014 and 2032. Included in the NOLs are state NOLs of $2.0 million attributable to excess tax benefits from the exercise of non-qualified stock options. The tax benefits attributable to these NOLs are credited directly to additional paid-in capital when realized. In addition, the Company had $14.9 million of federal credit carryforwards, which expire between 2019 and 2032, and $24.7 million of state tax credit carryforwards at December 31, 2013, $16.2 million of which expire between 2014 and 2028 and $8.5 million of which do not expire.

The increase in the NOL and credit carryforwards from the prior year primarily relate to NOLs and credit carryforwards that were acquired in connection with the acquisitions of Optimer and Trius. These tax attributes are subject to limitation under Internal Revenue Code, Section 382, which limits the amount of NOL and credit carryforwards that may be utilized following an ownership change.

In connection with the acquisition of Optimer, the Company acquired federal, foreign, and state NOL carryforwards of $282.6 million, $12.3 million, and $188.5 million, respectively. The Company expects that it will use all of the federal NOL carryforwards acquired, but has provided a full valuation allowance on the foreign and state NOLs as it is more likely than not that these NOLs will not be utilized. The Company utilized $11.4 million of Optimer federal NOL carryforwards during the year ended December 31, 2013. The Company also acquired federal and state research tax credit carryforwards of $7.8 million and $4.3 million, respectively. The Company expects that it will use all of the federal credit carryforwards acquired, but has provided a full valuation allowance on the state credit carryforwards as it has been determined that it is more likely than not that these credit carryforwards will not be utilized. See Note D., "Business Combinations and Acquisitions," for additional information.

In connection with the acquisition of Trius, the Company acquired federal and state NOL carryforwards of $192.0 million and $95.5 million, respectively. The Company expects that it will use all of the federal NOL carryforwards acquired, but has provided a full valuation allowance on the state NOLs as it is more likely than not that these NOLs will not be utilized. The Company utilized $17.5 million of Trius federal NOL carryforwards during the year ended December 31, 2013. The Company also acquired federal and state research tax credit carryforwards of $6.1 million and $2.6 million, respectively. The Company expects that it will use all of the federal credit carryforwards acquired, but has provided a full valuation allowance on the state credit carryforwards as it has been determined that it is more likely than not that these credit carryforwards will not be utilized. See Note D., "Business Combinations and Acquisitions," for additional information.

In connection with the acquisition of Adolor, the Company acquired federal NOL carryforwards of $166.4 million. The Company has utilized $66.4 million of Adolor federal NOL carryforwards from the date of acquisition through December 31, 2013.

At December 31, 2013 and 2012, the Company maintained a valuation allowance of $45.5 million and $13.3 million, respectively, primarily relating to state NOL and credit carryforwards acquired in connection with the acquisitions of Trius and Optimer, the Adynxx investment impairment, and realized capital losses incurred on the Company's investment in auction rate securities, which were sold in 2010. The capital loss carryforwards may only be utilized to the extent that the Company generates capital gains and expire in 2015.

Future ownership changes resulting from the issuance of capital stock may limit the amount of NOL and tax credit carryforwards that can be utilized annually to offset future taxable income. The amount of the annual limitation is determined based on Cubist's value immediately prior to the ownership change. Subsequent significant changes in ownership could affect the limitations in future years.

Uncertain Tax Positions

A reconciliation of the Company's changes in uncertain tax positions is as follows:


		For the Years Ended December 31,
		2013			2012			2011
		(in thousands)
Uncertain tax positions at the beginning of the year		$	36,115		$	27,774		$	8,216
Additions based on tax positions related to the current year			2,717			769			12,844
Additions for tax positions of prior years			5,393			24,299			7,321
Subtractions based on tax positions related to the current year			—			—			—
Subtractions for tax positions of prior years			(1,105	)		(16,727	)		(607	)


Balance at the end of the year		$	43,120		$	36,115		$	27,774





The increase in the Company's total uncertain tax positions during the year ended December 31, 2013, included an increase of $3.0 million related to federal and state research tax credits acquired in connection with the acquisition of Optimer, and $1.0 million related to federal research credits acquired in connection with the acquisition of Adolor. These increases were partially offset by the reversal of $1.1 million of gross uncertain tax positions related to a prior year state income tax award, which was reversed based upon authoritative guidance issued during 2013.

Of the total uncertain tax positions as of December 31, 2013, $16.4 million were included in other long-term liabilities within the consolidated balance sheets and $26.7 million were offset against deferred tax assets. The amount of uncertain tax positions that, if realized, would affect the Company's effective tax rate in future periods is approximately $40.9 million.

The statute of limitations for assessment by the Internal Revenue Service, or IRS, and state taxing authorities is closed for tax years prior to December 31, 2010, although carryforward tax attributes that were generated prior to 2010 may still be adjusted upon examination by the relevant taxing authorities if they are used in a future period.

The Company's 2011 federal income tax return is currently under audit by the IRS. Cubist is not able to determine any impact to its unrecognized tax benefits based on the preliminary stage of discussions with the IRS.

SEGMENT_INFORMATION

SEGMENT INFORMATION	12 Months Ended
SEGMENT INFORMATION	Dec. 31, 2013
SEGMENT INFORMATION	'
SEGMENT INFORMATION	'

	P. SEGMENT INFORMATION

	Cubist has one operating segment: the research, development and commercialization of pharmaceutical products that address unmet medical needs in the acute care environment. The Company's entire business is managed by a single management team, which reports to the Chief Executive Officer. For the years ended December 31, 2013, 2012 and 2011, 93%, 94% and 94%, respectively, of the Company's revenues were generated within the U.S., and substantially all of the Company's long-lived assets were held within the U.S.

SELECTED_QUARTERLY_FINANCIAL_D

SELECTED QUARTERLY FINANCIAL DATA (UNAUDITED)	12 Months Ended
SELECTED QUARTERLY FINANCIAL DATA (UNAUDITED)	Dec. 31, 2013
SELECTED QUARTERLY FINANCIAL DATA (UNAUDITED)	'
SELECTED QUARTERLY FINANCIAL DATA (UNAUDITED)	'

	Q. SELECTED QUARTERLY FINANCIAL DATA (UNAUDITED)

	The following table contains quarterly financial information for fiscal years 2013 and 2012. Cubist believes that the following information reflects all normal recurring adjustments necessary for a fair presentation of the information for the periods presented. The operating results for any quarter are not necessarily indicative of results for any future period.


		First		Second		Third			Fourth
		Quarter		Quarter		Quarter			Quarter
		(in thousands, except per share data)
	2013
	Total revenues, net	$	229,929	$	258,779	$	265,993		$	299,741
	Product revenues, net	$	225,651	$	254,462	$	256,583		$	295,737
	Cost of product revenues	$	55,675	$	63,041	$	60,989		$	80,605
	Net income (loss)	$	6,088	$	15,242	$	-33,895	-2	$	-6,006	-1
	Basic net income (loss) per share	$	0.09	$	0.23	$	-0.5	-2	$	-0.08	-1
	Diluted net income (loss) per share	$	0.09	$	0.23	$	-0.5	-2	$	-0.08	-1
	2012
	Total revenues, net	$	211,692	$	230,567	$	238,181		$	245,919
	Product revenues, net	$	206,803	$	221,249	$	230,313		$	241,460
	Cost of product revenues	$	53,952	$	58,891	$	55,740		$	61,474
	Net income	$	32,794	$	43,123	$	40,321		$	37,837	-1
	Basic net income per share	$	0.52	$	0.68	$	0.63		$	0.59	-1
	Diluted net income per share	$	0.45	$	0.58	$	0.55		$	0.51	-1


	-1
	During the fourth quarters of 2013 and 2012, Cubist recorded impairment charges of $35.3 million and $38.7 million, respectively, to write down the bevenopran IPR&D asset, which was acquired in connection with the acquisition of Adolor in December 2011, to its revised fair value. The impairment charges were offset by related contingent consideration income of $36.2 million and $37.0 million recorded during the fourth quarters of 2013 and 2012, respectively. In addition, during the fourth quarter of 2013, Cubist recorded an impairment charge of $20.0 million, representing the write-off of the non-refundable option payment to Adynxx, which resulted from management's decision to not exercise the option to acquire 100% of the outstanding shares of Adynxx.

	-2
	During the third quarter of 2013, Cubist recorded a $34.6 million loss on the induced conversion of $221.2 million of the principal amount of the Company's 2017 Notes in September 2013.

SCHEDULE_II_Valuation_and_Qual

SCHEDULE II Valuation and Qualifying Accounts and Reserves	12 Months Ended
SCHEDULE II Valuation and Qualifying Accounts and Reserves	Dec. 31, 2013
SCHEDULE II Valuation and Qualifying Accounts and Reserves	'
SCHEDULE II Valuation and Qualifying Accounts and Reserves	'

	SCHEDULE II

	Cubist Pharmaceuticals, Inc.
	Valuation and Qualifying Accounts and Reserves


	Description(1)	Balance at		Additions		Deductions			Balance at
		Beginning							End of Year
		of Year
		(in thousands)
	Year Ended December 31, 2011
	Medicaid rebates	$	6,279		23,796		(15,198	)	$	14,877
	Chargebacks	$	454		32,210		(32,026	)	$	638
	Prompt pay discounts	$	1,270		13,507		(13,333	)	$	1,444
	Sales returns and allowances and wholesaler fees	$	4,226		4,804		(2,914	)	$	6,116
	Valuation allowance against deferred tax assets	$	13,738		35		(603	)	$	13,170
	Year Ended December 31, 2012
	Medicaid and Medicare rebates	$	14,877		26,874		(21,186	)	$	20,565
	Chargebacks	$	638		46,298		(46,029	)	$	907
	Prompt pay discounts	$	1,444		16,943		(16,827	)	$	1,560
	Sales returns and allowances and wholesaler fees	$	6,116		5,990		(5,388	)	$	6,718
	Valuation allowance against deferred tax assets	$	13,170		185		(14	)	$	13,341
	Year Ended December 31, 2013
	Medicaid and Medicare rebates	$	20,565		23,558		(27,038	)	$	17,085
	Chargebacks	$	907		62,470		(61,579	)	$	1,798
	Prompt pay discounts	$	1,560		19,618		(19,124	)	$	2,054
	Commercial rebates	$	—		1,593		(83	)	$	1,510
	Sales returns and allowances and wholesaler fees	$	6,718		12,979		(7,575	)	$	12,122
	Valuation allowance against deferred tax assets	$	13,341		32,812		(692	)	$	45,461


	-1
	Additions to sales returns and allowances, chargebacks, prompt pay discounts, wholesaler fees, Medicaid program rebates and Medicare coverage gap discount program rebates are recorded as a reduction of revenue. Reserves for returns, chargebacks, prompt pay discounts and wholesaler management fees are offset against accounts receivable and reserves for Medicaid program rebates, Medicare coverage gap discount program rebates and commercial rebates are included in accrued liabilities. In addition, the year ended December 31, 2013, includes $9.3 million in additions that resulted from the acquisition of Optimer.

ACCOUNTING_POLICIES_Policies

ACCOUNTING POLICIES (Policies)	12 Months Ended
ACCOUNTING POLICIES (Policies)	Dec. 31, 2013
ACCOUNTING POLICIES	'
Basis of Presentation and Consolidation	'

	Basis of Presentation and Consolidation

	The accompanying consolidated financial statements have been prepared under accounting principles generally accepted in the U.S., or GAAP and include the accounts of Cubist and its wholly-owned subsidiaries. All intercompany balances and transactions have been eliminated in consolidation. The assets acquired and liabilities assumed in connection with the Company's acquisitions of Optimer and Trius were recorded at their fair values as of October 24, 2013, and September 11, 2013, respectively, the dates of acquisition. The operating results of Optimer and Trius have been consolidated with those of Cubist from the dates of acquisition. See Note D., "Business Combinations and Acquisitions," for additional information.

Use of Estimates	'

	Use of Estimates

	The preparation of financial statements in conformity with GAAP requires extensive use of estimates and assumptions that affect the reported amounts of assets, liabilities, revenues and expenses, and related disclosures. The most significant assumptions are employed in estimates used in determining values of: inventory; investments; acquisition-date fair value and subsequent fair value estimates used to assess impairment of long-lived assets, including goodwill, in-process research and development, or IPR&D, and other intangible assets; accrued clinical research costs; contingent consideration; income taxes; stock-based compensation; product rebate, chargeback and return accruals; as well as in estimates used in accounting for contingencies and revenue recognition. Actual results could differ from these estimates.

Fair Value Measurements	'

	Fair Value Measurements

	The accounting standard for fair value measurements defines fair value, establishes a framework for measuring fair value in accordance with GAAP, and requires detailed disclosures about fair value measurements. Under this standard, 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 valuation techniques are based on observable and unobservable inputs. Observable inputs reflect readily obtainable data from independent sources, while unobservable inputs reflect certain market assumptions. This standard classifies these inputs into the following hierarchy:

	Level 1 Inputs—Quoted prices for identical instruments in active markets.

	Level 2 Inputs—Quoted prices for similar instruments in active markets; quoted prices for identical or similar instruments in markets that are not active; and model-derived valuations whose inputs are observable or whose significant value drivers are observable.

	Level 3 Inputs—Instruments with primarily unobservable value drivers.

	The fair value hierarchy level is determined by asset class based on the lowest level of significant input. In periods of market inactivity, the observability of prices and inputs may be reduced for certain instruments. This condition could cause an instrument to be reclassified between levels. During the year ended December 31, 2013, there were no transfers between levels.

	The carrying amounts of Cubist's cash and cash equivalents, accounts receivable, net, accounts payable and accrued expenses approximate their fair value due to the short-term nature of these amounts. Short-term and long-term investments primarily consist of available-for-sale securities as of December 31, 2013 and 2012, and are carried at fair value.

Cash and Cash Equivalents	'

	Cash and Cash Equivalents

	Cash and cash equivalents consist of short-term, interest-bearing instruments with original maturities of 90 days or less at the date of purchase. These may include money market instruments, bank deposits, corporate and municipal notes, U.S. Treasury securities and federal agency securities.

Investments	'

	Investments

	Investments with original maturities of greater than 90 days and remaining maturities of less than one year are classified as short-term investments. Investments with remaining maturities of greater than one year from the balance sheet date are classified as long-term investments. Short-term and long-term investments may include bank deposits, corporate and municipal notes, U.S. Treasury securities and federal agency securities. See Note E., "Investments," for additional information.

	Unrealized gains and temporary losses on investments are included in accumulated other comprehensive income (loss) as a separate component of stockholders' equity. Realized gains and losses, dividends and declines in value judged to be other-than-temporary credit losses are included in other income (expense) within the consolidated statements of income. Any premium or discount arising at purchase is amortized and/or accreted to interest income within the consolidated statements of income.

Concentration of Risk	'

	Concentration of Risk

	Financial instruments, which potentially subject the Company to concentrations of credit risk, consist principally of cash and cash equivalents, investments and accounts receivable. The Company's cash and cash equivalents are held with several major financial institutions. The Company's investments are restricted, in accordance with its investment policy, to a concentration limit per institution.

	Cubist's accounts receivable, net at December 31, 2013 and 2012, represent amounts due to the Company from customers, including AmerisourceBergen Drug Corporation, Cardinal Health, Inc. and McKesson Corporation. Cubist performs ongoing credit evaluations of its customers, including key wholesalers and distributors, and generally does not require collateral. For the year ended December 31, 2013, Cubist did not have any significant write-offs of accounts receivable and its days sales outstanding has not significantly changed since December 31, 2012.


		Percentage of
		Total Accounts
		Receivable
		Balance as of
		December 31,
		2013			2012
	AmerisourceBergen Drug Corporation		18	%		22	%
	Cardinal Health, Inc.		17	%		18	%
	McKesson Corporation		18	%		20	%





		Percentage of Total
		Net Revenues for
		the Years Ended
		December 31,
		2013			2012			2011
	AmerisourceBergen Drug Corporation		19	%		20	%		21	%
	Cardinal Health, Inc.		17	%		18	%		21	%
	McKesson Corporation		18	%		18	%		17	%

	The Company depends on a single-source supplier of the active pharmaceutical ingredient, or API, in CUBICIN, and two suppliers to provide fill-finish services related to the manufacture of CUBICIN. If any of the Company's suppliers were to limit or terminate production, or otherwise fail to meet the quality or delivery requirements needed to supply CUBICIN at levels to meet market demand, the Company could experience a loss of revenue, which could materially and adversely impact its results of operations.

Inventory	'

	Inventory

	Inventory is stated at the lower of cost or market on a first-in, first-out (FIFO) basis. The Company analyzes its inventory levels on a quarterly basis and writes down inventory that is expected to expire prior to being sold, inventory in excess of expected sales requirements and inventory that fails to meet commercial sale specifications, with a corresponding charge to cost of product revenues. The Company disposes of its expired inventory. Inventory that is in excess of the amount expected to be sold within one year is classified as long-term inventory and is included in other assets within the consolidated balance sheets.

	The Company capitalizes inventory produced for commercial sales, including inventory produced for potential sales of a product candidate when it considers the probability of a product candidate's regulatory approval to be high and expects the future economic benefit from sales of the product to be realized. Inventory capitalization is assessed on a product-by-product basis, and begins either on or after the date the New Drug Application, or NDA, is accepted for filing by the U.S. Food and Drug Administration, or FDA, or an international equivalent. Determining whether or not to continue to record the commercial supply costs related to a product candidate as research and development expenses or to capitalize these costs as inventory involves significant judgment. The Company will assess the costs capitalized prior to regulatory approval each quarter for indicators of impairment, such as reduced likelihood of approval.

Property and Equipment, Net	'

	Property and Equipment, Net

	Property and equipment are recorded at cost and are depreciated when placed into service using the straight-line method, based on their estimated useful lives as follows:


	Asset Description	Estimated Useful Life
		(in years)
	Land		Indefinite
	Building		40
	Building enhancements		Not to exceed 20
	Furniture and fixtures		5 - 10
	Laboratory equipment		5
	Computer hardware and software		3

	Costs for capital assets not yet placed into service have been capitalized as construction-in-progress and will be depreciated in accordance with the above guidelines once placed into service. Costs for repairs and maintenance are expensed as incurred, while major betterments are capitalized. The Company capitalizes interest cost incurred on funds used to construct property and equipment. The capitalized interest is recorded as part of the asset to which it relates and is depreciated over the asset's estimated useful life. When assets are retired or otherwise disposed of, the assets and related allowances for depreciation or amortization are eliminated from the consolidated balance sheets and any resulting gain or loss is reflected in the consolidated statements of income.

IPR&D	'

	IPR&D

	IPR&D acquired in a business combination is capitalized on the Company's consolidated balance sheets at its acquisition-date fair value. Until the underlying project is completed, these assets are accounted for as indefinite-lived intangible assets and are subject to impairment testing. Once the project is completed, the carrying value of the IPR&D is amortized over the estimated useful life of the asset. Post-acquisition research and development expenses related to the IPR&D projects are expensed as incurred.

	The projected discounted cash flow models used to estimate the fair values of the Company's IPR&D reflect significant assumptions regarding the estimates a market participant would make in order to evaluate a drug development asset, including: (i) probability of successfully completing clinical trials and obtaining regulatory approval; (ii) market size, market growth projections, and market share; (iii) estimates regarding the timing of and the expected costs to advance Cubist's clinical programs to commercialization; (iv) estimates of future cash flows from potential product sales; and (v) a discount rate.

	The accounting standard for testing indefinite-lived intangible assets for impairment permits a company to first assess the qualitative factors to determine whether the existence of events and circumstances indicates that it is more likely than not that the indefinite-lived intangible asset is impaired. The more-likely-than-not threshold is defined as having a likelihood of more than 50%. If, after assessing the totality of events or circumstances, a company concludes it is more likely than not that the fair value of the indefinite-lived intangible asset exceeds its carrying value, then the company is not required to take further action. A company also has the option to bypass the qualitative assessment for any indefinite-lived intangible asset in any period and proceed directly to performing the quantitative impairment test and may resume performing the qualitative assessment in any subsequent period.

	IPR&D is tested for impairment on an annual basis or more frequently if impairment indicators are present. If IPR&D becomes impaired or is abandoned, the carrying value of the IPR&D is written down to its revised fair value with the related impairment charge recognized in the period in which the impairment occurs. If the carrying value of the asset becomes impaired as the result of unfavorable data from any ongoing or future clinical trial, changes in assumptions that negatively impact projected cash flows, or because of any other information regarding the prospects of successfully developing or commercializing the Company's programs, Cubist could incur significant charges in the period in which the impairment occurs. The valuation techniques utilized in performing quantitative impairment tests incorporate significant assumptions and judgments to estimate the fair value. The use of different valuation techniques or assumptions could result in materially different fair value estimates. The Company recorded impairment charges of $35.3 million and $38.7 million during the years ended December 31, 2013 and 2012, respectively, to write down its bevenopran IPR&D asset to its revised fair value. See Note I., "Goodwill, IPR&D and Other Intangible Assets, Net," and Note F., "Fair Value Measurements," for additional information. Cubist did not recognize any impairment charges related to IPR&D during the year ended December 31, 2011.

Goodwill	'

	Goodwill

	Goodwill relates to amounts that arose in connection with the acquisitions of Optimer and Trius in 2013, as well as Adolor Corporation, or Adolor, in 2011, and Calixa Therapeutics Inc., or Calixa, in 2009. Goodwill represents the excess of the purchase price over the fair value of the net assets acquired when accounted for using the acquisition method of accounting for business combinations. Goodwill is not amortized but is evaluated for impairment within the Company's single reporting unit on an annual basis, during the fourth quarter, or more frequently if an event occurs or circumstances change that would more-likely-than-not reduce the fair value of the Company's reporting unit below its carrying amount. Cubist performed step one of the two-step goodwill impairment test by assessing the fair value of its reporting unit as compared to its carrying value, including goodwill. The Company determined that the carrying value of its single reporting unit did not exceed its fair value, and therefore, goodwill was not impaired as of December 31, 2013. The Company did not recognize any impairment charges related to goodwill during the years ended December 31, 2013, 2012 and 2011.

Other Intangible Assets	'

	Other Intangible Assets

	Other intangible assets consist of patents, acquired intellectual property, acquired technology rights, manufacturing rights, contract intangibles, and other intangibles with finite lives. The Company amortizes its intangible assets using the straight-line method over their estimated economic lives, which range from nine to 14 years. The fair values of patents obtained through an acquisition transaction are capitalized and amortized over the lesser of the patent's remaining legal life or its useful life. Costs to obtain, maintain and defend the Company's patents are expensed as incurred. Cubist evaluates the potential impairment of other intangible assets if events or changes in circumstances indicate that the carrying amount of the assets may not be fully recoverable or that the useful lives of these assets are no longer appropriate. The impairment test is based on a comparison of the undiscounted cash flows expected to be generated from the use of the asset group and its eventual disposition to the carrying value of the asset group. If impairment is indicated, the asset is written down by the amount by which the carrying value of the asset exceeds the related fair value of the asset. Cubist did not recognize an impairment charge related to other intangible assets during the years ended December 31, 2013, 2012 and 2011.

Revenue Recognition	'

	Revenue Recognition

	The Company's principal sources of revenue during the reporting period were: (i) product sales of CUBICIN, DIFICID and ENTEREG in the U.S.; (ii) revenues derived from sales of CUBICIN and DIFICID by Cubist's international distribution partners; (iii) license fees and milestone payments that are derived from collaboration, license and commercialization agreements with other biopharmaceutical companies; and (iv) prior to Cubist's acquisition of Optimer, service revenues derived from Cubist's co-promotion agreement with Optimer for the promotion and support of DIFICID in the U.S., which was terminated on October 24, 2013, as a result of Cubist's acquisition of Optimer. In all instances, revenue is recognized only when the price is fixed or determinable, persuasive evidence of an arrangement exists, delivery has occurred or services have been rendered, and collectibility of the resulting receivable is reasonably assured.

	Multiple-Element Arrangements

	Cubist accounts for revenue arrangements with multiple elements entered into or materially modified after January 1, 2011, by separating and allocating consideration according to the relative selling price of each deliverable. The selling price 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 will be separate units of accounting, provided (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 Company's control.

	Cubist's other license and collaboration agreements continue to be accounted for under previously-issued revenue recognition guidance for multiple-element arrangements. Under this guidance, the Company recognizes non-refundable upfront license payments as revenue upon receipt if the license has standalone value and the fair value of the undelivered obligations, if any, can be determined. If the license is considered to have standalone value but the fair value of any of the undelivered items cannot be determined, the license payments are recognized as revenue over the period of Cubist's performance for such undelivered items or services. License fees with ongoing involvement or performance obligations are recorded as deferred revenue once received, and generally are recognized ratably over the period of such performance obligation only after both the license period has commenced and the technology has been delivered by Cubist.

	U.S. Product Revenues, net

	All revenues from product sales are recorded net of applicable provisions for returns, chargebacks, discounts, wholesaler management fees, government and commercial rebates, and other applicable allowances in the same period the related sales are recorded.

	Gross U.S. product revenues were offset by provisions for the years ended December 31, 2013, 2012 and 2011, as follows:


		For the Years Ended December 31,
		2013			2012			2011
		(in thousands)
	Gross U.S. product revenues	$	1,116,870		$	977,874		$	802,457
	Provisions offsetting U.S. product revenues
	Contractual adjustments		(61,448	)		(55,331	)		(45,093	)
	Governmental rebates		(84,226	)		(73,172	)		(55,997	)


	Total provisions, net offsetting U.S. product revenues		(145,674	)		(128,503	)		(101,090	)


	U.S. product revenues, net	$	971,196		$	849,371		$	701,367





	Certain product sales qualify for rebates or discounts from standard list pricing due to government sponsored programs or other contractual agreements. Contractual adjustments include provisions for returns, pricing and early payment discounts extended to the Company's external customers, as well as wholesaler distribution fees, volume-based rebates and other commercial rebates. The Company allows customers to return product within a specified period prior to and subsequent to the product's expiration date and in the event of certain circumstances, such as a product recall. The estimate of the provision for returns is analyzed quarterly and is based upon many factors, including historical experience of actual returns, analysis of the level of inventory in the distribution channel, if any, and reorder rates of end users. In certain circumstances, for example, in the event of a product recall or similar circumstance outside of the customers' control, Cubist may issue the customer replacement product for product returned. In these limited circumstances, expected costs of the replacement product are recognized within cost of product revenues, whereas expected refunds or credits granted to the customer are recognized as revenue deductions at full sales value within provisions for product returns.

	Governmental rebates represent estimated amounts for government-mandated rebates and discounts relating to federal and state programs, such as Medicaid, the Veterans' Administration and Department of Defense programs, the Medicare Part D Coverage Gap Discount Program and certain other qualifying federal and state government programs. Estimates and assumptions for reserves are analyzed quarterly. Reserves for government and commercial rebates and chargebacks represent the Company's estimates of outstanding claims for end-user rebate-eligible sales that have occurred, but for which related claim submissions have not been received. The estimates are based on an analysis of customer sales mix data, prior claims history and third-party studies to determine which sales may flow through to a rebate- or chargeback-eligible customer.

	Effective March 23, 2010, the Patient Protection and Affordable Care Act, as amended by the Health Care and Education reconciliation Act of 2010, or the Affordable Care Act, extended Medicaid rebates to drug volume issued to Medicaid patients whose drug coverage is managed by managed care organizations, or MCOs, under individual agreements with states. The Company accrues for the expected liability at the time it records the sale; however, the time lag between sale and payment of Medicaid program rebates and Medicare coverage gap discount program rebates can be lengthy. In addition, the Company continues to experience delays in billing by certain state authorities under the MCO plans. As a result, in any particular period, Medicaid and Medicare rebate adjustments may incorporate revisions of accruals for several periods.

	Reserves for returns, discounts, chargebacks, wholesaler management fees and doubtful accounts are offset against accounts receivable and were $16.0 million and $9.2 million at December 31, 2013 and 2012, respectively. Reserves for governmental and commercial rebates are included in accrued liabilities and were $18.6 million and $20.6 million at December 31, 2013 and 2012, respectively. The Company reversed $18.0 million of revenue reserves during the year ended December 31, 2013, which includes $10.0 million related to Medicaid program rebate reserves that had been accrued since the enactment of the Affordable Care Act. The change in estimate for Medicaid rebates was based on receipt of claims information from certain state governments and other additional data during 2013, as a result of lower than estimated usage of CUBICIN by MCOs.

	International Product Revenues

	The Company's principal sources of international product revenues during the period were sales of CUBICIN and DIFICID to international distribution partners. Sales with international distribution partners are based upon contractually predetermined transfer price arrangements. Once Cubist's distribution partner sells the product to a third party, Cubist may also be owed an additional payment or royalty. Certain agreements with the Company's distribution partners contain multiple elements in which Cubist has continuing performance obligations. In such arrangements in which the Company determined that the undelivered elements in each arrangement did not have objective evidence of fair value, payments from distribution partners are recorded as deferred revenue. The Company amortizes deferred revenue to international product revenue over the remaining performance obligation. Total deferred revenue related to international product revenues was $20.5 million and $20.4 million at December 31, 2013 and 2012, respectively.

	Service Revenues

	Service revenues for the years ended December 31, 2013, 2012 and 2011, were $12.3 million, $23.2 million and $6.7 million, respectively. Service revenues represent the ratable recognition of the quarterly service fee earned in accordance with the co-promotion agreement with Optimer, which the Company entered into in April 2011 and terminated in October 2013, as described in Note D., "Business Combinations and Acquisitions." In addition, service revenues during the year ended December 31, 2012, include $8.5 million related to a bonus payment received from Optimer for the achievement of an annual sales target and Cubist's portion of Optimer's gross profits on net sales of DIFICID in the U.S. that exceeded the annual sales target for the first sales year, as stipulated in the co-promotion agreement.

	Other Revenues

	Other revenues include revenue related to upfront license payments, license fees and milestone payments received through Cubist's license, collaboration and commercialization agreements. Milestone payments received in accordance with these agreements and in which there are continuing performance obligations are recognized under accounting guidance for milestone payments. Consideration for an event that meets the definition of a milestone in accordance with the accounting guidance for the milestone method of revenue recognition is recognized as revenue in its entirety in the period in which the milestone is achieved only if all of the following conditions are met, and therefore, the milestone is considered substantive: (i) the milestone is commensurate with either Cubist's performance to achieve the milestone or the enhancement of the value of the delivered item as a result of a specific outcome resulting from the Company's performance to achieve the milestone; (ii) the consideration relates solely to past performance; and (iii) the amount of the milestone consideration is reasonable relative to all of the deliverables and payment terms, including other potential milestone consideration, within the arrangement. Otherwise, the milestone payments are not considered to be substantive and are, therefore, recognized as revenue as Cubist completes its remaining performance obligations. Total deferred revenue related to other revenues was $16.9 million and $20.5 million at December 31, 2013 and 2012, respectively.

Research and Development	'

	Research and Development

	Research and development costs, including upfront fees and milestones paid to collaborators who are performing research and development activities under contractual agreement with the Company, are expensed as incurred if no planned alternative future use exists for the technology and if the payment is not payment for future services. The Company defers and capitalizes its nonrefundable advance payments that are for research and development activities until the related goods are delivered or the related services are performed. When the Company is reimbursed by a collaboration partner for work the Company performs, it records the costs incurred as research and development expenses and the related reimbursement as a reduction to research and development expenses in its consolidated statement of income. Research and development expenses primarily consist of employee-related expenses, clinical and non-clinical activities performed by contract research organizations, or CROs, lab services, purchases of drug product materials, manufacturing development costs, general overhead and facilities, and upfront and milestone payments related to the licensing or purchase of research and development assets that did not qualify as business combinations.

Stock-Based Compensation	'

	Stock-Based Compensation

	The Company expenses the fair value of employee stock-based compensation using the straight-line recognition method over the employees' service periods, which are generally the vesting period of the equity award. Compensation expense is measured using the fair value of the award at the grant date, adjusted for estimated forfeitures. In order to determine the fair value of each option award on the grant date, the Company uses the Black-Scholes option-pricing model. Inherent in this model are assumptions related to expected stock price volatility, estimated option life, risk-free interest rate and dividend yield. Cubist's expected stock price volatility assumption is based on the historical volatility of the Company's stock price, which is obtained from public data sources. In prior years, the Company also utilized peer group data to derive its expected stock price volatility. Expected stock price volatility is determined based on the instrument's expected term. The expected life represents the weighted average period of time that stock-based awards are expected to be outstanding giving consideration to vesting schedules, historical exercise patterns and post-vesting cancellations for terminated employees that have been exhibited historically, adjusted for specific factors that may influence future exercise patterns. The risk-free interest rate is a less subjective assumption as it is based on factual data derived from public sources. Cubist uses a dividend yield of zero as it has never paid cash dividends and has no intention of paying cash dividends in the foreseeable future.

	The Company estimates forfeitures of awards based on its historical experience of pre-vesting cancellations for terminated employees. Its estimated forfeiture rate is applied to all equity awards, which includes option awards and restricted stock units. The Company believes that its estimates are based on outcomes that are reasonably likely to occur. To the extent actual forfeitures differ from its estimates, such amounts will be recorded as a cumulative adjustment in the period the estimates are revised. See Note L., "Employee Stock Benefit Plans," for additional information.

Income Taxes	'

	Income Taxes

	Cubist accounts for income taxes under the asset and liability method. Under this method, deferred tax assets and liabilities are recognized for the estimated future tax consequences attributable to differences between the financial statement carrying amounts of existing assets and liabilities and their respective tax bases. Deferred tax assets and liabilities are measured using enacted rates in effect for the year in which those temporary differences are expected to be recovered or settled. A deferred tax asset is established for the expected future benefit of net operating loss, or NOL, and credit carryforwards. A valuation allowance against net deferred tax assets is required if, based upon available evidence, it is more-likely-than-not that some or all of the deferred tax assets will not be realized.

	The Company recognizes the tax benefit from an uncertain tax position only if it is more-likely-than-not that the tax position will be sustained upon examination by the taxing authorities, based on the technical merits of the tax position. 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; and changes in facts or circumstances related to a tax position. Any changes to these estimates, based on the actual results obtained and/or a change in assumptions, could impact the Company's income tax provision in future periods. Interest and penalty charges, if any, related to unrecognized tax benefits would be classified as a provision for income tax in the consolidated statements of income. See Note O., "Income Taxes," for additional information.

Basic and Diluted Net (Loss) Income Per Common Share	'

	Basic and Diluted Net (Loss) Income Per Common Share

	Basic net (loss) income per common share has been computed by dividing net (loss) income by the weighted average number of shares outstanding during the period. Diluted net (loss) income per share has been computed by dividing diluted net (loss) income by the diluted number of shares outstanding during the period. Except where the result would be antidilutive to income from continuing operations, diluted net (loss) income per share has been computed assuming the conversion of convertible obligations and the elimination of the interest expense related to the Company's 2.25% convertible subordinated notes due June 2013, or 2013 Notes, 2.50% convertible senior notes due 2017, or 2017 Notes, 1.125% convertible senior notes due 2018, or 2018 Notes, 1.875% convertible senior notes due 2020, or 2020 Notes, the exercise of stock options, the exercise of warrants issued in connection with the convertible bond hedge transactions discussed below, and the vesting of restricted stock units, or RSUs, as well as their related income tax effects. In 2012, Cubist retired the remainder of its 2013 Notes.

	In September 2013, in connection with the issuance of the 2018 Notes and 2020 Notes, the Company entered into convertible bond hedge transactions, or convertible bond hedges. The convertible bond hedges are not considered for purposes of calculating the number of diluted shares outstanding, as their effect would be antidilutive. The convertible bond hedges are generally expected, but not guaranteed, to reduce the potential dilution and/or offset the cash payments Cubist is required to make upon conversion of the 2018 Notes and 2020 Notes. See Note K., "Debt," for additional information.

	The following table sets forth the computation of basic and diluted net (loss) income per common share:


		For the Years Ended December 31,
		2013			2012			2011
		(in thousands, except share and per share data)
	Basic net (loss) income	$	(18,571	)	$	154,075		$	33,023
	Effect of dilutive securities:
	Interest on 2017 Notes, net of tax		—			7,088			—
	Debt issuance costs related to 2017 Notes, net of tax		—			936			—
	Debt discount amortization related to 2017 Notes, net of tax		—			8,705			—


	Diluted net (loss) income	$	(18,571	)	$	170,804		$	33,023




	Shares used in calculating basic net (loss) income per common share		68,160,798			63,766,209			60,839,128
	Effect of dilutive securities:
	Options to purchase shares of common stock and RSUs		—			2,254,294			2,098,013
	2017 Notes payable convertible into shares of common stock		—			15,424,155			—


	Shares used in calculating diluted net (loss) income per common share		68,160,798			81,444,658			62,937,141




	Basic net (loss) income per share	$	(0.27	)	$	2.42		$	0.54
	Diluted net (loss) income per share	$	(0.27	)	$	2.1		$	0.52

	Potential shares of common stock excluded from the calculation of diluted net (loss) income per share as their inclusion would have been antidilutive, were:


		For the Years Ended December 31,
		2013			2012			2011
	Options to purchase shares of common stock and RSUs		8,360,441			2,449,796			1,962,363
	Warrants		9,705,442			—			—
	2020 Notes convertible into shares of common stock		5,459,311			—			—
	2018 Notes convertible into shares of common stock		4,246,131			—			—
	2017 Notes convertible into shares of common stock		7,842,943			—			15,424,155
	2013 Notes convertible into shares of common stock		—			1,962,273			3,549,377
Accumulated Other Comprehensive Income	'

	Accumulated Other Comprehensive Income

	In February 2013, the Financial Accounting Standards Board, or FASB, issued amended accounting guidance for reporting accumulated other comprehensive income. The amendments require a company to provide information about the amounts reclassified out of accumulated other comprehensive income by component. In addition, a company is required to present, either on the face of the statement where 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. The Company adopted this guidance on January 1, 2013. The Company had de minimis realized gains or losses from sales of its available-for-sale securities and did not reclassify any amounts out of accumulated other comprehensive income during the year ended December 31, 2013.

Subsequent Events	'

	Subsequent Events

	Cubist considers events or transactions that have occurred after the balance sheet date of December 31, 2013, but prior to the filing of the financial statements with the Securities and Exchange Commission, or SEC, to provide additional evidence relative to certain estimates or to identify matters that require additional recognition or disclosure. Subsequent events have been evaluated through the filing of the financial statements accompanying this Annual Report on Form 10-K.

Recent Accounting Pronouncements	'

	Recent Accounting Pronouncements

	In July 2013, the FASB issued an accounting standards update clarifying the presentation of an unrecognized tax benefit when an NOL carryforward, a similar tax loss, or a tax credit carryforward exists. The updated guidance requires the netting of unrecognized tax benefits against a deferred tax asset for a loss or other carryforward when settlement of the liability for an unrecognized tax benefit in this manner is available. The update is effective prospectively for reporting periods beginning after December 15, 2013, and early adoption and retrospective adoption are permitted. The adoption of this guidance is not expected to have an impact on the Company's consolidated financial statements.

ACCOUNTING_POLICIES_Tables

ACCOUNTING POLICIES (Tables)	12 Months Ended
ACCOUNTING POLICIES (Tables)	Dec. 31, 2013
ACCOUNTING POLICIES	'
Concentration of risk	'




		Percentage of
		Total Accounts
		Receivable
		Balance as of
		December 31,
		2013			2012
	AmerisourceBergen Drug Corporation		18	%		22	%
	Cardinal Health, Inc.		17	%		18	%
	McKesson Corporation		18	%		20	%





		Percentage of Total
		Net Revenues for
		the Years Ended
		December 31,
		2013			2012			2011
	AmerisourceBergen Drug Corporation		19	%		20	%		21	%
	Cardinal Health, Inc.		17	%		18	%		21	%
	McKesson Corporation		18	%		18	%		17	%
Schedule of estimated useful lives of property and equipment	'




	Asset Description	Estimated Useful Life
		(in years)
	Land		Indefinite
	Building		40
	Building enhancements		Not to exceed 20
	Furniture and fixtures		5 - 10
	Laboratory equipment		5
	Computer hardware and software		3
Schedule of gross U.S. product revenues offset by provisions	'




		For the Years Ended December 31,
		2013			2012			2011
		(in thousands)
	Gross U.S. product revenues	$	1,116,870		$	977,874		$	802,457
	Provisions offsetting U.S. product revenues
	Contractual adjustments		(61,448	)		(55,331	)		(45,093	)
	Governmental rebates		(84,226	)		(73,172	)		(55,997	)


	Total provisions, net offsetting U.S. product revenues		(145,674	)		(128,503	)		(101,090	)


	U.S. product revenues, net	$	971,196		$	849,371		$	701,367




Computation of basic and diluted net (loss) income per common share	'




		For the Years Ended December 31,
		2013			2012			2011
		(in thousands, except share and per share data)
	Basic net (loss) income	$	(18,571	)	$	154,075		$	33,023
	Effect of dilutive securities:
	Interest on 2017 Notes, net of tax		—			7,088			—
	Debt issuance costs related to 2017 Notes, net of tax		—			936			—
	Debt discount amortization related to 2017 Notes, net of tax		—			8,705			—


	Diluted net (loss) income	$	(18,571	)	$	170,804		$	33,023




	Shares used in calculating basic net (loss) income per common share		68,160,798			63,766,209			60,839,128
	Effect of dilutive securities:
	Options to purchase shares of common stock and RSUs		—			2,254,294			2,098,013
	2017 Notes payable convertible into shares of common stock		—			15,424,155			—


	Shares used in calculating diluted net (loss) income per common share		68,160,798			81,444,658			62,937,141




	Basic net (loss) income per share	$	(0.27	)	$	2.42		$	0.54
	Diluted net (loss) income per share	$	(0.27	)	$	2.1		$	0.52
Potential common shares excluded from calculation of diluted net (loss) income per share, as their inclusion would have been antidilutive	'




		For the Years Ended December 31,
		2013			2012			2011
	Options to purchase shares of common stock and RSUs		8,360,441			2,449,796			1,962,363
	Warrants		9,705,442			—			—
	2020 Notes convertible into shares of common stock		5,459,311			—			—
	2018 Notes convertible into shares of common stock		4,246,131			—			—
	2017 Notes convertible into shares of common stock		7,842,943			—			15,424,155
	2013 Notes convertible into shares of common stock		—			1,962,273			3,549,377

BUSINESS_COMBINATIONS_AND_ACQU1

BUSINESS COMBINATIONS AND ACQUISITIONS (Tables)	12 Months Ended
BUSINESS COMBINATIONS AND ACQUISITIONS (Tables)	Dec. 31, 2013
Optimer Pharmaceuticals, Inc.	'
Business combinations and acquisitions	'
Schedule of acquisition-date fair value of the consideration transferred	'




		Total
		Acquisition-
		Date
		Fair Value
		(in thousands)
	Cash transferred	$	569,452
	Contingent consideration (CVRs)		115,634


	Total consideration transferred	$	685,086




Summary of estimated fair values of the assets acquired and liabilities assumed	'




		October 24,
		2013
		(in thousands)
	Cash	$	31,466
	Investments		42,067
	Inventory		32,000
	DIFICID intangible asset		561,000
	Contract intangible asset		36,000
	Deferred tax assets		116,199
	Goodwill		108,631
	Other assets acquired		15,942


	Total assets acquired		943,305


	Deferred tax liabilities		(224,110	)
	Other liabilities assumed		(34,109	)


	Total liabilities assumed		(258,219	)


	Total net assets acquired	$	685,086




Schedule of supplemental unaudited pro forma information	'

	The following supplemental unaudited pro forma information presents Cubist's financial results as if the acquisition of Optimer had occurred on January 1, 2012 (in thousands):


		For the Years Ended
		December 31,
		2013			2012
		(unaudited)
	Total revenues, net	$	1,101,824		$	1,004,641
	Net (loss) income	$	(91,973	)	$	26,100
Trius Therapeutics, Inc.	'
Business combinations and acquisitions	'
Schedule of acquisition-date fair value of the consideration transferred	'




		Total
		Acquisition-
		Date Fair
		Value
		(in thousands)
	Cash transferred, including transaction costs	$	695,710
	Contingent consideration (CVRs)		4,603


	Total consideration transferred	$	700,313




Summary of estimated fair values of the assets acquired and liabilities assumed	'




		September 11,
		2013
		(in thousands)
	Cash	$	22,697
	Investments		39,513
	IPR&D		659,000
	Deferred tax assets		92,567
	Goodwill		160,257
	Other assets acquired		5,522


	Total assets acquired		979,556


	Deferred tax liabilities		(248,884	)
	Other liabilities assumed		(30,359	)


	Total liabilities assumed		(279,243	)


	Total net assets acquired	$	700,313




Schedule of supplemental unaudited pro forma information	'

	The following supplemental unaudited pro forma information presents Cubist's financial results as if the acquisition of Trius had occurred on January 1, 2012 (in thousands):


		For the Years Ended
		December 31,
		2013			2012
		(unaudited)
	Total revenues, net	$	1,054,442		$	938,460
	Net (loss) income	$	(28,312	)	$	75,594
Adolor Corporation	'
Business combinations and acquisitions	'
Schedule of supplemental unaudited pro forma information	'

	The following supplemental unaudited pro forma information presents Cubist's financial results as if the acquisition of Adolor had occurred on January 1, 2010 (in thousands):


		For the Year
		Ended
		December 31, 2011
		(unaudited)
	Total revenues, net	$	809,416
	Net income	$	29,147

INVESTMENTS_Tables

INVESTMENTS (Tables)	12 Months Ended
INVESTMENTS (Tables)	Dec. 31, 2013
INVESTMENTS	'
Amortized cost and estimated fair value of marketable securities, which are considered to be available-for-sale investments	'




		Amortized		Unrealized		Unrealized			Fair
		Cost		Gains		Losses			Value
		(in thousands)
	Balance at December 31, 2013:
	Bank deposits	$	40,000	$	—	$	—		$	40,000
	U.S. Treasury securities		67,648		6		(4	)		67,650
	Corporate and municipal notes		362,561		173		(36	)		362,698


	Total	$	470,209	$	179	$	(40	)	$	470,348




	Balance at December 31, 2012:
	Bank deposits	$	61,000	$	—	$	—		$	61,000
	U.S. Treasury securities		114,041		4		(3	)		114,042
	Corporate and municipal notes		640,234		158		(215	)		640,177


	Total	$	815,275	$	162	$	(218	)	$	815,219




Contractual maturities of investments	'




		December 31,
		2013				2012
		Amortized		Fair		Amortized			Fair
		Cost		Value		Cost			Value
		(in thousands)
	Within 1 year	$	470,209	$	470,348	$	812,104		$	812,052
	1 - 2 years		—		—		3,171			3,167


	Total	$	470,209	$	470,348	$	815,275		$	815,219

FAIR_VALUE_MEASUREMENTS_Tables

FAIR VALUE MEASUREMENTS (Tables)	12 Months Ended
FAIR VALUE MEASUREMENTS (Tables)	Dec. 31, 2013
FAIR VALUE MEASUREMENTS	'
Assets and liabilities measured at fair value on a recurring basis	'




		December 31, 2013
		Fair Value Measurements Using
		Level 1			Level 2			Level 3			Total
		(in thousands)
	Assets
	Cash and cash equivalents:(1)
	Money market funds	$	146		$	—		$	—		$	146
	Short-term investments:(2)
	Bank deposits		—			40,000			—			40,000
	U.S. Treasury securities		67,650			—			—			67,650
	Corporate and municipal notes		—			362,698			—			362,698


	Total assets	$	67,796		$	402,698		$	—		$	470,494




	Liabilities
	Contingent consideration—Optimer CVRs	$	68,561		$	—		$	—		$	68,561
	Contingent consideration—other		—			—			154,761			154,761


	Total liabilities	$	68,561		$	—		$	154,761		$	223,322









		December 31, 2012
		Fair Value Measurements Using
		Level 1			Level 2			Level 3			Total
		(in thousands)
	Assets
	Cash and cash equivalents:(1)
	Corporate and municipal notes	$	—		$	18,422		$	—		$	18,422
	Short-term and long-term investments:(2)
	Bank deposits		—			61,000			—			61,000
	U.S. Treasury securities		114,042			—			—			114,042
	Corporate and municipal notes		—			640,177			—			640,177


	Total assets	$	114,042		$	719,599		$	—		$	833,641




	Liabilities
	Contingent consideration—other	$	—		$	—		$	189,213		$	189,213


	Total liabilities	$	—		$	—		$	189,213		$	189,213






-1
Excludes $90.9 million and $85.6 million of cash as of December 31, 2013 and 2012, respectively.

-2
Excludes certificates of deposit of $17.2 million and $60.1 million recorded at cost as of December 31, 2013 and 2012, respectively.

Quantitative information associated with fair value measurement of the Company's contingent consideration using Level 3 inputs	'






		Contingent Consideration
		Trius		Adolor		Calixa
	Fair value as of December 31, 2013: (in thousands)	$5,012		$44,161		$105,588
	Valuation technique	Probability-adjusted		Probability-adjusted		Probability-adjusted
	Valuation technique	discounted cash flow		discounted cash flow		discounted cash flow
	Unobservable input
	Probabilities of success—range	4.0% - 6.5%		25.0% - 30.0%		40.0% - 86.0%
	(weighted average)	-5.80%		-27.00%		-65.00%
	Periods in which milestones are projected to be achieved	2016		2018 - 2022		2014 - 2018
	Discount rate	8.00%		5.3% / 13.0%		5.30%
Schedule of changes in the fair value of contingent consideration based upon Level 3 inputs	'




		Contingent
		Consideration
		(in thousands)
	Balance at December 31, 2011	$	248,234
	Contingent consideration income		(29,021	)
	Contingent consideration milestone payment		(30,000	)


	Balance at December 31, 2012		189,213
	Contingent consideration liability recorded upon acquisition		4,879
	Contingent consideration expense		669
	Milestone payment		(40,000	)


	Balance at December 31, 2013	$	154,761




Schedule of estimated fair values of the Convertible Senior Notes	'




		December 31,
		2013			2012
		(in thousands)
	2020 Notes	$	516,843		$	—
	2018 Notes		403,473			—
	2017 Notes		550,317			699,750


	Total estimated fair value of Convertible Senior Notes	$	1,470,633		$	699,750




Non-recurring Level 3 fair value measurement of the impairment analysis	'




		Fair Value as of			Valuation Technique		Unobservable Input		Percentage
		December 31,
		2013
		(in thousands)
	IPR&D asset (bevenopran)	$	43,400		Income approach -		Discount rate			13	%
					Probability-adjusted
					discounted cash flow

INVENTORY_Tables

INVENTORY (Tables)	12 Months Ended
INVENTORY (Tables)	Dec. 31, 2013
INVENTORY	'
Schedule of inventory	'




		December 31,
		2013		2012
		(in thousands)
	Raw materials	$	17,904	$	9,132
	Work-in-process		8,104		8,485
	Finished goods		31,655		24,330


	Inventory		57,663		41,947
	Included in other assets:
	Raw materials		57,284		34,091
	Work-in-process		1,882		1,733
	Finished goods		—		1,669


	Total	$	116,829	$	79,440

PROPERTY_AND_EQUIPMENT_NET_Tab

PROPERTY AND EQUIPMENT, NET (Tables)	12 Months Ended
PROPERTY AND EQUIPMENT, NET (Tables)	Dec. 31, 2013
PROPERTY AND EQUIPMENT, NET	'
Schedule of property and equipment, net	'




		December 31,
		2013			2012
		(in thousands)
	Land and buildings	$	172,199		$	166,659
	Laboratory equipment		48,997			35,961
	Furniture and fixtures		4,923			3,351
	Computer hardware and software		28,126			20,903
	Construction-in-progress		1,256			3,120


			255,501			229,994
	Less: accumulated depreciation		(77,957	)		(63,529	)


	Property and equipment, net	$	177,544		$	166,465

GOODWILL_IPR_AND_D_AND_OTHER_I1

GOODWILL, IPR AND D AND OTHER INTANGIBLE ASSETS, NET (Tables)	12 Months Ended
	Dec. 31, 2013
GOODWILL, IPR&D AND OTHER INTANGIBLE ASSETS, NET	'
Schedule of the Company's goodwill balance	'




		Goodwill
		(in thousands)
	Beginning balance as of December 31, 2012	$	114,130
	Goodwill acquired		268,888


	Ending balance as of December 31, 2013	$	383,018




Schedule of carrying value of the Company's IPR&D assets	'




		December 31,
		2013			2012
		(in thousands)
	Development and potential commercialization of:
	Tedizolid phosphate	$	659,000		$	—
	Bevenopran		43,400			78,700
	Ceftolozane/tazobactam for HABP and VABP		174,000			174,000
	Ceftolozane/tazobactam for cUTI and cIAI		20,000			20,000


	Total IPR&D	$	896,400		$	272,700




Schedule of finite-lived other intangible assets, net	'




		December 31,
		2013			2012
		(in thousands)
	Patents	$	2,627		$	2,627
	Acquired technology rights		788,800			191,800


	Other intangible assets, gross		791,427			194,427
	Less: accumulated amortization—patents		(2,493	)		(2,431	)
	accumulated amortization—acquired technology rights		(67,868	)		(39,166	)


	Other intangible assets, net	$	721,066		$	152,830




Schedule of estimated aggregate amortization of intangible assets	'




		(in thousands)
	2014	$	64,741
	2015		64,741
	2016		63,460
	2017		62,221
	2018		62,221
	2019 and thereafter		403,682


	Total	$	721,066

ACCRUED_LIABILITIES_Tables

ACCRUED LIABILITIES (Tables)	12 Months Ended
ACCRUED LIABILITIES (Tables)	Dec. 31, 2013
ACCRUED LIABILITIES	'
Schedule of accrued liabilities	'




		December 31,
		2013		2012
		(in thousands)
	Accrued royalties	$	83,591	$	72,103
	Accrued bonus		24,540		13,971
	Accrued Medicaid, Medicare and commercial rebates		18,595		20,565
	Accrued clinical trials		44,830		29,143
	Accrued benefits and incentive compensation		18,183		8,603
	Accrued restructuring		19,753		933
	Other accrued costs		35,586		18,315


	Accrued liabilities	$	245,078	$	163,633

DEBT_Tables

DEBT (Tables)	12 Months Ended
DEBT (Tables)	Dec. 31, 2013
DEBT	'
Schedule of components of the Company's Convertible Senior Notes	'




		December 31,
		2013			2012
		(in thousands)
	2020 Convertible Senior Notes
	Principal amount outstanding	$	450,000		$	—
	Unamortized discount		(111,015	)		—


	Net carrying amount		338,985			—


	2018 Convertible Senior Notes
	Principal amount outstanding		350,000			—
	Unamortized discount		(65,733	)		—


	Net carrying amount		284,267			—


	2017 Convertible Senior Notes
	Principal amount outstanding		228,822			450,000
	Unamortized discount		(34,244	)		(82,189	)


	Net carrying amount		194,578			367,811


	Total Convertible Senior Notes
	Principal amount outstanding		1,028,822			450,000
	Unamortized discount		(210,992	)		(82,189	)


	Net carrying amount	$	817,830		$	367,811




Schedule of interest expense on Convertible Senior Notes and other interest expense, which includes interest expense for the payable to Glaxo	'




		For the Years Ended
		December 31,
		2013			2012			2011
		(in thousands)
	Contractual interest coupon payment	$	13,370		$	12,667		$	13,707
	Amortization of discount on debt		20,333			17,244			18,447
	Amortization debt issuance costs		3,048			1,971			1,828
	Other interest expense		851			1,109			—
	Capitalized interest		—			—			(2,567	)


	Total interest expense	$	37,602		$	32,991		$	31,415




Schedule of future payments of principal and interest on existing debt and the payable to Glaxo	'




		Principal
		(in thousands)
	2014	$	3,500
	2015		3,500
	2016		4,500
	2017		233,322
	2018		350,000
	2019 and thereafter		450,000


	Total payments		1,044,822
	Less current portion		(3,500	)


	Total long-term debt and payable obligations	$	1,041,322

EMPLOYEE_STOCK_BENEFIT_PLANS_T

EMPLOYEE STOCK BENEFIT PLANS (Tables)	12 Months Ended
EMPLOYEE STOCK BENEFIT PLANS (Tables)	Dec. 31, 2013
EMPLOYEE STOCK BENEFIT PLANS	'
Schedule of stock-based compensation expense	'




		For the Years Ended December 31,
		2013			2012			2011
		(in thousands)
	Stock-based compensation expense allocation:
	Cost of product revenues	$	525		$	497		$	264
	Research and development		12,249			9,100			6,623
	Selling, general and administrative		19,583			16,105			12,481


	Total stock-based compensation		32,357			25,702			19,368
	Income tax effect		(11,454	)		(9,510	)		(7,449	)


	After-tax effect of stock-based compensation expense	$	20,903		$	16,192		$	11,919




Schedule of weighted-average assumptions used to calculate the fair value of each stock-based option award under the Black-Scholes option-pricing model	'




		For the Years Ended December 31,
		2013		2012		2011
	Expected stock price volatility	36.20%		39.60%		41.00%
	Risk-free interest rate	0.7% - 1.7%		0.6% - 1.1%		0.9% - 2.4%
	Expected annual dividend yield per share	—		—		—
	Expected life of options	4.5 years		4.6 years		4.6 years
Schedule of option activity	'




		Number of			Weighted-			Aggregate			Weighted-
		Shares			Average			Intrinsic Value			Average
					Exercise Price						Contractual
											Life
								(in thousands)			(in years)
	Outstanding as of December 31, 2012		8,025,194		$	27.31		$	333,507
	Granted		1,288,393		$	45.83		$	29,688
	Exercised		(1,695,244	)	$	21.73		$	58,051
	Canceled		(140,174	)	$	35.91		$	4,620


	Outstanding as of December 31, 2013		7,478,169		$	31.61		$	278,661			6.6




	Vested and exercisable as of December 31, 2013		4,654,759		$	25.99		$	199,619			5.6
	Expected to vest as of December 31, 2013		2,437,787		$	40.87		$	68,247			8.4
Schedule of RSU activity, including PRSUs	'




		Number of			Weighted-			Aggregate
		Shares			Average Grant			Intrinsic Value
					Date Fair Value
								(in thousands)
	Nonvested as of December 31, 2012		735,939		$	35.33		$	50,684
	Granted		457,820		$	44.75		$	31,530
	Vested		(278,874	)	$	32.71		$	19,206
	Canceled		(32,613	)	$	37.44		$	2,246


	Nonvested as of December 31, 2013		882,272		$	40.97		$	60,762




	Expected to vest as of December 31, 2013		584,061		$	40.97		$	40,224

COMMITMENTS_AND_CONTINGENCIES_

COMMITMENTS AND CONTINGENCIES (Tables)	12 Months Ended
COMMITMENTS AND CONTINGENCIES (Tables)	Dec. 31, 2013
COMMITMENTS AND CONTINGENCIES	'
Schedule of future minimum payments under non-cancelable leases	'




		(in thousands)
	2014	$	2,950
	2015		2,623
	2016		2,687
	2017		2,686
	2018		2,352
	2019 and thereafter		7,116


	Total	$	20,414

RESTRUCTURING_Tables

RESTRUCTURING (Tables)	12 Months Ended
RESTRUCTURING (Tables)	Dec. 31, 2013
RESTRUCTURING	'
Schedule of activity in restructuring liability included in accrued liabilities and other long-term liabilities	'




		Employee-			Lease			Total
		Related			Restructuring
		Severance
		(in thousands)
	Balance at December 31, 2011	$	8,089		$	1,190		$	9,279
	Cash payments made		(7,156	)		(1,190	)		(8,346	)


	Balance at December 31, 2012		933			—			933
	Restructuring expense		19,824			4,495			24,319
	Cash payments made		(1,584	)		—			(1,584	)


	Balance at December 31, 2013	$	19,173		$	4,495		$	23,668

INCOME_TAXES_Tables

INCOME TAXES (Tables)	12 Months Ended
INCOME TAXES (Tables)	Dec. 31, 2013
INCOME TAXES	'
Schedule of components of federal and state income tax expense (benefit)	'




		For the Years Ended December 31,
		2013			2012			2011
		(in thousands)
	Current income tax expense
	Federal	$	9,163		$	74,744		$	55,656
	State		4,748			3,719			7,393


	Total current income tax expense		13,911			78,463			63,049


	Deferred income tax (benefit) expense
	Federal		(32,449	)		(15,874	)		10,112
	State		(6,535	)		(17,068	)		(1,395	)


	Total deferred income tax (benefit) expense		(38,984	)		(32,942	)		8,717


	Total current and deferred income tax (benefit) expense	$	(25,073	)	$	45,521		$	71,766




Schedule of the reconciliation of the federal statutory tax rate to the effective tax rates and the related impact to the (benefit) provision for income taxes	'




		For the Years Ended December 31,
		2013						2012						2011
		Amount			Tax Rate			Amount			Tax Rate			Amount			Tax Rate
		(in thousands, except for percentages)
	Federal statutory tax rate applied to (loss) income before taxes	$	(15,275	)		35	%	$	69,859			35	%	$	36,676			35	%
	Differential arising from:
	State		(1,161	)		2.7	%		2,247			1.1	%		3,899			3.7	%
	Non-deductible expenses		1,606			(3.7	)%		1,284			0.6	%		1,386			1.3	%
	Current year federal research credit		(6,176	)		14.2	%		—			—	%		(1,763	)		(1.7	)%
	Prior year federal research credits		(4,399	)		10.1	%		—			—	%		—			—	%
	Impact of reserve for uncertain tax positions		(192	)		0.4	%		(10,923	)		(5.5	)%		—			—	%
	Domestic manufacturing deduction		(262	)		0.6	%		(5,820	)		(2.9	)%		—			—	%
	Transaction costs		3,797			(8.7	)%		—			—	%		967			1	%
	Loss on extinguishment of 2017 Notes		8,070			(18.5	)%		—			—	%		—			—	%
	Contingent consideration		(19,147	)		43.9	%		(12,029	)		(6.0	)%		29,881			28.5	%
	Valuation allowance on Adynxx impairment		7,000			(16.0	)%		—			—	%		—			—	%
	Other		1,066			(2.6	)%		903			0.5	%		720			0.7	%


	Total	$	(25,073	)		57.4	%	$	45,521			22.8	%	$	71,766			68.5	%




Schedule of components of the net deferred tax assets and the related valuation allowance	'




		December 31,
		2013			2012
		(in thousands)
	Deferred income tax assets:
	NOL carryforwards	$	215,155		$	50,043
	Deferred revenues		12,539			10,141
	Research and development costs		17,461			517
	Tax credit carryforwards		30,815			9,357
	Stock-based compensation		21,136			18,485
	Capital loss carryforward		10,472			11,118
	Investment impairment		7,341			—
	Other		15,721			8,868


	Total deferred tax assets	$	330,640		$	108,529
	Deferred income tax liabilities:
	Prepaid expenses	$	(2,066	)	$	(2,669	)
	Debt discount		(12,220	)		(29,919	)
	IPR&D		(327,272	)		(100,104	)
	Other intangible assets		(226,408	)		(32,880	)
	Inventory		(13,871	)		(14,539	)
	Depreciation		(9,036	)		(3,968	)


	Total deferred tax liabilities		(590,873	)		(184,079	)


	Total deferred tax assets and liabilities		(260,233	)		(75,550	)
	Valuation allowance		(45,461	)		(13,341	)


	Net deferred tax liabilities	$	(305,694	)	$	(88,891	)




Schedule of reconciliation of changes in uncertain tax positions	'




		For the Years Ended December 31,
		2013			2012			2011
		(in thousands)
	Uncertain tax positions at the beginning of the year	$	36,115		$	27,774		$	8,216
	Additions based on tax positions related to the current year		2,717			769			12,844
	Additions for tax positions of prior years		5,393			24,299			7,321
	Subtractions based on tax positions related to the current year		—			—			—
	Subtractions for tax positions of prior years		(1,105	)		(16,727	)		(607	)


	Balance at the end of the year	$	43,120		$	36,115		$	27,774

SELECTED_QUARTERLY_FINANCIAL_D1

SELECTED QUARTERLY FINANCIAL DATA (UNAUDITED) (Tables)	12 Months Ended
SELECTED QUARTERLY FINANCIAL DATA (UNAUDITED) (Tables)	Dec. 31, 2013
SELECTED QUARTERLY FINANCIAL DATA (UNAUDITED)	'
Schedule of selected quarterly financial data	'






		First		Second		Third			Fourth
		Quarter		Quarter		Quarter			Quarter
		(in thousands, except per share data)
	2013
	Total revenues, net	$	229,929	$	258,779	$	265,993		$	299,741
	Product revenues, net	$	225,651	$	254,462	$	256,583		$	295,737
	Cost of product revenues	$	55,675	$	63,041	$	60,989		$	80,605
	Net income (loss)	$	6,088	$	15,242	$	-33,895	-2	$	-6,006	-1
	Basic net income (loss) per share	$	0.09	$	0.23	$	-0.5	-2	$	-0.08	-1
	Diluted net income (loss) per share	$	0.09	$	0.23	$	-0.5	-2	$	-0.08	-1
	2012
	Total revenues, net	$	211,692	$	230,567	$	238,181		$	245,919
	Product revenues, net	$	206,803	$	221,249	$	230,313		$	241,460
	Cost of product revenues	$	53,952	$	58,891	$	55,740		$	61,474
	Net income	$	32,794	$	43,123	$	40,321		$	37,837	-1
	Basic net income per share	$	0.52	$	0.68	$	0.63		$	0.59	-1
	Diluted net income per share	$	0.45	$	0.58	$	0.55		$	0.51	-1


	-1
	During the fourth quarters of 2013 and 2012, Cubist recorded impairment charges of $35.3 million and $38.7 million, respectively, to write down the bevenopran IPR&D asset, which was acquired in connection with the acquisition of Adolor in December 2011, to its revised fair value. The impairment charges were offset by related contingent consideration income of $36.2 million and $37.0 million recorded during the fourth quarters of 2013 and 2012, respectively. In addition, during the fourth quarter of 2013, Cubist recorded an impairment charge of $20.0 million, representing the write-off of the non-refundable option payment to Adynxx, which resulted from management's decision to not exercise the option to acquire 100% of the outstanding shares of Adynxx.

	-2
	During the third quarter of 2013, Cubist recorded a $34.6 million loss on the induced conversion of $221.2 million of the principal amount of the Company's 2017 Notes in September 2013.

NATURE_OF_BUSINESS_Details

NATURE OF BUSINESS (Details)	12 Months Ended
	Dec. 31, 2013
	candidate
	product
NATURE OF BUSINESS	'
Number of marketed products	3
Number of late-stage product candidates	4

ACCOUNTING_POLICIES_Details

ACCOUNTING POLICIES (Details) (USD $)	12 Months Ended
ACCOUNTING POLICIES (Details) (USD $)	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Fair Value Measurements	'	'	'
Assets transferred out of Level 1 to Level 2	0	'	'
Assets transferred out of Level 2 to Level 1	0	'	'
Liabilities transferred out of Level 1 to Level 2	0	'	'
Liabilities transferred out of Level 2 to Level 1	0	'	'
Assets transferred out of Level 2 to Level 3	0	'	'
Assets transferred out of Level 3 to Level 2	0	'	'
Liabilities transferred out of Level 2 to Level 3	0	'	'
Liabilities transferred out of Level 3 to Level 2	0	'	'
Concentration of Risk	'	'	'
Number of suppliers in order to provide fill finish services related to manufacture of CUBICIN	2	'	'
Accounts receivable \| AmerisourceBergen Drug Corporation	'	'	'
Concentration of risk	'	'	'
Benchmark percentage Concentration of risk	18.00%	22.00%	'
Accounts receivable \| Cardinal Health, Inc.	'	'	'
Concentration of risk	'	'	'
Benchmark percentage Concentration of risk	17.00%	18.00%	'
Accounts receivable \| McKesson Corporation	'	'	'
Concentration of risk	'	'	'
Benchmark percentage Concentration of risk	18.00%	20.00%	'
Revenues \| AmerisourceBergen Drug Corporation	'	'	'
Concentration of risk	'	'	'
Benchmark percentage Concentration of risk	19.00%	20.00%	21.00%
Revenues \| Cardinal Health, Inc.	'	'	'
Concentration of risk	'	'	'
Benchmark percentage Concentration of risk	17.00%	18.00%	21.00%
Revenues \| McKesson Corporation	'	'	'
Concentration of risk	'	'	'
Benchmark percentage Concentration of risk	18.00%	18.00%	17.00%

ACCOUNTING_POLICIES_Details_2

ACCOUNTING POLICIES (Details 2) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012
Intangible Assets, Net	'	'
Impairment charges related to IPR&D asset	$35,300	$38,700
Minimum	'	'
Intangible Assets, Net	'	'
Other intangible assets, estimated economic lives	'9 years	'
Maximum	'	'
Intangible Assets, Net	'	'
Other intangible assets, estimated economic lives	'14 years	'
Building	'	'
Property and equipment, net	'	'
Estimated Useful Life	'40 years	'
Building enhancements \| Maximum	'	'
Property and equipment, net	'	'
Estimated Useful Life	'20 years	'
Furniture and fixtures \| Minimum	'	'
Property and equipment, net	'	'
Estimated Useful Life	'5 years	'
Furniture and fixtures \| Maximum	'	'
Property and equipment, net	'	'
Estimated Useful Life	'10 years	'
Laboratory equipment	'	'
Property and equipment, net	'	'
Estimated Useful Life	'5 years	'
Computer hardware and software	'	'
Property and equipment, net	'	'
Estimated Useful Life	'3 years	'

ACCOUNTING_POLICIES_Details_3

ACCOUNTING POLICIES (Details 3) (USD $)	12 Months Ended
ACCOUNTING POLICIES (Details 3) (USD $)	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Gross U.S. product revenues offset by provisions	'	'	'
Gross U.S. product revenues	$1,116,870,000	$977,874,000	$802,457,000
Provisions offsetting U.S. product revenues	'	'	'
Contractual adjustments	-61,448,000	-55,331,000	-45,093,000
Governmental rebates	-84,226,000	-73,172,000	-55,997,000
Total provisions, net offsetting U.S. product revenues	-145,674,000	-128,503,000	-101,090,000
U.S. product revenues, net	971,196,000	849,371,000	701,367,000
Reserves for returns, discounts, chargebacks, wholesaler management fees and doubtful accounts offset against accounts receivable	16,000,000	9,200,000	'
Reserves for governmental and commercial rebates included in accrued liabilities	18,600,000	20,600,000	'
Revenue reserves reversed	18,000,000	'	'
Reversal of revenue reserves related to Medicaid program	10,000,000	'	'
International Product Revenues	'	'	'
Total deferred revenue related to international product revenues	20,500,000	20,400,000	'
Service Revenues	'	'	'
Service revenues	12,287,000	23,249,000	6,725,000
Other Revenues	'	'	'
Total deferred revenue related to other revenues	16,900,000	20,500,000	'
Stock-Based Compensation	'	'	'
Dividend yield assumption used in the Black-Scholes option-pricing model (as a percent)	0.00%	'	'
License agreement with Optimer	'	'	'
Milestones	'	'	'
Bonus for achieving an annual sales target	'	$8,500,000	'

ACCOUNTING_POLICIES_Details_4

ACCOUNTING POLICIES (Details 4) (USD $)	3 Months Ended								12 Months Ended
In Thousands, except 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
Basic and diluted net (loss) income per share	'	'	'	'	'	'	'	'	'	'	'
Basic net (loss) income	($6,006)	($33,895)	$15,242	$6,088	$37,837	$40,321	$43,123	$32,794	($18,571)	$154,075	$33,023
Effect of dilutive securities:	'	'	'	'	'	'	'	'	'	'	'
Debt issuance costs, net of tax	'	'	'	'	'	'	'	'	3,048	1,971	1,828
Debt discount amortization, net of tax	'	'	'	'	'	'	'	'	20,333	17,244	18,447
Diluted net (loss) income	'	'	'	'	'	'	'	'	-18,571	170,804	33,023
Reconciliation of basic and diluted shares	'	'	'	'	'	'	'	'	'	'	'
Shares used in calculating basic net (loss) income per common share	'	'	'	'	'	'	'	'	68,160,798	63,766,209	60,839,128
Options to purchase shares of common stock and RSUs (in shares)	'	'	'	'	'	'	'	'	'	2,254,294	2,098,013
Shares used in calculating diluted net (loss) income per common share	'	'	'	'	'	'	'	'	68,160,798	81,444,658	62,937,141
Basic net (loss) income per share (in dollars per share)	($0.08)	($0.50)	$0.23	$0.09	$0.59	$0.63	$0.68	$0.52	($0.27)	$2.42	$0.54
Diluted net (loss) income per share (in dollars per share)	($0.08)	($0.50)	$0.23	$0.09	$0.51	$0.55	$0.58	$0.45	($0.27)	$2.10	$0.52
2.25% Convertible subordinated notes due June 2013 (2013 Notes)	'	'	'	'	'	'	'	'	'	'	'
Computation of basic and diluted net (loss) income per common share	'	'	'	'	'	'	'	'	'	'	'
Notes stated interest rate percentage	2.25%	'	'	'	'	'	'	'	2.25%	'	'
2.50% convertible senior notes due November 2017 (2017 Notes)	'	'	'	'	'	'	'	'	'	'	'
Computation of basic and diluted net (loss) income per common share	'	'	'	'	'	'	'	'	'	'	'
Notes stated interest rate percentage	2.50%	'	'	'	'	'	'	'	2.50%	'	'
Effect of dilutive securities:	'	'	'	'	'	'	'	'	'	'	'
Interest on convertible notes, net of tax	'	'	'	'	'	'	'	'	'	7,088	'
Debt issuance costs, net of tax	'	'	'	'	'	'	'	'	'	936	'
Debt discount amortization, net of tax	'	'	'	'	'	'	'	'	'	$8,705	'
Reconciliation of basic and diluted shares	'	'	'	'	'	'	'	'	'	'	'
Notes payable convertible into common stock (in shares)	'	'	'	'	'	'	'	'	'	15,424,155	'
1.125% convertible senior notes due 2018 (2018 Notes)	'	'	'	'	'	'	'	'	'	'	'
Computation of basic and diluted net (loss) income per common share	'	'	'	'	'	'	'	'	'	'	'
Notes stated interest rate percentage	1.13%	'	'	'	'	'	'	'	1.13%	'	'
1.875% convertible senior notes due 2020 (2020 Notes)	'	'	'	'	'	'	'	'	'	'	'
Computation of basic and diluted net (loss) income per common share	'	'	'	'	'	'	'	'	'	'	'
Notes stated interest rate percentage	1.88%	'	'	'	'	'	'	'	1.88%	'	'

ACCOUNTING_POLICIES_Details_5

ACCOUNTING POLICIES (Details 5)	12 Months Ended
ACCOUNTING POLICIES (Details 5)	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Options to purchase shares of common stock and RSUs	'	'	'
Potential common shares excluded from the calculation of diluted net (loss) income per share	'	'	'
Antidilutive securities related to potential shares excluded from calculation of net (loss) income per share (in shares)	8,360,441	2,449,796	1,962,363
Warrants	'	'	'
Potential common shares excluded from the calculation of diluted net (loss) income per share	'	'	'
Antidilutive securities related to potential shares excluded from calculation of net (loss) income per share (in shares)	9,705,442	'	'
1.875% convertible senior notes due 2020 (2020 Notes)	'	'	'
Potential common shares excluded from the calculation of diluted net (loss) income per share	'	'	'
Antidilutive securities related to potential shares excluded from calculation of net (loss) income per share (in shares)	5,459,311	'	'
1.125% convertible senior notes due 2018 (2018 Notes)	'	'	'
Potential common shares excluded from the calculation of diluted net (loss) income per share	'	'	'
Antidilutive securities related to potential shares excluded from calculation of net (loss) income per share (in shares)	4,246,131	'	'
2.50% convertible senior notes due November 2017 (2017 Notes)	'	'	'
Potential common shares excluded from the calculation of diluted net (loss) income per share	'	'	'
Antidilutive securities related to potential shares excluded from calculation of net (loss) income per share (in shares)	7,842,943	'	15,424,155
2.25% Convertible subordinated notes due June 2013 (2013 Notes)	'	'	'
Potential common shares excluded from the calculation of diluted net (loss) income per share	'	'	'
Antidilutive securities related to potential shares excluded from calculation of net (loss) income per share (in shares)	'	1,962,273	3,549,377

BUSINESS_AGREEMENTS_Details

BUSINESS AGREEMENTS (Details) (USD $)	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2013	Dec. 31, 2011	Mar. 31, 2005	Mar. 31, 2005	Dec. 31, 2013	Sep. 30, 2003
			CUBICIN	CUBICIN	CUBICIN	CUBICIN	CUBICIN	CUBICIN
			License and manufacturing and supply agreements	License and manufacturing and supply agreements	License agreement	License agreement	License agreement	License agreement
			Novartis AG	Novartis AG	Eli Lilly & Co.	Eli Lilly & Co.	Eli Lilly & Co.	Eli Lilly & Co.
						Royalty rates payable	Royalty rates payable	Additional funding
Milestones	'	'	'	'	'	'	'	'
Receipt on achievement of certain sales milestones	'	'	$5,000,000	$5,000,000	'	'	'	'
Maximum payments to be received upon the achievement of certain milestones	'	'	15,000,000	'	'	'	'	'
Number of shares issued during the period	'	'	'	'	'	2,599,792	'	'
Values of shares issued during the period	'	'	'	'	'	28,000,000	'	'
Number of shares issued	74,428,087	64,713,695	'	'	'	'	'	38,922
Value of shares issued	74,000	65,000	'	'	'	'	'	500,000
Payment for license agreement	'	'	'	'	28,500,000	'	'	'
Cumulative royalties paid on sales of CUBICIN	'	'	'	'	'	'	$588,600,000	'

BUSINESS_AGREEMENTS_Details_2

BUSINESS AGREEMENTS (Details 2)	25 Months Ended	1 Months Ended			12 Months Ended	1 Months Ended	12 Months Ended	25 Months Ended
In Millions, unless otherwise specified	Dec. 31, 2013	Jun. 30, 2012	Mar. 31, 2011	Dec. 31, 2013	Dec. 31, 2013	Dec. 31, 2011	Dec. 31, 2013	Dec. 31, 2013
	Adolor	DIFICID	DIFICID	DIFICID	DIFICID	ENTEREG	ENTEREG	ENTEREG
	USD ($)	Collaboration and license and supply agreement	Collaboration and license and supply agreement	Collaboration and license and supply agreement	Buy-back agreement	License agreement	License agreement	License agreement
		Astellas Europe	Astellas Europe	Astellas Europe	Par	Glaxo	Glaxo	Glaxo
		Optimer	Optimer	Optimer	Optimer	Adolor	Adolor	Adolor
		EUR (€)	USD ($)	EUR (€)		USD ($)	USD ($)	USD ($)
Licensing and Collaboration Agreements	'	'	'	'	'	'	'	'
Upfront, non-refundable payment, received prior to acquisition	'	'	$69.20	'	'	'	'	'
Receipt of potential milestone payments prior to acquisition	'	50	'	'	'	'	'	'
Receipt of regulatory approval milestone payment prior to acquisition	'	40	'	'	'	'	'	'
Milestone payment received for the first commercial launch of DIFICLIR prior to acquisition	'	10	'	'	'	'	'	'
Maximum payments to be received upon the achievement of certain milestones	'	'	'	65	'	'	'	'
Term of net sales royalty payment on a country-by-country basis	'	'	'	'	'7 years	'	'	'
Term of net revenues royalties payment	'	'	'	'	'7 years	'	'	'
Aggregated original payments assumed	'	'	'	'	'	25	'	'
Payments made prior to acquisition	'	'	'	'	'	2.5	'	'
Payments made under the agreement	6.5	'	'	'	'	'	'	6.5
Milestone payable on achievement of certain levels of sales	'	'	'	'	'	'	$15	'

BUSINESS_AGREEMENTS_Details_3

BUSINESS AGREEMENTS (Details 3) (USD $)	12 Months Ended		1 Months Ended			1 Months Ended
In Millions, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2013	Jul. 31, 2011	Sep. 30, 2013	Dec. 31, 2013	Mar. 31, 2013	Dec. 31, 2013
	Settlement and license agreement	Tedizolid phosphate	Tedizolid phosphate	Tedizolid phosphate	Tedizolid phosphate	Ceftolozane/tazobactam	Ceftolozane/tazobactam
	Teva and its affiliates	Collaboration and license agreement	Collaboration and license agreement	License agreement	License agreement	License agreement	License agreement
	component	Bayer Pharma AG	Bayer Pharma AG	Dong-A ST Co., Ltd.	Dong-A ST Co., Ltd.	Astellas Pharma Inc.	Astellas Pharma Inc.
			Trius	Trius	Trius
Licensing and Collaboration Agreements	'	'	'	'	'	'	'
Upfront, non-refundable payment, received prior to acquisition	'	'	$25	'	'	'	'
Percentage of future development costs of tedizolid required for global approval agreed to be reimbursed	'	'	25.00%	'	'	'	'
Percentage of future development costs for local approval agreed to be reimbursed	'	'	100.00%	'	'	'	'
Maximum payments to be received upon the achievement of certain milestones	'	55	'	'	'	'	'
Potential obligation of milestone payments	'	'	'	11.5	8.5	'	40
Minimum period after the date of the first commercial sale over which royalties on annual net worldwide sales would be paid	'	'	'	'12 years	'	'	'
Payment for license agreement	'	'	'	'	'	$25	'
Number of components based on which payments will be received under supply terms	2	'	'	'	'	'	'

BUSINESS_COMBINATIONS_AND_ACQU2

BUSINESS COMBINATIONS AND ACQUISITIONS (Details) (USD $)

3 Months Ended

12 Months Ended

3 Months Ended

12 Months Ended

0 Months Ended

12 Months Ended

0 Months Ended

12 Months Ended

0 Months Ended

12 Months Ended

0 Months Ended

12 Months Ended

0 Months Ended

1 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, 2011

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Oct. 24, 2013

Dec. 31, 2013

Dec. 31, 2012

Oct. 24, 2013

Dec. 31, 2013

Sep. 11, 2013

Dec. 31, 2013

Dec. 31, 2012

Sep. 11, 2013

Dec. 31, 2013

Dec. 12, 2011

Dec. 31, 2011

Dec. 31, 2013

Dec. 12, 2011

Dec. 31, 2013

Dec. 12, 2011

Dec. 31, 2011

Bevenopran (formerly known as CB-5945)

Research and development expense

Selling, general and administrative expense

Optimer Pharmaceuticals, Inc.

Trius Therapeutics, Inc.

Adolor Corporation

right

Contract intangibles

DIFICID

Cempra

Research and development expense

Selling, general and administrative expense

right

Tedizolid phosphate

Research and development expense

Selling, general and administrative expense

ENTEREG

Bevenopran (formerly known as CB-5945)

Selling, general and administrative expense

BUSINESS COMBINATIONS AND ACQUISITIONS

Percentage of issued and outstanding shares purchased

100.00%

Tender offer purchase price of outstanding common stock of acquiree (in dollars per share)

$10.75

$13.50

Number of contingent value rights receivable by stockholders of acquiree

Maximum additional cash payment per share (in dollars per share)

Undiscounted contingent consideration payout

$253,900,000

$108,400,000

$233,800,000

Total Acquisition-Date Fair Value

Cash transferred

569,452,000

Contingent consideration (CVRs)

115,634,000

4,603,000

110,200,000

Total consideration transferred

685,086,000

700,313,000

Carrying value of the investment

25,000,000

Cash transferred, including transaction costs

544,500,000

695,710,000

220,800,000

Transaction costs paid on behalf of acquiree

13,700,000

Charges for stock-based compensation

32,357,000

25,702,000

19,368,000

12,249,000

9,100,000

6,623,000

19,583,000

16,105,000

12,481,000

7,200,000

1,800,000

5,400,000

22,700,000

11,000,000

11,700,000

Estimated fair values of the assets acquired and liabilities assumed

Cash

31,466,000

22,697,000

Investments

42,067,000

39,513,000

Inventory

32,000,000

IPR&D

659,000,000

117,400,000

Intangible asset

36,000,000

561,000,000

163,300,000

Deferred tax assets

116,199,000

92,567,000

Goodwill

383,018,000

114,130,000

383,018,000

114,130,000

108,631,000

160,257,000

Other assets acquired

15,942,000

5,522,000

Total assets acquired

943,305,000

979,556,000

Deferred tax liabilities

-224,110,000

-248,884,000

Other liabilities assumed

-34,109,000

-30,359,000

Total liabilities assumed

-258,219,000

-279,243,000

Total net assets acquired

685,086,000

700,313,000

Fair value of IPR&D asset, bevenopran

43,400,000

Discount rate for determining fair value of acquired asset (as a percent)

13.00%

14.50%

16.00%

8.00%

9.50%

Expected useful life of intangible assets

'14 years

'11 years

Revenues of acquiree included in the income statement of combined entity

14,700,000

2,000,000

Operating loss of acquiree included in the income statement of combined entity

11,000,000

23,400,000

Transaction costs

12,400,000

10,200,000

8,100,000

Revenues

299,741,000

265,993,000

258,779,000

229,929,000

245,919,000

238,181,000

230,567,000

211,692,000

1,054,442,000

926,359,000

753,972,000

2,600,000

Supplemental unaudited pro forma information

Total revenues, net

1,101,824,000

1,004,641,000

1,054,442,000

938,460,000

809,416,000

Net (loss) income

($91,973,000)

$26,100,000

($28,312,000)

$75,594,000

$29,147,000

BUSINESS_COMBINATIONS_AND_ACQU3

BUSINESS COMBINATIONS AND ACQUISITIONS (Details 2) (USD $)

3 Months Ended

12 Months Ended

1 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

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Optimer Pharmaceuticals, Inc.

Trius Therapeutics, Inc.

Adolor Corporation

Amortization of intangible asset

Transaction costs

Stock-based compensation expense related to the acceleration of vesting of previously unvested awards

Restructuring charges

Intercompany revenues related to the co-promotion DIFICID

Additional interest expense

Transaction costs

Stock-based compensation expense related to the acceleration of vesting of previously unvested awards

Compensation expense related to severance and retention agreements and restructuring charges

Research and development

Amortization of intangible asset

Transaction costs

Restructuring charges

Recurring and non-recurring adjustments to pro forma information

Net income

($6,006)

($33,895)

$15,242

$6,088

$37,837

$40,321

$43,123

$32,794

($18,571)

$154,075

$33,023

($35,600)

($44,000)

$34,300

($34,300)

$7,200

($7,200)

$21,600

($21,600)

($29,700)

($41,500)

$24,900

($24,900)

$22,700

($22,700)

$9,400

($9,400)

($4,100)

($15,100)

($20,200)

$13,100

$9,300

Revenues

$299,741

$265,993

$258,779

$229,929

$245,919

$238,181

$230,567

$211,692

$1,054,442

$926,359

$753,972

($12,300)

($23,200)

$2,600

INVESTMENTS_Details

INVESTMENTS (Details) (USD $)	Dec. 31, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012
Available-for-sale investments	'	'
Amortized Cost	$470,209	$815,275
Unrealized Gains	179	162
Unrealized Losses	-40	-218
Total	470,348	815,219
Bank deposits	'	'
Available-for-sale investments	'	'
Amortized Cost	40,000	61,000
Total	40,000	61,000
U.S. Treasury securities	'	'
Available-for-sale investments	'	'
Amortized Cost	67,648	114,041
Unrealized Gains	6	4
Unrealized Losses	-4	-3
Total	67,650	114,042
Corporate and municipal notes	'	'
Available-for-sale investments	'	'
Amortized Cost	362,561	640,234
Unrealized Gains	173	158
Unrealized Losses	-36	-215
Total	$362,698	$640,177

INVESTMENTS_Details_2

INVESTMENTS (Details 2) (USD $)	12 Months Ended		1 Months Ended	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Feb. 28, 2013	Dec. 31, 2013	Dec. 31, 2013	Dec. 31, 2012
			Option agreement	Option agreement	Excluded portion	Excluded portion
			Adynxx	Adynxx
Amortized Cost	'	'	'	'	'	'
Within 1 year, Amortized Cost	$470,209,000	$812,104,000	'	'	'	'
1-2 years, Amortized Cost	'	3,171,000	'	'	'	'
Total	470,209,000	815,275,000	'	'	'	'
Fair Value	'	'	'	'	'	'
Within 1 year, Fair Value	470,348,000	812,052,000	'	'	'	'
1-2 years, Fair Value	'	3,167,000	'	'	'	'
Total	470,348,000	815,219,000	'	'	'	'
Certificates of deposit	'	'	'	'	17,200,000	60,100,000
Payment for purchase option, non-refundable except in limited circumstances	20,000,000	'	20,000,000	'	'	'
Percentage of outstanding shares to be acquired under option in exchange for $20.0 million non-refundable payment	'	'	100.00%	'	'	'
Maximum number of days purchase option was exercisable	'	'	'60 days	'	'	'
Impairment charge of option	'	'	'	$20,000,000	'	'

FAIR_VALUE_MEASUREMENTS_Detail

FAIR VALUE MEASUREMENTS (Details) (USD $)	Dec. 31, 2013	Dec. 31, 2012
Optimer CVRs	'	'
Liabilities	'	'
Contingent consideration	$68,600,000	'
Excluded portion	'	'
Assets	'	'
Cash	90,900,000	85,600,000
Certificate of deposit excluded and recorded at cost	17,200,000	60,100,000
Recurring Basis \| Level 1	'	'
Assets	'	'
Total assets	67,796,000	114,042,000
Liabilities	'	'
Total liabilities	68,561,000	'
Recurring Basis \| Level 1 \| Optimer CVRs	'	'
Liabilities	'	'
Contingent consideration	68,561,000	'
Recurring Basis \| Level 1 \| Money market funds	'	'
Assets	'	'
Cash and cash equivalents:	146,000	'
Recurring Basis \| Level 1 \| U.S. Treasury securities	'	'
Assets	'	'
Short-term and long-term investments:	67,650,000	114,042,000
Recurring Basis \| Level 2	'	'
Assets	'	'
Total assets	402,698,000	719,599,000
Recurring Basis \| Level 2 \| Bank deposits	'	'
Assets	'	'
Short-term and long-term investments:	40,000,000	61,000,000
Recurring Basis \| Level 2 \| Corporate and municipal notes	'	'
Assets	'	'
Cash and cash equivalents:	'	18,422,000
Short-term and long-term investments:	362,698,000	640,177,000
Recurring Basis \| Level 3	'	'
Liabilities	'	'
Total liabilities	154,761,000	189,213,000
Recurring Basis \| Level 3 \| Other	'	'
Liabilities	'	'
Contingent consideration	154,761,000	189,213,000
Recurring Basis \| Total Fair Value	'	'
Assets	'	'
Total assets	470,494,000	833,641,000
Liabilities	'	'
Total liabilities	223,322,000	189,213,000
Recurring Basis \| Total Fair Value \| Optimer CVRs	'	'
Liabilities	'	'
Contingent consideration	68,561,000	'
Recurring Basis \| Total Fair Value \| Other	'	'
Liabilities	'	'
Contingent consideration	154,761,000	189,213,000
Recurring Basis \| Total Fair Value \| Money market funds	'	'
Assets	'	'
Cash and cash equivalents:	146,000	'
Recurring Basis \| Total Fair Value \| Bank deposits	'	'
Assets	'	'
Short-term and long-term investments:	40,000,000	61,000,000
Recurring Basis \| Total Fair Value \| U.S. Treasury securities	'	'
Assets	'	'
Short-term and long-term investments:	67,650,000	114,042,000
Recurring Basis \| Total Fair Value \| Corporate and municipal notes	'	'
Assets	'	'
Cash and cash equivalents:	'	18,422,000
Short-term and long-term investments:	$362,698,000	$640,177,000

FAIR_VALUE_MEASUREMENTS_Detail1

FAIR VALUE MEASUREMENTS (Details 2) (USD $)

3 Months Ended

12 Months Ended

3 Months Ended

12 Months Ended

25 Months Ended

12 Months Ended

3 Months Ended

1 Months Ended

12 Months Ended

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

Oct. 24, 2013

Dec. 31, 2013

Sep. 11, 2013

Dec. 31, 2013

Dec. 31, 2011

Dec. 31, 2013

Dec. 31, 2012

Aug. 31, 2013

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

2020 Notes

2018 Notes

2017 Notes

Bevenopran (formerly known as CB-5945)

Optimer Pharmaceuticals, Inc.

Trius Therapeutics, Inc.

Adolor Corporation

Calixa Therapeutics Inc.

Level 2

Contingent Consideration

right

Minimum

Maximum

Weighted Average

AnnualPayment

Minimum

Maximum

Weighted Average

Bevenopran (formerly known as CB-5945)

Minimum

Maximum

Weighted Average

Ceftolozane/tazobactam

2020 Notes

2018 Notes

2017 Notes

Level 3

Contingent Consideration

Number of transferable CVRs received by stockholders of acquiree

Undiscounted contingent consideration, low range

Undiscounted contingent consideration, high range

253,900,000

108,400,000

233,800,000

180,000,000

Payment for contingent consideration

15,746,000

12,592,000

16,791,000

40,000,000

Level 3 Disclosures

Contingent consideration

68,600,000

5,012,000

44,161,000

77,000,000

105,588,000

112,200,000

Probability of success (as a percent)

4.00%

6.50%

5.80%

25.00%

30.00%

27.00%

40.00%

86.00%

65.00%

Discount rate (as a percent)

13.00%

8.00%

5.30%

13.00%

5.30%

Reconciliation of fair value using Level 3 inputs, liabilities

Balance at the beginning of the period

189,213,000

248,234,000

Contingent consideration liability recorded upon acquisition

4,879,000

Contingent consideration (income) expense

-36,200,000

-37,000,000

-32,800,000

669,000

-29,021,000

Milestone payment

-40,000,000

-30,000,000

Balance at the end of the period

154,761,000

189,213,000

Other Fair Value Measurements

Estimated fair value of Convertible Senior Notes

516,800,000

403,500,000

550,300,000

1,470,633,000

699,750,000

516,843,000

403,473,000

550,317,000

699,750,000

Aggregate payments assumed

22,500,000

Amount paid to Glaxo under termination agreement

6,500,000

Number of remaining annual payments under termination agreement

Net carrying amount of the total payable to Glaxo outstanding at the end of the period

16,000,000

Impairment charge recognized

35,300,000

38,700,000

35,300,000

38,700,000

35,300,000

38,700,000

Non-recurring Level 3 fair value measurements of the impairment analysis

IPR&D asset (bevenopran)

$43,400,000

INVENTORY_Details

INVENTORY (Details) (USD $)	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2013	Dec. 31, 2013	Dec. 31, 2013	Dec. 31, 2013
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	DIFICID	DIFICID API	ENTEREG	ENTEREG API
INVENTORY	'	'	'	'	'	'
Raw materials	$17,904	$9,132	'	'	'	'
Work-in-process	8,104	8,485	'	'	'	'
Finished goods	31,655	24,330	'	'	'	'
Inventory	57,663	41,947	'	'	'	'
Included in other assets:	'	'	'	'	'	'
Raw materials	57,284	34,091	'	'	'	'
Work-in-process	1,882	1,733	'	'	'	'
Finished goods	'	1,669	'	'	'	'
Total	$116,829	$79,440	'	'	'	'
INVENTORY	'	'	'	'	'	'
Period in which inventory is expected to be sold	'	'	'1 year	'	'1 year	'
Shelf-life	'	'	'3 years	'3 years	'3 years	'5 years
Period over which the entity expects to consume substantially all of the inventory	'	'	'	'3 years	'	'7 years

PROPERTY_AND_EQUIPMENT_NET_Det

PROPERTY AND EQUIPMENT, NET (Details) (USD $)	12 Months Ended
PROPERTY AND EQUIPMENT, NET (Details) (USD $)	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Property and equipment, net	'	'	'
Property and equipment, gross	$255,501,000	$229,994,000	'
Less: accumulated depreciation	-77,957,000	-63,529,000	'
Property and equipment, net	177,544,000	166,465,000	'
Depreciation expense	14,400,000	12,400,000	9,000,000
Land and buildings	'	'	'
Property and equipment, net	'	'	'
Property and equipment, gross	172,199,000	166,659,000	'
Laboratory equipment	'	'	'
Property and equipment, net	'	'	'
Property and equipment, gross	48,997,000	35,961,000	'
Furniture and fixtures	'	'	'
Property and equipment, net	'	'	'
Property and equipment, gross	4,923,000	3,351,000	'
Computer hardware and software	'	'	'
Property and equipment, net	'	'	'
Property and equipment, gross	28,126,000	20,903,000	'
Construction-in-progress	'	'	'
Property and equipment, net	'	'	'
Property and equipment, gross	$1,256,000	$3,120,000	'

GOODWILL_IPR_AND_D_AND_OTHER_I2

GOODWILL, IPR AND D AND OTHER INTANGIBLE ASSETS, NET (Details) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013
Goodwill	'
Balance at the beginning of the period	$114,130
Goodwill acquired	268,888
Balance at the end of the period	383,018
Accumulated impairment losses	$0

GOODWILL_IPR_AND_D_AND_OTHER_I3

GOODWILL, IPR AND D AND OTHER INTANGIBLE ASSETS, NET (Details 2) (USD $)

12 Months Ended

1 Months Ended

12 Months Ended

1 Months Ended

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Oct. 31, 2013

Sep. 11, 2013

Dec. 31, 2013

Sep. 30, 2013

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

Oct. 31, 2013

Patents

Acquired technology rights

Optimer

Trius

Tedizolid phosphate

Bevenopran (formerly known as CB-5945)

Ceftolozane/tazobactam (formerly known as CXA-201) for HABP and VABP

Ceftolozane/tazobactam (formerly known as CXA-201) for cUTI and cIAI

ENTEREG

DIFICID

Contract intangibles

Trius

Optimer

Other intangible assets, net

Total IPR&D

$896,400,000

$272,700,000

$659,000,000

$43,400,000

$78,700,000

$174,000,000

$20,000,000

IPR&D asset (bevenopran)

43,400,000

Impairment charges recorded

35,300,000

38,700,000

35,300,000

38,700,000

Finite-lived intangible assets

Other intangible assets, gross

791,427,000

194,427,000

2,627,000

788,800,000

191,800,000

Less: accumulated amortization

-2,493,000

-2,431,000

-67,868,000

-39,166,000

Acquired finite-lived other intangible assets

597,000,000

36,000,000

561,000,000

Period of amortization

'9 years

Amortization expense

28,800,000

20,900,000

3,500,000

Estimated aggregate amortization of intangible assets

2014

64,741,000

2015

64,741,000

2016

63,460,000

2017

62,221,000

2018

62,221,000

2019 and thereafter

403,682,000

Total

$721,066,000

$152,830,000

ACCRUED_LIABILITIES_Details

ACCRUED LIABILITIES (Details) (USD $)	Dec. 31, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012
ACCRUED LIABILITIES	'	'
Accrued royalties	$83,591	$72,103
Accrued bonus	24,540	13,971
Accrued Medicaid, Medicare and commercial rebates	18,595	20,565
Accrued clinical trials	44,830	29,143
Accrued benefits and incentive compensation	18,183	8,603
Accrued restructuring	19,753	933
Other accrued costs	35,586	18,315
Accrued liabilities	$245,078	$163,633

DEBT_Details

DEBT (Details) (USD $)

1 Months Ended

12 Months Ended

1 Months Ended

3 Months Ended

12 Months Ended

1 Months Ended

12 Months Ended

1 Months Ended

Sep. 30, 2013

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Sep. 30, 2013

Dec. 31, 2013

Sep. 30, 2013

Dec. 31, 2013

Sep. 30, 2013

Oct. 31, 2010

Sep. 30, 2013

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Oct. 31, 2010

Nov. 30, 2012

Oct. 31, 2012

Jun. 30, 2012

Dec. 31, 2012

Dec. 31, 2013

Oct. 31, 2012

2018 Convertible Senior Notes and 2020 Convertible Senior Notes

2020 Convertible Senior Notes

2018 Convertible Senior Notes

2017 Convertible Senior Notes

2013 Convertible Subordinated Notes

noteseries

Minimum

Maximum

noteseries

Minimum

Maximum

Minimum

Debt

Principal amount outstanding

$1,028,822,000

$450,000,000

$350,000,000

$228,822,000

$450,000,000

Unamortized discount

-210,992,000

-82,189,000

-111,015,000

-65,733,000

-34,244,000

-82,189,000

Net carrying amount

817,830,000

367,811,000

338,985,000

284,267,000

194,578,000

367,811,000

Redemption of remaining convertible subordinated debt

34,500,000

Percentage of convertible debt principal that may be redeemed for cash

100.00%

Aggregate principal amount of notes issued

800,000,000

450,000,000

350,000,000

450,000,000

Number of note series

Net proceeds after debt issuance cost

775,600,000

436,000,000

Conversion rate of common stock

0.0121318

0.0342759

0.0324981

Initial conversion price of shares (in dollars per share)

$82.43

$29.18

$30.77

Average price per share of convertible debt instrument settled in cash (in dollar per share)

$42.14

Repurchase of convertible subordinated debt including accrued interest and transaction fees

102,600,000

Repurchase of convertible subordinated debt

109,218,000

47,200,000

74,700,000

Conversion rate of average repurchase price per $100 of debt

1.3607

Number of days within 30 consecutive trading days in which the closing price of the entity's common stock must exceed the conversion price for the notes to be redeemable

Number of consecutive trading days during which the closing price of the entity's common stock must exceed the conversion price for at least 20 days in order for the notes to be redeemable

'30 days

Convertibility of debt, closing price of stock test, percentage of stock price to conversion price that must be exceeded

130.00%

150.00%

Number of consecutive business days immediately after any five consecutive trading day period during the note measurement period

'5 days

Number of consecutive trading days before five consecutive business days during the note measurement period

'5 days

Conversion ratio, principal amount

1,000

Convertibility of debt, trading price of debt test, percentage of closing price of stock used in calculation

98.00%

Notes stated interest rate percentage

1.88%

1.13%

2.50%

2.25%

Fair value of the remaining aggregate principal amount of the outstanding notes

516,800,000

403,500,000

550,300,000

Issuance costs incurred

24,400,000

Equity component of convertible debt issuance, net of tax and issuance costs

113,053,000

-40,343,000

5,600,000

Debt issuance costs allocated to the liability components

18,800,000

Expected life of debt discount

'7 years

'5 years

'7 years

Carrying value of equity component

70,500,000

42,600,000

33,800,000

66,400,000

Effective interest rate on liability component (as a percent)

6.40%

5.70%

7.00%

If-converted value in excess of the principal amount of debt

311,300,000

Principal amount of the 2017 Notes converted

221,200,000

Common stock issued on conversion of senior notes (in shares)

7,580,923

Transaction or solicitation fees incurred for the conversion of debt to stock

Aggregate loss on conversion

34,600,000

Excess of the fair value of consideration issuable in accordance with the original conversion terms

22,000,000

Difference between the net carrying value and the fair value of the liability component of the principal at the time of each conversion

12,600,000

-4,400,000

Convertible Bond Hedge

Common stock covered under convertible bond hedge (in shares)

9,705,442

Exercise price (in dollars per unit)

$82.43

Purchase of convertible bond hedge

179,390,000

Warrant Transactions

Number of common stock called by warrants (in shares)

9,705,442

Exercise price (in dollars per share)

$96.43

Number of trading days over which warrants are exercisable

'80 days

Amount received on warrants sold

121,675,000

Interest expense incurred

Contractual interest coupon payment

13,370,000

12,667,000

13,707,000

Amortization of discount on debt

20,333,000

17,244,000

18,447,000

8,705,000

Amortization debt issuance costs

3,048,000

1,971,000

1,828,000

936,000

Other interest expense

851,000

1,109,000

Capitalized interest

-2,567,000

Total interest expense

37,602,000

32,991,000

31,415,000

Principal amount

2014

3,500,000

2015

3,500,000

2016

4,500,000

2017

233,322,000

2018

350,000,000

2019 and thereafter

450,000,000

Total payments

1,044,822,000

Less current portion

-3,500,000

Total long-term debt and payable obligations

$1,041,322,000

DEBT_Details_2

DEBT (Details 2) (Senior secured revolving credit facility, USD $)

1 Months Ended

12 Months Ended

In Millions, unless otherwise specified

Nov. 30, 2012

Dec. 31, 2013

Dec. 31, 2012

Sep. 30, 2013

Dec. 31, 2013

Maximum

Base rate

Prime rate

Federal funds rate

One month adjusted Eurodollar rate

Eurodollar rate

Minimum

Maximum

Minimum

Maximum

Credit Facility

Maximum borrowing capacity under credit facility

$150

Term of credit facility

'3 years

Additional borrowing allowed subject to pro forma compliance with financial covenants

150

Outstanding credit facility

Variable rate basis

'Base rate

'prime rate

'Federal funds rate

'One month adjusted Eurodollar rate

'Eurodollar rate

Basis spread on variable rate (as a percent)

1.25%

2.00%

0.50%

1.00%

2.25%

3.00%

Interest period of deposits used as reference

'1 month

EMPLOYEE_STOCK_BENEFIT_PLANS_D

EMPLOYEE STOCK BENEFIT PLANS (Details)	12 Months Ended
EMPLOYEE STOCK BENEFIT PLANS (Details)	Dec. 31, 2013
Employee Stock Purchase Plan	'
Summary of Stock-based Compensation Plans	'
Shares of common stock reserved for grant	1,250,000
Shares of common stock available for grant	131,369
Period of interval for purchase of common stock	'6 months
Percentage of the lower of fair market value of common stock at the beginning or end of the period	85.00%
Maximum percentage of payroll deductions on annual compensation	15.00%
2012 Equity Incentive Plan	'
Summary of Stock-based Compensation Plans	'
Shares of common stock reserved for grant	5,000,000
Shares of common stock available for grant	2,974,464

EMPLOYEE_STOCK_BENEFIT_PLANS_D1

EMPLOYEE STOCK BENEFIT PLANS (Details 2) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Summary of Stock-based Compensation Expense	'	'	'
Total stock-based compensation	$32,357	$25,702	$19,368
Income tax effect	-11,454	-9,510	-7,449
After-tax effect of stock-based compensation expense	20,903	16,192	11,919
Trius Therapeutics, Inc.	'	'	'
Summary of Stock-based Compensation Expense	'	'	'
Total stock-based compensation	22,700	'	'
Optimer	'	'	'
Summary of Stock-based Compensation Expense	'	'	'
Total stock-based compensation	7,200	'	'
Trius and Optimer	'	'	'
Summary of Stock-based Compensation Expense	'	'	'
Total stock-based compensation	29,900	'	'
Cost of product revenues	'	'	'
Summary of Stock-based Compensation Expense	'	'	'
Total stock-based compensation	525	497	264
Research and development	'	'	'
Summary of Stock-based Compensation Expense	'	'	'
Total stock-based compensation	12,249	9,100	6,623
Research and development \| Trius Therapeutics, Inc.	'	'	'
Summary of Stock-based Compensation Expense	'	'	'
Total stock-based compensation	11,000	'	'
Research and development \| Optimer	'	'	'
Summary of Stock-based Compensation Expense	'	'	'
Total stock-based compensation	1,800	'	'
Research and development \| Trius and Optimer	'	'	'
Summary of Stock-based Compensation Expense	'	'	'
Total stock-based compensation	12,800	'	'
Selling, general and administrative	'	'	'
Summary of Stock-based Compensation Expense	'	'	'
Total stock-based compensation	19,583	16,105	12,481
Selling, general and administrative \| Trius Therapeutics, Inc.	'	'	'
Summary of Stock-based Compensation Expense	'	'	'
Total stock-based compensation	11,700	'	'
Selling, general and administrative \| Optimer	'	'	'
Summary of Stock-based Compensation Expense	'	'	'
Total stock-based compensation	5,400	'	'
Selling, general and administrative \| Trius and Optimer	'	'	'
Summary of Stock-based Compensation Expense	'	'	'
Total stock-based compensation	$17,100	'	'

EMPLOYEE_STOCK_BENEFIT_PLANS_D2

EMPLOYEE STOCK BENEFIT PLANS (Details 3) (USD $)	12 Months Ended
EMPLOYEE STOCK BENEFIT PLANS (Details 3) (USD $)	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Weighted-average assumptions used to calculate the fair value of stock-based option award under the Black-Scholes option pricing model	'	'	'
Expected stock price volatility (as a percent)	36.20%	39.60%	41.00%
Risk free interest rate, low end of range (as a percent)	0.70%	0.60%	0.90%
Risk free interest rate, high end of range (as a percent)	1.70%	1.10%	2.40%
Expected life of options	'4 years 6 months	'4 years 7 months 6 days	'4 years 7 months 6 days
Stock options	'	'	'
Number of options	'	'	'
Outstanding as of beginning of the period (in shares)	8,025,194	'	'
Granted (in shares)	1,288,393	'	'
Exercised (in shares)	-1,695,244	'	'
Canceled (in shares)	-140,174	'	'
Outstanding as of end of the period (in shares)	7,478,169	8,025,194	'
Vested and exercisable as of end of the period (in shares)	4,654,759	'	'
Expected to vest at the end of the period (in shares)	2,437,787	'	'
Weighted Average Exercise Price	'	'	'
Outstanding as of beginning of the period (in dollars per share)	27.31	'	'
Granted (in dollars per share)	45.83	'	'
Exercised (in dollars per share)	21.73	'	'
Canceled (in dollars per share)	35.91	'	'
Outstanding as of end of the period (in dollars per share)	31.61	27.31	'
Vested and exercisable as of end of the period (in dollars per share)	25.99	'	'
Expected to vest at the end of the period (in dollars per share)	40.87	'	'
Aggregate Intrinsic Value	'	'	'
Outstanding at the beginning of the period	333,507,000	'	'
Granted	29,688,000	'	'
Exercised	58,051,000	39,100,000	42,200,000
Canceled	4,620,000	'	'
Outstanding at the end of the period	278,661,000	333,507,000	'
Vested and exercisable at the end of the period	199,619,000	'	'
Expected to vest at the end of the period	68,247,000	'	'
Weighted-Average Contractual Life	'	'	'
Outstanding at the end of the period	'6 years 7 months 6 days	'	'
Vested and exercisable at the end of the period	'5 years 7 months 6 days	'	'
Expected to vest at the end of the period	'8 years 4 months 24 days	'	'
Stock options, intrinsic value	'	'	'
Total intrinsic value of options exercised	58,051,000	39,100,000	42,200,000
Details of unrecognized stock-based compensation expense	'	'	'
Total unrecognized compensation cost	30,400,000	'	'
Expected weighted average period for recognition of compensation costs	'1 year 2 months 12 days	'	'
Details of fully vested and exercisable options and expected to vest options	'	'	'
Fair value of shares vested	19,100,000	17,300,000	14,300,000
Weighted average grant-date fair value of options granted during the period (in dollars per share)	14.23	14.37	12.46
Weighted average grant-date fair value of options vested (in dollars per share)	10.2	9.23	8.46
Restricted stock units	'	'	'
Details of unrecognized stock-based compensation expense	'	'	'
Total unrecognized compensation cost	22,700,000	'	'
Expected weighted average period for recognition of compensation costs	'1 year 3 months 18 days	'	'
Number of restricted stock units	'	'	'
Nonvested as of beginning of the period (in shares)	735,939	'	'
Granted (in shares)	457,820	'	'
Vested (in shares)	-278,874	'	'
Canceled (in shares)	-32,613	'	'
Nonvested as of end of the period (in shares)	882,272	'	'
Expected to vest at the end of the period (in shares)	584,061	'	'
Weighted Average Grant Date Fair Value	'	'	'
Nonvested stock as of beginning of the period (in dollars per share)	35.33	'	'
Granted (in dollars per share)	44.75	'	'
Vested (in dollars per share)	32.71	'	'
Canceled (in dollars per share)	37.44	'	'
Nonvested stock as of end of the period (in dollars per share)	40.97	'	'
Expected to vest at the end of the period (in dollars per share)	40.97	'	'
Aggregate Intrinsic Value	'	'	'
Nonvested stock at the beginning of the period	50,684,000	'	'
Granted	31,530,000	'	'
Vested	19,206,000	'	'
Canceled	2,246,000	'	'
Nonvested stock at the end of the period	60,762,000	'	'
Expected to vest at the end of the period	40,224,000	'	'

COMMITMENTS_AND_CONTINGENCIES_1

COMMITMENTS AND CONTINGENCIES (Details) (USD $)	12 Months Ended
In Millions, unless otherwise specified	Dec. 31, 2013
Optimer	'
LEGAL PROCEEDINGS	'
Amount of potentially improper payment to research laboratory identified	$0.30
Hospira, Inc.	'
LEGAL PROCEEDINGS	'
Period for which filing of lawsuit prevents the FDA from approving the ANDA under U.S. law	'30 months
Strides, Inc.	'
LEGAL PROCEEDINGS	'
Period for which filing of lawsuit prevents the FDA from approving the ANDA under U.S. law	'30 months

COMMITMENTS_AND_CONTINGENCIES_2

COMMITMENTS AND CONTINGENCIES (Details 2) (USD $)	12 Months Ended
COMMITMENTS AND CONTINGENCIES (Details 2) (USD $)	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Other commitments	'	'	'
Rent expense	$1,000,000	$700,000	$2,500,000
Future minimum lease payments	'	'	'
2014	2,950,000	'	'
2015	2,623,000	'	'
2016	2,687,000	'	'
2017	2,686,000	'	'
2018	2,352,000	'	'
2019 and thereafter	7,116,000	'	'
Total	20,414,000	'	'
Third-party contract manufacturers	'	'	'
Other commitments	'	'	'
Purchase commitments, time period (in years)	'P5Y	'	'
Purchase commitments	172,900,000	'	'
Clinical trial payment obligations	'	'	'
Other commitments	'	'	'
Purchase commitments, time period (in years)	'P5Y	'	'
Purchase commitments	$8,100,000	'	'

RESTRUCTURING_Details

RESTRUCTURING (Details) (USD $)	12 Months Ended			3 Months Ended	12 Months Ended		3 Months Ended	12 Months Ended			3 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2011	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2013	Dec. 31, 2011
				Adolor Corporation	Employee-Related Severance	Employee-Related Severance	Employee-Related Severance	Lease Restructuring	Lease Restructuring	Lease Restructuring	Lease Restructuring
							Adolor Corporation			Optimer	Adolor Corporation
Activity in the restructuring liability	'	'	'	'	'	'	'	'	'	'	'
Balance at the beginning of the period	$933	$9,279	'	'	$933	$8,089	'	'	$1,190	'	'
Restructuring expense	24,319	'	9,279	9,300	19,824	'	8,100	4,495	'	4,500	1,200
Cash payments made	-1,584	-8,346	'	'	-1,584	-7,156	'	'	-1,190	'	'
Balance at the end of the period	$23,668	$933	$9,279	'	$19,173	$933	'	$4,495	'	'	'

INCOME_TAXES_Details

INCOME TAXES (Details) (USD $)	1 Months Ended	3 Months Ended	12 Months Ended
INCOME TAXES (Details) (USD $)	Sep. 30, 2013	Jun. 30, 2012	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Current income tax expense	'	'	'	'	'
Federal	'	'	$9,163,000	$74,744,000	$55,656,000
State	'	'	4,748,000	3,719,000	7,393,000
Total current income tax expense	'	'	13,911,000	78,463,000	63,049,000
Deferred income tax (benefit) expense	'	'	'	'	'
Federal	'	'	-32,449,000	-15,874,000	10,112,000
State	'	'	-6,535,000	-17,068,000	-1,395,000
Total deferred income tax (benefit) expense	'	'	-38,984,000	-32,942,000	8,717,000
Total current and deferred income tax (benefit) expense	'	'	-25,073,000	45,521,000	71,766,000
Effective Tax Amount	'	'	'	'	'
Federal statutory tax rate applied to (loss) income before taxes	'	'	-15,275,000	69,859,000	36,676,000
Differential arising from:	'	'	'	'	'
State	'	'	-1,161,000	2,247,000	3,899,000
Non-deductible expenses	'	'	1,606,000	1,284,000	1,386,000
Current year federal research credit	'	'	-6,176,000	'	-1,763,000
Prior year federal research credits	'	'	-4,399,000	'	'
Impact of reserve for uncertain tax positions	'	'	-192,000	-10,923,000	'
Domestic manufacturing deduction	'	'	-262,000	-5,820,000	'
Transaction costs	'	'	3,797,000	'	967,000
Loss on extinguishment of 2017 Notes	'	'	8,070,000	'	'
Contingent consideration	'	'	-19,147,000	-12,029,000	29,881,000
Valuation allowance on Adynxx impairment	'	'	7,000,000	'	'
Other	'	'	1,066,000	903,000	720,000
Total current and deferred income tax (benefit) expense	'	'	-25,073,000	45,521,000	71,766,000
Federal statutory tax rate applied to (loss) income before taxes (as a percent)	'	'	35.00%	35.00%	35.00%
Differential arising from:	'	'	'	'	'
State (as a percent)	'	'	2.70%	1.10%	3.70%
Non-deductible expenses (as a percent)	'	'	-3.70%	0.60%	1.30%
Current year federal research credit (as a percent)	'	'	14.20%	'	-1.70%
Prior year federal research credits (as a percent)	'	'	10.10%	'	'
Impact of reserve for uncertain tax positions (as a percent)	'	'	0.40%	-5.50%	'
Domestic manufacturing deduction (as a percent)	'	'	0.60%	-2.90%	'
Transaction costs (as a percent)	'	'	-8.70%	'	1.00%
Loss on extinguishment of 2017 Notes (as a percent)	'	'	-18.50%	'	'
Contingent consideration (as a percent)	'	'	43.90%	-6.00%	28.50%
Valuation allowance on Adynxx impairment (as a percent)	'	'	-16.00%	'	'
Other (as a percent)	'	'	-2.60%	0.50%	0.70%
Total (as a percent)	'	'	57.40%	22.80%	68.50%
Non-deductible losses incurred in connection with the induced conversion of the 2017 Notes	23,100,000	'	'	'	'
Principal amount of the 2017 Notes converted	221,200,000	'	'	'	'
Gross uncertain tax positions amount impacting effective tax rate (in dollars)	'	$11,000,000	'	'	'

INCOME_TAXES_Details_2

INCOME TAXES (Details 2) (USD $)	Dec. 31, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012
Deferred income tax assets:	'	'
NOL carryforwards	$215,155	$50,043
Deferred revenues	12,539	10,141
Research and development costs	17,461	517
Tax credit carryforwards	30,815	9,357
Stock-based compensation	21,136	18,485
Capital loss carryforward	10,472	11,118
Investment impairment	7,341	'
Other	15,721	8,868
Total deferred tax assets	330,640	108,529
Deferred income tax liabilities:	'	'
Prepaid expenses	-2,066	-2,669
Debt discount	-12,220	-29,919
IPR&D	-327,272	-100,104
Other intangible assets	-226,408	-32,880
Inventory	-13,871	-14,539
Depreciation	-9,036	-3,968
Total deferred tax liabilities	-590,873	-184,079
Total deferred tax assets and liabilities	-260,233	-75,550
Valuation allowance	-45,461	-13,341
Net deferred tax liabilities	($305,694)	($88,891)

INCOME_TAXES_Details_3

INCOME TAXES (Details 3) (USD $)	Dec. 31, 2012	Dec. 31, 2013	Dec. 31, 2013	Dec. 31, 2013	Dec. 31, 2013	Dec. 31, 2013	Dec. 31, 2013	Dec. 31, 2013	Dec. 31, 2013	Dec. 31, 2013
		Federal	Federal	Federal	Federal	Foreign	Foreign	State	State	State
			Optimer	Trius	Adolor Corporation		Optimer		Optimer	Trius
Operating loss and tax credit carryforwards	'	'	'	'	'	'	'	'	'	'
NOL carryforwards	'	$551,700,000	$282,600,000	$192,000,000	$166,400,000	$15,800,000	$12,300,000	$318,500,000	$188,500,000	$95,500,000
NOL carryforwards utilized	'	'	11,400,000	17,500,000	66,400,000	'	'	'	'	'
State NOLs attributable to excess tax benefits from the exercise of non-qualified stock options	-88,891,000	'	'	'	'	'	'	2,000,000	'	'
Tax credit carryforwards	'	14,900,000	7,800,000	6,100,000	'	'	'	24,700,000	4,300,000	2,600,000
Tax credit carryforwards which expire between 2014 and 2028	'	'	'	'	'	'	'	16,200,000	'	'
Tax credit carryforwards which do not expire	'	'	'	'	'	'	'	$8,500,000	'	'

INCOME_TAXES_Details_4

INCOME TAXES (Details 4) (USD $)	12 Months Ended
INCOME TAXES (Details 4) (USD $)	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Reconciliation of the Company's changes in uncertain tax positions	'	'	'
Balance at the beginning of the period	$36,115,000	$27,774,000	$8,216,000
Additions based on tax positions related to the current year	2,717,000	769,000	12,844,000
Additions for tax positions of prior years	5,393,000	24,299,000	7,321,000
Subtractions for tax positions of prior years	-1,105,000	-16,727,000	-607,000
Balance at the end of the period	43,120,000	36,115,000	27,774,000
Uncertain tax positions offset against deferred tax assets	26,700,000	'	'
Uncertain tax positions included in other long-term liabilities	16,400,000	'	'
Amount impacting the effective tax rate	40,900,000	'	'
Optimer Pharmaceuticals, Inc.	'	'	'
Uncertain Tax Positions	'	'	'
Increase in uncertain tax positions	3,000,000	'	'
Adolor Corporation	'	'	'
Uncertain Tax Positions	'	'	'
Increase in uncertain tax positions	$1,000,000	'	'

SEGMENT_INFORMATION_Details

SEGMENT INFORMATION (Details)	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
	segment	Dec. 31, 2012	Dec. 31, 2011
SEGMENT INFORMATION	'	'	'
Number of operating segments	1	'	'
Approximate percentage of revenues generated within the U. S.	93.00%	94.00%	94.00%

SELECTED_QUARTERLY_FINANCIAL_D2

SELECTED QUARTERLY FINANCIAL DATA (UNAUDITED) (Details) (USD $)

3 Months Ended

12 Months Ended

3 Months Ended

1 Months Ended

12 Months Ended

3 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, 2011

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Option agreement

Adolor Corporation

Bevenopran

Adynxx

Adolor Corporation

Selected quarterly financial data

Total revenues, net

$299,741,000

$265,993,000

$258,779,000

$229,929,000

$245,919,000

$238,181,000

$230,567,000

$211,692,000

$1,054,442,000

$926,359,000

$753,972,000

$2,600,000

Product revenues, net

295,737,000

256,583,000

254,462,000

225,651,000

241,460,000

230,313,000

221,249,000

206,803,000

Cost of product revenues

80,605,000

60,989,000

63,041,000

55,675,000

61,474,000

55,740,000

58,891,000

53,952,000

260,310,000

230,057,000

172,864,000

Net income (loss)

-6,006,000

-33,895,000

15,242,000

6,088,000

37,837,000

40,321,000

43,123,000

32,794,000

-18,571,000

154,075,000

33,023,000

Basic net income per share (in dollars per share)

($0.08)

($0.50)

$0.23

$0.09

$0.59

$0.63

$0.68

$0.52

($0.27)

$2.42

$0.54

Diluted net income per share (in dollars per share)

($0.08)

($0.50)

$0.23

$0.09

$0.51

$0.55

$0.58

$0.45

($0.27)

$2.10

$0.52

Selected quarterly financial data

Impairment charges recorded

35,300,000

38,700,000

35,300,000

38,700,000

35,300,000

38,700,000

Impairment charge recorded

20,000,000

Contingent consideration income (loss)

$36,200,000

$37,000,000

$32,800,000

Percentage of outstanding shares to be acquired under exercise of option

100.00%

SELECTED_QUARTERLY_FINANCIAL_D3

SELECTED QUARTERLY FINANCIAL DATA (UNAUDITED) (Details 2) (USD $)	1 Months Ended	3 Months Ended	12 Months Ended
In Millions, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2013	Dec. 31, 2013
Selected quarterly financial data	'	'	'
Principal amount of the 2017 Notes converted	$221.20	'	'
2.50% convertible senior notes due November 2017 (2017 Notes)	'	'	'
Selected quarterly financial data	'	'	'
Loss on the induced conversion	'	34.6	34.6
Principal amount of the 2017 Notes converted	$221.20	'	'

SCHEDULE_II_Valuation_and_Qual1

SCHEDULE II Valuation and Qualifying Accounts and Reserves (Details) (USD $)	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Sales Returns & Allowances, Chargebacks, Prompt Pay Discounts, Wholesaler Fees, Commercial Rebates and Medicaid and Medicare Rebates	'	'	'
Additions that resulted from the acquisition of Optimer	$9,300,000	'	'
Medicaid rebates	'	'	'
Sales Returns & Allowances, Chargebacks, Prompt Pay Discounts, Wholesaler Fees, Commercial Rebates and Medicaid and Medicare Rebates	'	'	'
Balance at Beginning of Year	'	'	6,279,000
Additions	'	'	23,796,000
Deductions	'	'	-15,198,000
Balance at End of Year	'	'	14,877,000
Medicaid and Medicare rebates	'	'	'
Sales Returns & Allowances, Chargebacks, Prompt Pay Discounts, Wholesaler Fees, Commercial Rebates and Medicaid and Medicare Rebates	'	'	'
Balance at Beginning of Year	20,565,000	14,877,000	'
Additions	23,558,000	26,874,000	'
Deductions	-27,038,000	-21,186,000	'
Balance at End of Year	17,085,000	20,565,000	'
Chargebacks	'	'	'
Sales Returns & Allowances, Chargebacks, Prompt Pay Discounts, Wholesaler Fees, Commercial Rebates and Medicaid and Medicare Rebates	'	'	'
Balance at Beginning of Year	907,000	638,000	454,000
Additions	62,470,000	46,298,000	32,210,000
Deductions	-61,579,000	-46,029,000	-32,026,000
Balance at End of Year	1,798,000	907,000	638,000
Prompt pay discounts	'	'	'
Sales Returns & Allowances, Chargebacks, Prompt Pay Discounts, Wholesaler Fees, Commercial Rebates and Medicaid and Medicare Rebates	'	'	'
Balance at Beginning of Year	1,560,000	1,444,000	1,270,000
Additions	19,618,000	16,943,000	13,507,000
Deductions	-19,124,000	-16,827,000	-13,333,000
Balance at End of Year	2,054,000	1,560,000	1,444,000
Commercial rebates	'	'	'
Sales Returns & Allowances, Chargebacks, Prompt Pay Discounts, Wholesaler Fees, Commercial Rebates and Medicaid and Medicare Rebates	'	'	'
Additions	1,593,000	'	'
Deductions	-83,000	'	'
Balance at End of Year	1,510,000	'	'
Sales returns and allowances and wholesaler fees	'	'	'
Sales Returns & Allowances, Chargebacks, Prompt Pay Discounts, Wholesaler Fees, Commercial Rebates and Medicaid and Medicare Rebates	'	'	'
Balance at Beginning of Year	6,718,000	6,116,000	4,226,000
Additions	12,979,000	5,990,000	4,804,000
Deductions	-7,575,000	-5,388,000	-2,914,000
Balance at End of Year	12,122,000	6,718,000	6,116,000
Valuation allowance against deferred tax assets	'	'	'
Sales Returns & Allowances, Chargebacks, Prompt Pay Discounts, Wholesaler Fees, Commercial Rebates and Medicaid and Medicare Rebates	'	'	'
Balance at Beginning of Year	13,341,000	13,170,000	13,738,000
Additions	32,812,000	185,000	35,000
Deductions	-692,000	-14,000	-603,000
Balance at End of Year	$45,461,000	$13,341,000	$13,170,000