Cubist Pharmaceuticals (CBST) 10-Q 12 Nov 13 2013 Q3 Quarterly report Financial data

Document_and_Entity_Informatio

Document and Entity Information	9 Months Ended
	Sep. 30, 2013	Oct. 30, 2013
Document and Entity Information	'	'
Entity Registrant Name	'CUBIST PHARMACEUTICALS INC	'
Entity Central Index Key	'0000912183	'
Document Type	'10-Q	'
Document Period End Date	30-Sep-13	'
Amendment Flag	'false	'
Current Fiscal Year End Date	'--12-31	'
Entity Current Reporting Status	'Yes	'
Entity Filer Category	'Large Accelerated Filer	'
Entity Common Stock, Shares Outstanding	'	74,060,500
Document Fiscal Year Focus	'2013	'
Document Fiscal Period Focus	'Q3	'

CONDENSED_CONSOLIDATED_BALANCE

CONDENSED CONSOLIDATED BALANCE SHEETS (USD $)	Sep. 30, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified
Current assets:	'	'
Cash and cash equivalents	$538,504	$104,041
Short-term investments	382,681	872,188
Accounts receivable, net	106,451	93,467
Inventory	55,079	41,947
Deferred tax assets, net	38,383	14,190
Prepaid expenses and other current assets	82,016	31,217
Total current assets	1,203,114	1,157,050
Property and equipment, net	170,122	166,465
In-process research and development	931,700	272,700
Goodwill	273,572	114,130
Other intangible assets, net	137,411	152,830
Long-term investments	76,640	3,167
Other assets	73,673	66,043
Total assets	2,866,232	1,932,385
Current liabilities:	'	'
Accounts payable	36,061	45,603
Accrued liabilities	160,644	163,633
Short-term deferred revenue	7,417	6,784
Short-term contingent consideration	'	38,998
Other current liabilities	3,500	3,500
Total current liabilities	207,622	258,518
Long-term deferred revenue	31,952	34,091
Long-term deferred tax liabilities, net	252,398	103,081
Long-term contingent consideration	161,372	150,215
Long-term debt, net	809,539	367,811
Other long-term liabilities	27,766	27,921
Total liabilities	1,490,649	941,637
Commitments and contingencies (Notes E, J, L and N)	'	'
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; 74,011,707 and 64,713,695 shares issued and outstanding as of September 30, 2013 and December 31, 2012, respectively	74	65
Additional paid-in capital	1,338,259	940,969
Accumulated other comprehensive income (loss)	42	-59
Retained earnings	37,208	49,773
Total stockholders' equity	1,375,583	990,748
Total liabilities and stockholders' equity	$2,866,232	$1,932,385

CONDENSED_CONSOLIDATED_BALANCE1

CONDENSED CONSOLIDATED BALANCE SHEETS (Parenthetical) (USD $)	Sep. 30, 2013	Dec. 31, 2012
CONDENSED 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	74,011,707	64,713,695
Common stock, shares outstanding	74,011,707	64,713,695

CONDENSED_CONSOLIDATED_STATEME

CONDENSED CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME (USD $)	3 Months Ended		9 Months Ended
In Thousands, except Share data, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012
Revenues:	'	'	'	'
U.S. product revenues, net	$243,596	$218,354	$696,347	$622,389
International product revenues	12,987	11,959	40,349	35,976
Service revenues	3,755	7,215	11,044	19,544
Other revenues	5,655	653	6,961	2,531
Total revenues, net	265,993	238,181	754,701	680,440
Costs and expenses:	'	'	'	'
Cost of product revenues	60,989	55,740	179,705	168,583
Research and development	123,423	70,197	352,822	188,575
Contingent consideration	2,641	1,473	7,280	6,996
Selling, general and administrative	74,884	40,420	172,974	124,455
Total costs and expenses	261,937	167,830	712,781	488,609
Operating income	4,056	70,351	41,920	191,831
Other income (expense):	'	'	'	'
Interest income	624	817	2,084	2,233
Interest expense	-8,924	-7,629	-23,358	-25,538
Other expense	-34,871	-3,359	-34,777	-6,652
Total other income (expense), net	-43,171	-10,171	-56,051	-29,957
(Loss) income before income taxes	-39,115	60,180	-14,131	161,874
(Benefit) provision for income taxes	-5,220	19,859	-1,566	45,636
Net (loss) income	-33,895	40,321	-12,565	116,238
Basic net (loss) income per common share (in dollars per share)	($0.50)	$0.63	($0.19)	$1.83
Diluted net (loss) income per common share (in dollars per share)	($0.50)	$0.55	($0.19)	$1.59
Shares used in calculating:	'	'	'	'
Basic net (loss) income per common share (in shares)	67,841,665	64,048,673	66,122,521	63,521,491
Diluted net (loss) income per common share (in shares)	67,841,665	82,856,912	66,122,521	81,251,074
Total comprehensive (loss) income	($33,351)	$40,570	($12,464)	$116,497

CONDENSED_CONSOLIDATED_STATEME1

CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS (USD $)	9 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2012
Cash flows from operating activities:	'	'
Net (loss) income	($12,565)	$116,238
Adjustments to reconcile net (loss) income to net cash (used in) provided by operating activities:	'	'
Loss on extinguishment of convertible debt, including write-off of debt issuance costs	12,592	3,542
Depreciation and amortization	25,866	24,900
Amortization and accretion of investments	8,680	6,584
Amortization of debt discount and debt issuance costs, excluding write-off of debt issuance costs	13,382	14,740
Deferred income taxes	-23,068	-14,012
Stock-based compensation	24,104	19,244
Contingent consideration	7,280	6,996
Payment of contingent consideration	-24,254	-17,408
Premium paid for convertible subordinated debt repurchase	'	-26,945
Loss on disposal of property and equipment	'	3,248
Other non-cash	-7,198	7,806
Changes in assets and liabilities, net of effects from acquisitions:	'	'
Accounts receivable	-12,984	-6,561
Inventory	-13,370	-5,679
Prepaid expenses and other current assets	1,871	384
Other assets	-219	5,754
Accounts payable and accrued liabilities	-29,669	-28,059
Deferred revenue and other liabilities	1,171	2,942
Total adjustments	-15,816	-2,524
Net cash (used in) provided by operating activities	-28,381	113,714
Cash flows from investing activities:	'	'
Acquisition of business, net of acquired cash	-671,729	'
Purchase of non-voting preferred stock	-25,000	'
Purchases of property and equipment	-11,691	-14,279
Purchases of investments	-736,469	-1,170,611
Proceeds from maturities of investments	1,183,443	978,161
Payment for purchase option	-20,000	'
Net cash used in investing activities	-281,446	-206,729
Cash flows from financing activities:	'	'
Payment of contingent consideration	-15,746	-12,592
Issuance of common stock, net	29,621	28,825
Excess tax benefit on stock-based awards	12,861	9,085
Extinguishment of convertible debt	'	-74,704
Proceeds from issuance of convertible debt	800,000	'
Payment of debt issuance costs	-24,731	'
Proceeds from issuance of warrants	121,675	'
Purchase of convertible bond hedge	-179,390	'
Net cash provided by (used in) financing activities	744,290	-49,386
Net increase (decrease) in cash and cash equivalents	434,463	-142,401
Cash and cash equivalents at beginning of period	104,041	197,618
Cash and cash equivalents at end of period	$538,504	$55,217

CONDENSED_CONSOLIDATED_STATEME2

CONDENSED CONSOLIDATED STATEMENT OF CHANGES IN STOCKHOLDERS' EQUITY (USD $)	Total	Common Stock	Additional Paid-in Capital	Accumulated Other Comprehensive Income (Loss)	Retained Earnings
In Thousands, except Share data, unless otherwise specified
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 loss	-12,464	'	'	101	-12,565
Sale of warrants	121,675	'	121,675	'	'
Purchase of convertible bond hedge, net of tax	-113,379	'	-113,379	'	'
Equity component of convertible debt extinguishment, 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	27,404	1	27,403	'	'
Exercise of stock options and vesting of restricted stock units (in shares)	'	1,581,809	'	'	'
Shares issued in connection with employee stock purchase plan and 401(k) plan	5,767	'	5,767	'	'
Shares issued in connection with employee stock purchase plan and 401(k) plan (in shares)	'	135,280	'	'	'
Tax benefit on stock-based awards	12,861	'	12,861	'	'
Stock-based compensation	24,190	'	24,190	'	'
Balance at Sep. 30, 2013	$1,375,583	$74	$1,338,259	$42	$37,208
Balance (in shares) at Sep. 30, 2013	'	74,011,707	'	'	'

BASIS_OF_PRESENTATION_AND_ACCO

BASIS OF PRESENTATION AND ACCOUNTING POLICIES	9 Months Ended
	Sep. 30, 2013
BASIS OF PRESENTATION AND ACCOUNTING POLICIES	'
BASIS OF PRESENTATION AND ACCOUNTING POLICIES	'
	A.   BASIS OF PRESENTATION AND ACCOUNTING POLICIES
	Basis of Presentation and Consolidation
	The accompanying condensed consolidated financial statements are unaudited and have been prepared by Cubist Pharmaceuticals, Inc. (“Cubist” or the “Company”) in accordance with accounting principles generally accepted in the United States of America, or GAAP, and pursuant to the instructions to Form 10-Q and Article 10 of Regulation S-X. The year-end condensed consolidated financial statements were derived from audited financial statements, but certain information and footnote disclosures required by GAAP normally included in the Company’s annual consolidated financial statements have been condensed or omitted. These interim condensed consolidated financial statements should be read in conjunction with the audited consolidated financial statements for the year ended December 31, 2012, which are contained in the Company’s Annual Report on Form 10-K filed with the Securities and Exchange Commission, or SEC, on February 27, 2013. The condensed consolidated financial statements, in the opinion of management, reflect all normal and recurring adjustments necessary for a fair statement of the Company’s financial position and results of operations.
	The accompanying condensed consolidated financial statements include the accounts of the Company 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 acquisition of Trius Therapeutics, Inc., or Trius, on September 11, 2013, were recorded at their fair values as of the date of acquisition. The operating results of Trius have been consolidated with those of Cubist from the date of acquisition. See Note C., “Business Combinations and Acquisitions,” for additional information. The results of operations for the interim periods are not necessarily indicative of the results of operations to be expected for any future period or the entire fiscal year. The accompanying condensed consolidated financial statements do not contemplate the impact of the Company’s acquisition of Optimer Pharmaceuticals, Inc., or Optimer, which was completed on October 24, 2013. See Note O., “Subsequent Events,” for additional information.
	Use of Estimates
	The preparation of financial statements in conformity with GAAP requires the extensive use of estimates and assumptions that affect the reported amounts of assets, liabilities, revenues, 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; accounting for 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 Level 1 and Level 2 or between Level 2 and Level 3. During the three and nine months ended September 30, 2013, there were no transfers between Level 1, Level 2 and Level 3.
	The carrying amounts of Cubist’s cash and cash equivalents, accounts receivable, 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 September 30, 2013 and December 31, 2012, and are carried at fair value.
	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 as of September 30, 2013 and December 31, 2012, primarily represent amounts due to the Company from wholesalers, including AmerisourceBergen Drug Corporation, Cardinal Health, Inc. and McKesson Corporation. Cubist performs ongoing credit evaluations of its key wholesalers, distributors and other customers and generally does not require collateral. For the three and nine months ended September 30, 2013 and 2012, 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
		September 30,		December 31,
		2013		2012
	AmerisourceBergen Drug Corporation	20	%	22	%
	Cardinal Health, Inc.	17	%	18	%
	McKesson Corporation	20	%	20	%
		Percentage of Total				Percentage of Total
		Net Revenues for				Net Revenues for
		the Three Months Ended				the Nine Months Ended
		September 30,				September 30,
		2013		2012		2013		2012
	AmerisourceBergen Drug Corporation	18	%	20	%	19	%	20	%
	Cardinal Health, Inc.	17	%	18	%	17	%	19	%
	McKesson Corporation	18	%	18	%	18	%	18	%
	IPR&D
	IPR&D acquired in a business combination is capitalized on the Company’s condensed 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, 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 acquired IPR&D are expensed as incurred.
	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 fair 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 product candidates, Cubist could incur significant charges in the period in which the impairment occurs. The valuation techniques utilized in performing impairment tests incorporate significant assumptions and judgments to estimate the fair value. The use of different valuation techniques or different assumptions could result in materially different fair value estimates.
	Revenue Recognition
	The Company’s principal sources of revenue during the reporting period were: (i) sales of CUBICIN® (daptomycin for injection) and ENTEREG® (alvimopan) in the United States, or U.S.; (ii) revenues derived from sales of CUBICIN 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) service revenues derived from Cubist’s co-promotion agreement with Optimer for the promotion and support of DIFICID® (fidaxomicin) in the U.S., which was terminated on October 24, 2013, as a result of the completion of Cubist’s acquisition of Optimer. See Note O., “Subsequent Events,” for additional information. 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.
	U.S. Product Revenues, net
	All revenues from product sales are recorded net of applicable provisions for returns, chargebacks, Medicaid program rebates, Medicare coverage gap discount program rebates, wholesaler management fees, volume-based rebates and discounts in the same period the related sales are recorded.
	Gross U.S. product revenues were offset by provisions for the three and nine months ended September 30, 2013 and 2012, as follows:
		Three Months Ended						Nine Months Ended
		September 30,						September 30,
		2013			2012			2013			2012
		(in thousands)
	Gross U.S. product revenues	$	277,999		$	250,881		$	796,217		$	716,906
	Provisions offsetting U.S. product revenues:
	Contractual adjustments	(13,249		)	(13,535		)	(43,281		)	(40,516		)
	Governmental rebates	(21,154		)	(18,992		)	(56,589		)	(54,001		)
	Total provisions offsetting product revenues	(34,403		)	(32,527		)	(99,870		)	(94,517		)
	U.S. product revenues, net	$	243,596		$	218,354		$	696,347		$	622,389
	Certain product sales qualify for rebates or discounts from standard list pricing due to government-sponsored programs or other contractual agreements. Contractual adjustments in the table above include provisions for returns, volume-based rebates, and pricing and early payment discounts extended to the Company’s external customers, as well as wholesaler distribution fees. Governmental rebates in the table above represent estimated amounts for Medicaid program rebates, Medicare coverage gap discount program rebates and chargebacks related to 340B/Public Health Service and Federal Supply Schedule drug pricing programs. Estimates and assumptions for reserves are analyzed quarterly. The Company reversed approximately $6.0 million and $14.1 million of revenue reserves, primarily consisting of Medicaid program rebates as a result of receiving claims information from certain state governments and additional data regarding the usage of CUBICIN by managed care organizations during the three and nine months ended September 30, 2013, respectively.
	Basic and Diluted Net (Loss) Income Per 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 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 J., “Debt,” and Note K., “Employee Stock Benefit Plans,” for additional information.
	The following table sets forth the computation of basic and diluted net (loss) income per common share:
		Three Months Ended						Nine Months Ended
		September 30,						September 30,
		2013			2012			2013			2012
		(in thousands, except share and per share amounts)
	Net (loss) income, basic	$	(33,895	)	$	40,321		$	(12,565	)	$	116,238
	Effect of dilutive securities:
	Interest on 2017 Notes, net of tax	—			1,853			—			5,469
	Debt issuance costs related to 2017 Notes, net of tax	—			245			—			723
	Debt discount amortization related to 2017 Notes, net of tax	—			2,296			—			6,659
Interest on 2013 Notes, net of tax	—			128			—			—
Debt issuance costs related to 2013 Notes, net of tax	—			17			—			—
Debt discount amortization related to 2013 Notes, net of tax	—			316			—			—
Net (loss) income, diluted	$	(33,895	)	$	45,176		$	(12,565	)	$	129,089
Shares used in calculating basic net (loss) income per common share	67,841,665			64,048,673			66,122,521			63,521,491
Effect of dilutive securities:
Options to purchase shares of common stock and RSUs	—			2,262,445			—			2,305,428
2017 Notes convertible into shares of common stock	—			15,424,155			—			15,424,155
2013 Notes convertible into shares of common stock	—			1,121,639			—			—
Shares used in calculating diluted net (loss) income per common share	67,841,665			82,856,912			66,122,521			81,251,074
Net (loss) income per share, basic	$	(0.50	)	$	0.63		$	(0.19	)	$	1.83
Net (loss) income per share, diluted	$	(0.50	)	$	0.55		$	(0.19	)	$	1.59
Potential common shares excluded from the calculation of diluted net (loss) income per share, as their inclusion would have been antidilutive, were:
	Three Months Ended				Nine Months Ended
	September 30,				September 30,
	2013		2012		2013		2012
Options to purchase shares of common stock and RSUs	8,739,777		2,059,361		8,739,777		2,535,235
Warrants	9,705,442		—		9,705,442		—
2020 Notes convertible into shares of common stock	5,459,311		—		5,459,311		—
2018 Notes convertible into shares of common stock	4,246,131		—		4,246,131		—
2017 Notes convertible into shares of common stock	7,842,943		—		7,842,943		—
2013 Notes convertible into shares of common stock	—		—		—		2,521,856
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 did not recognize any 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 three and nine months ended September 30, 2013.
Subsequent Events
Cubist considers events or transactions that have occurred after the balance sheet date of September 30, 2013, but prior to the filing of the financial statements with the SEC on this Form 10-Q to provide additional evidence relative to certain estimates or to identify matters that require additional recognition or disclosure. On October 24, 2013, Cubist completed the acquisition of Optimer. See Note O., “Subsequent Events,” for additional information.
Recent Accounting Pronouncements
In July 2013, the FASB issued an accounting standards update clarifying the presentation of an unrecognized tax benefit when a net operating loss, or 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	9 Months Ended
	Sep. 30, 2013
BUSINESS AGREEMENTS	'
BUSINESS AGREEMENTS	'
	B.    BUSINESS AGREEMENTS
	Licensing and Collaboration Agreements
	Dong-A ST Co., Ltd.
	In connection with the Company’s acquisition of Trius in September 2013, Cubist acquired the rights to tedizolid phosphate. See Note C., “Business Combinations and Acquisitions,” for additional information. Trius licensed tedizolid phosphate from Dong-A ST Co., Ltd., or 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. 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 patent covering tedizolid phosphate in such country. The license agreement terminates upon the expiration of all of the royalty obligations under the agreement. Cubist may terminate the license agreement if Cubist decides to discontinue development or commercialization of licensed products and Dong-A may terminate the license agreement if Cubist fails to meet certain specified development and commercialization obligations within specified time periods.
	Hydra Biosciences, Inc.
	In October 2009, Cubist entered into a collaboration and license agreement with Hydra Biosciences, Inc., or Hydra, under which the Company provided funding for the research and development of potential therapeutics for the management of pain. In June 2013, the Company entered into an agreement to amend and restate the original collaboration and license agreement with Hydra. Pursuant to the terms of the restated agreement, each party granted to the other an exclusive license to research, develop, manufacture and commercialize certain Transient Receptor Potential Ankyrin repeat 1, or TRPA1, inhibitor compounds. Cubist paid Hydra an upfront, non-refundable payment of $15.0 million as consideration for the arrangement, which was recorded within research and development expense in the condensed consolidated statement of comprehensive income for the nine months ended September 30, 2013, as it was not accounted for as a business combination and the asset has no alternative future use. All potential future milestone payments under the original agreement were eliminated, and each party agreed to pay low single-digit royalties to the other party for worldwide net sales of its respectively licensed products. The agreement expires upon the later of: (i) the expiration of the last licensed patent claim covering a licensed TRPA1 inhibitor product in any country; or (ii) the last tenth anniversary of the date of the first commercial sale of any licensed TRPA1 inhibitor product in any country, following the cessation of all research, development, manufacturing and commercialization of licensed products by or on behalf of Cubist and Hydra and their respective affiliates.
	Astellas Pharma Inc.
	In connection with the Company’s acquisition of Calixa Therapeutics Inc., or Calixa, in December 2009, Cubist acquired the rights to ceftolozane (formerly known as CXA-101), which Calixa had licensed from Astellas Pharma Inc., or Astellas. In March 2013, the license agreement with Astellas was amended to expand the territory in which Cubist holds the rights to manufacture, market and sell any eventual products that incorporate ceftolozane, including ceftolozane/tazobactam (formerly known as CXA-201), to include the Asia-Pacific and Middle East territories that Astellas had retained under the original agreement. Effective as of this amendment, Cubist owns 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 in the condensed consolidated statement of comprehensive income for the nine months ended September 30, 2013, as the acquisition of these rights was not accounted for as a business combination and the asset has no alternative future use.
	Bayer Pharma AG
	In connection with the Company’s acquisition of Trius in September 2013, Cubist acquired a 2011 collaboration and license agreement between Trius and Bayer Pharma AG, or Bayer. See Note C., “Business Combinations and Acquisitions,” for additional information. 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, Africa, Latin America and the Middle East, excluding North and South Korea, or the Bayer Licensed Territory. Trius retained full development and commercialization rights outside the Bayer Licensed Territory, including the U.S., Canada and the European Union, but excluding North and South Korea where 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 pneumonia, 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 up to $69.1 million under the agreement upon the achievement of certain development, regulatory, and commercial milestones and will receive double-digit royalties on net sales of tedizolid phosphate in the Bayer Licensed Territory.
	Commercialization and Distribution Agreements
	Optimer Co-Promotion Agreement
	On July 30, 2013, in connection with the Optimer merger agreement, Cubist entered into an amendment to its existing co-promotion agreement with Optimer which was due to expire on July 31, 2013. The amendment extended the term of the existing co-promotion agreement in substantially its current form through the earlier of July 31, 2014, or the completion of the merger, subject to early termination by either party of the Optimer merger agreement. The co-promotion agreement was terminated upon Cubist’s completion of the acquisition of Optimer on October 24, 2013. See Note O., “Subsequent Events,” for additional information.

BUSINESS_COMBINATIONS_AND_ACQU

BUSINESS COMBINATIONS AND ACQUISITIONS	9 Months Ended
	Sep. 30, 2013
BUSINESS COMBINATIONS AND ACQUISITIONS	'
BUSINESS COMBINATIONS AND ACQUISITIONS	'
	C.   BUSINESS COMBINATIONS AND ACQUISITIONS
	On September 11, 2013, Cubist completed its acquisition of Trius, a publicly-held biopharmaceutical company focused on the discovery and development of innovative antibiotics for serious infections. The transaction provides Cubist with an existing late-stage antibiotic candidate, tedizolid phosphate, which is in development for the potential treatment of certain Gram-positive infections.
	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 contingent value right, or CVR, per share, which entitles the holder to receive an additional cash payment of up to $2.00 per CVR for a total maximum undiscounted 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 and is based on significant unobservable inputs. See Note E., “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	$	694,426
	Contingent consideration (CVRs)	4,603
	Total consideration transferred	$	699,029
	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 $24.0 million of 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 September 30, 2013. The total $24.0 million charge was comprised of $12.4 million of research and development expense and $11.6 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 assets 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	159,442
	Other assets acquired	5,522
	Total assets acquired	978,741
	Deferred tax liabilities	(249,353		)
	Other liabilities assumed	(30,359		)
	Total liabilities assumed	(279,712		)
	Total net assets acquired	$	699,029
	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 September 11, 2013, the acquisition date.
	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. The goodwill 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 deferred tax assets of $92.6 million are primarily related to federal NOL carryforwards, capitalized research and development costs and federal research tax credits. See Note L., “Income Taxes,” for additional information. The deferred tax liability of $249.4 million primarily relates to the temporary differences associated with acquired IPR&D, which is not deductible for tax purposes.
	The fair value of the acquired IPR&D asset relates to tedizolid phosphate, a novel antibiotic drug candidate, currently in Phase 3 development for the treatment of serious Gram-positive bacterial infections, including those caused by methicillin-resistant staphylococcus aureus, or MRSA. The fair value was determined using an income approach, including a discount rate of 9.5%, applied to the probability-adjusted after-tax cash flows. The Company believes the assumptions are representative of those a market participant would use in estimating fair value.
	The operating results of Trius for the period from September 12, 2013 to September 30, 2013, including an operating loss of $4.8 million, have been included in the Company’s condensed consolidated financial statements as of and for the three and nine months ended September 30, 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 condensed consolidated statement of comprehensive income for the three and nine months ended September 30, 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:
		Nine Months Ended
		September 30,
		2013			2012
		(in thousands)
	Total revenues, net	$	754,701		$	689,440
	Net (loss) income	(27,912		)	52,214
	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 primarily relating to the following 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 nine months ended September 30, 2013, and inclusion of these transaction costs in the nine months ended September 30, 2012;
	(ii) elimination of $24.0 million of stock-based compensation expense related to the acceleration of vesting of previously unvested Trius awards in connection with the acquisition from the nine months ended September 30, 2013, and inclusion of this charge in the nine months ended September 30, 2012;
	(iii) elimination of $2.1 million of expense related to severance and retention agreements from the nine months ended September 30, 2013, and inclusion of the severance and retention agreements in the nine months ended September 30, 2012;
	(iv) tax effect of the unaudited pro forma consolidated net income and adjustments for the nine months ended September 30, 2013 and 2012; and
	(v) reclassification of certain Trius revenues related to research and development expense reimbursement to research and development expense for the nine months ended September 30, 2013 and 2012, in accordance with Cubist accounting policy.

INVESTMENTS

INVESTMENTS	9 Months Ended
	Sep. 30, 2013
INVESTMENTS	'
INVESTMENTS	'
	D.   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 condensed consolidated balance sheets:
		Amortized		Unrealized		Unrealized			Fair
		Cost		Gains		Losses			Value
		(in thousands)
	Balance as of September 30, 2013
	Bank deposits	$	20,000	$	—	$	—		$	20,000
	U.S. Treasury securities	75,021		18		—			75,039
	Corporate and municipal notes	352,099		86		(55		)	352,130
	Total	$	447,120	$	104	$	(55	)	$	447,169
	Balance as of 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 marketable securities:
		September 30, 2013				December 31, 2012
		Amortized		Fair		Amortized			Fair
		Cost		Value		Cost			Value
		(in thousands)
	Within 1 year	$	370,450	$	370,530	$	812,104		$	812,052
	1-2 years	76,670		76,639		3,171			3,167
	Total	$	447,120	$	447,169	$	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 condensed consolidated balance sheets and are not included in the tables above. In addition, certificates of deposit of $12.2 million and $60.1 million as of September 30, 2013 and December 31, 2012, respectively, were included within short-term investments in the condensed consolidated balance sheets but are excluded from the tables above as they were not deemed to be securities.
	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 is non-refundable except in limited circumstances, and obtained an exclusive option to acquire 100% of the outstanding shares of Adynxx. The option is exercisable any time prior to sixty 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. Adynxx is studying AYX1 as a potential treatment for the reduction of acute pain and prevention of persistent and chronic pain following surgery. If Cubist exercises the option, Cubist would make an additional payment of $40.0 million to acquire Adynxx, net of any cash acquired and liabilities assumed, and would be obligated to make certain additional payments to the stockholders of Adynxx that are contingent upon the achievement of certain development, regulatory and sales milestones.
	The Company has concluded that Adynxx is a variable interest entity, or VIE, in which Cubist is not the primary beneficiary. Cubist does not have power, through its variable interest, to direct the activities that most significantly impact the economic performance of Adynxx. Specifically, Cubist does not have any voting rights or other decision-making authority over Adynxx’s operational or financial activities, and it does not participate on any joint steering or oversight committees of Adynxx. Accordingly, the Company did not consolidate Adynxx as of September 30, 2013. Cubist accounted for the $20.0 million payment, which represents the maximum exposure to any potential losses associated with this VIE, at cost, subject to impairment testing. The $20.0 million was included in prepaid expenses and other current assets within the condensed consolidated balance sheet as of September 30, 2013.
	Optimer Preferred Stock
	In connection with the merger agreement between Cubist and Optimer, Cubist agreed to provide Optimer with $25.0 million per quarter, up to $75.0 million in aggregate funding, to fund Optimer’s operations in the ordinary course of business through the completion of the merger in exchange for non-voting senior preferred stock of Optimer. Accordingly, on September 16, 2013, Cubist and Optimer entered into a Series A Convertible Preferred Stock Purchase Agreement, pursuant to which Optimer issued to Cubist a total of $25.0 million of non-voting senior preferred stock. On October 24, 2013, Cubist completed its acquisition of Optimer. See Note O., “Subsequent Events,” for additional information. The non-voting senior preferred stock owned by Cubist at the completion of the merger was extinguished for no consideration and will be treated as consideration transferred at its fair value under the acquisition method of accounting for business combinations. As of September 30, 2013, the non-voting senior preferred stock was accounted for as a cost method investment and was included in prepaid expenses and other current assets within the condensed consolidated balance sheet.

FAIR_VALUE_MEASUREMENTS

FAIR VALUE MEASUREMENTS	9 Months Ended
	Sep. 30, 2013
FAIR VALUE MEASUREMENTS	'
FAIR VALUE MEASUREMENTS	'
	E.    FAIR VALUE MEASUREMENTS
	The following tables set forth the Company’s assets and liabilities that are measured at fair value on a recurring basis as of September 30, 2013:
		September 30, 2013
		Fair Value Measurements Using
		Level 1			Level 2		Level 3		Total
		(in thousands)
	Assets
	Cash and cash equivalents: (1)
	Money market funds	$	146,595		$	—	$	—	$	146,595
	U.S. Treasury securities	59,999			—		—		59,999
	Corporate and municipal notes	—			170,217		—		170,217
	Short-term and long-term investments: (2)
	Bank deposits	—			20,000		—		20,000
	U.S. Treasury securities	75,039			—		—		75,039
	Corporate and municipal notes	—			352,130		—		352,130
	Total assets	$	281,633		$	542,347	$	—	$	823,980
	Liabilities
	Contingent consideration	$	—		$	—	$	161,372	$	161,372
	Total liabilities	$	—		$	—	$	161,372	$	161,372
	(1)   Excludes $161.7 million of cash as of September 30, 2013.
	(2)   Excludes certificates of deposit of $12.2 million recorded at cost as of September 30, 2013.
	Marketable Securities
	The Company classifies its money market funds and U.S. Treasury securities as a Level 1 input 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 a Level 2 input 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
	In connection with the acquisitions of Trius, Adolor Corporation, or Adolor, and Calixa, Cubist recorded contingent consideration pertaining to the amounts potentially payable to the former stockholders of each company. Contingent consideration is measured at fair value and is based on significant inputs not observable in the market, which represents a Level 3 measurement 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 condensed consolidated statements of comprehensive 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 Level 3 inputs:
		Contingent Consideration
		Trius		Adolor		Calixa
	Fair value as of September 30, 2013 (in thousands)	$4,879		$80,401		$76,092
	Valuation technique	Probability-adjusted discounted cash flow		Probability-adjusted discounted cash flow		Probability-adjusted discounted cash flow
	Unobservable input
	Probabilities of success - range (weighted average)	4% - 7%		29% - 54%		29% - 63%
		-6%		-43%		-48%
	Periods in which milestones are expected to be achieved	2016		2016 - 2020		2014 - 2018
	Discount rate	8.00%		5.3% / 16%		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 the milestones will be achieved would result in a significantly lower or higher fair value measurement, respectively.
	Trius
	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 $4.9 million as of September 30, 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 treatment of serious Gram-positive bacterial infections, including those caused by MRSA.
	Adolor
	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 (formerly known as CB-5945), was estimated to be $80.4 million and $77.0 million as of September 30, 2013 and December 31, 2012, respectively. The change in the fair value of the contingent consideration liability during the three and nine months ended September 30, 2013, is due to the time value of money. The aggregate remaining, 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
	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 $76.1 million and $112.2 million as of September 30, 2013 and December 31, 2012, respectively. The change in fair value for the three and nine months ended September 30, 2013, is primarily due to the $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 ventilator-associated bacterial pneumonia, or VABP and the time value of money. The aggregate remaining, undiscounted amount of contingent consideration that Cubist could pay to the former stockholders of Calixa under the merger agreement is $180.0 million. Ceftolozane/tazobactam is being developed as a potential treatment for complicated urinary tract infections, or cUTI, complicated intra-abdominal infections, or cIAI, hospital-acquired bacterial pneumonia, or HABP, and VABP.
	Changes in the fair value of contingent consideration based upon unobservable inputs that are Level 3 measurements, were as follows:
		Contingent
		Consideration
		(in thousands)
	Beginning balance as of December 31, 2012	$	189,213
	Contingent consideration liability recorded upon acquisition of Trius	4,879
	Contingent consideration expense	7,280
	Contingent consideration milestone payment	(40,000		)
	Ending balance as of September 30, 2013	$	161,372
	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 2020 Notes, 2018 Notes and 2017 Notes were $480.8 million, $379.3 million and $526.2 million, respectively, as of September 30, 2013. See Note J., “Debt,” for additional information.
	Payable to Glaxo
	In connection with the acquisition of Adolor in December 2011, Cubist assumed the obligation to pay Glaxo Group Limited, or Glaxo, six annual payments aggregating to $22.5 million as a result of Adolor’s termination of its collaboration agreement with Glaxo in September 2011. The amount payable to Glaxo was recorded at its estimated fair value at the time of acquisition and is allocated between current and non-current liabilities within the condensed 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. As of September 30, 2013, the carrying value of the remaining annual payments to Glaxo of $14.1 million approximates its fair value. Imputed interest on the amount payable to Glaxo is recorded as interest expense within the condensed consolidated statements of comprehensive income.

INVENTORY

INVENTORY	9 Months Ended
	Sep. 30, 2013
INVENTORY	'
INVENTORY	'
	F.   INVENTORY
	Inventory consisted of the following at:
		September 30,		December 31,
		2013		2012
		(in thousands)
	Raw materials	$	12,957	$	9,132
	Work-in-process	5,657		8,485
	Finished goods	36,465		24,330
	Inventory	55,079		41,947
	Included in other assets:
	Raw materials	30,436		34,091
	Work-in-process	2,702		1,733
	Finished goods	—		1,669
	Total	$	88,217	$	79,440
	Inventory included in other assets within the condensed consolidated balance sheets as of September 30, 2013 and December 31, 2012, represents the amount of ENTEREG inventory held that is in excess of the amount expected to be sold within one year. In connection with the acquisition of Adolor in December 2011, Cubist recorded the acquired ENTEREG inventory at its fair value, which required a step-up adjustment to recognize the inventory at its expected net realizable value.
	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 condensed consolidated statements of comprehensive income in the period in which the inventory is sold. The ENTEREG Active Pharmaceutical Ingredient, or API, which is classified as raw materials, has a shelf-life of 60 months 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	9 Months Ended
	Sep. 30, 2013
PROPERTY AND EQUIPMENT, NET	'
PROPERTY AND EQUIPMENT, NET	'
	G.   PROPERTY AND EQUIPMENT, NET
	Property and equipment, net consisted of the following at:
		September 30,			December 31,
		2013			2012
		(in thousands)
	Land and buildings	$	171,299		$	166,659
	Laboratory equipment	43,042			35,961
	Furniture and fixtures	3,908			3,351
	Computer hardware and software	23,490			20,903
	Construction-in-progress	2,358			3,120
		244,097			229,994
	Less: accumulated depreciation	(73,975		)	(63,529		)
	Property and equipment, net	$	170,122		$	166,465
	Depreciation expense was $3.5 million and $3.1 million for the three months ended September 30, 2013 and 2012, respectively, and $10.4 million and $9.2 million for the nine months ended September 30, 2013 and 2012, respectively.

GOODWILL_IPRANDD_AND_OTHER_INT

GOODWILL IPRANDD AND OTHER INTANGIBLE ASSETS, NET	9 Months Ended
	Sep. 30, 2013
GOODWILL, IPR&D AND OTHER INTANGIBLE ASSETS, NET	'
GOODWILL, IPR&D AND OTHER INTANGIBLE ASSETS, NET	'
	H.   GOODWILL, IPR&D AND OTHER INTANGIBLE ASSETS, NET
	Goodwill
	The Company’s goodwill balance as of September 30, 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		159,442
	Ending balance as of September 30, 2013		$	273,572
	Goodwill of $159.4 million was recognized in connection with the acquisition of Trius in September 2013. See Note C., “Business Combinations and Acquisitions,” for additional information. As of September 30, 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 M., “Segment Information,” for additional information.
	IPR&D
	The carrying value of the Company’s IPR&D assets consisted of the following at:
			September 30,			December 31,
			2013			2012
			(in thousands)
	Development and potential commercialization of:
	Tedizolid phosphate		$	659,000		$	—
	Bevenopran		78,700			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		$	931,700		$	272,700
	IPR&D of $659.0 million was recognized in connection with the acquisition of Trius in September 2013. See Note C., “Business Combinations and Acquisitions,” for additional information.
	Other Intangible Assets
	Other intangible assets, net consisted of the following at:
				September 30,			December 31,
				2013			2012
				(in thousands)
	Patents			$	2,627		$	2,627
	Acquired technology rights			191,800			191,800
				194,427			194,427
	Less:	accumulated amortization — patents		(2,477		)	(2,431		)
		accumulated amortization — acquired technology rights		(54,539		)	(39,166		)
	Other intangible assets, net			$	137,411		$	152,830
	Amortization expense was $5.2 million for each of the three months ended September 30, 2013 and 2012, and $15.4 million and $15.7 million for the nine months ended September 30, 2013 and 2012, respectively.
	The estimated aggregate amortization of intangible assets as of September 30, 2013, for each of the five succeeding years and thereafter is as follows:
			(in thousands)
	Remainder of 2013		$	5,182
	2014		20,729
	2015		20,729
	2016		19,449
	2017		18,210
	2018 and thereafter		53,112
	Total		$	137,411

ACCRUED_LIABILITIES

ACCRUED LIABILITIES	9 Months Ended
	Sep. 30, 2013
ACCRUED LIABILITIES	'
ACCRUED LIABILITIES	'
	I.   ACCRUED LIABILITIES
	Accrued liabilities consisted of the following at:
		September 30,		December 31,
		2013		2012
		(in thousands)
	Accrued royalties	$	42,700	$	72,103
	Accrued clinical trials	39,921		29,143
	Accrued Medicaid and Medicare rebates	14,707		20,565
	Accrued bonus	18,141		13,971
	Accrued benefits and incentive compensation	14,359		8,603
	Other accrued costs	30,816		19,248
	Accrued liabilities	$	160,644	$	163,633

DEBT

DEBT	9 Months Ended
	Sep. 30, 2013
DEBT	'
DEBT	'
	J.   DEBT
	Convertible Senior Notes
	Long-term debt, net is comprised of the Company’s Convertible Senior Notes, as follows:
		September 30,			December 31,
		2013			2012
		(in thousands)
	2020 Convertible Senior Notes
	Principal amount outstanding	$	450,000		$	—
	Unamortized discount	(114,323		)	—
	Net carrying amount	335,677			—
	2018 Convertible Senior Notes
	Principal amount outstanding	350,000			—
	Unamortized discount	(68,784		)	—
	Net carrying amount	281,216			—
	2017 Convertible Senior Notes
	Principal amount outstanding	228,822			450,000
	Unamortized discount	(36,176		)	(82,189		)
	Net carrying amount	192,646			367,811
	Total Convertible Senior Notes
	Principal amount outstanding	1,028,822			450,000
	Unamortized discount	(219,283		)	(82,189		)
	Net carrying amount	$	809,539		$	367,811
	In accordance with accounting guidance for debt with conversion and other options, Cubist accounted for 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 1st and September 1st of each year, beginning on March 1, 2014. As of September 30, 2013, the “if-converted value” did not exceed the principal amount of the 2018 Notes and 2020 Notes.
	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 discount 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 September 30, 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 September 30, 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 the 2017 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 1st and November 1st of each year. As of September 30, 2013, the “if-converted value” exceeded the remaining principal amount of the 2017 Notes by $269.6 million.
	The Company determined the expected life of the debt discount for the 2017 Notes to be equal to the original seven-year term of each of the 2017 Notes, resulting in an amortization period ending November 1, 2017. For the nine months ended September 30, 2013, 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 three months ended September 30, 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 condensed consolidated statement of comprehensive 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 hedge transaction 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. 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.
	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, as administrative agent. On September 3, 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 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. As a result, 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. The credit facility, which includes a sublimit for letters of credit, will be used for general corporate purposes. There were no outstanding borrowings under the credit facility as of September 30, 2013 or December 31, 2012.

EMPLOYEE_STOCK_BENEFIT_PLANS

EMPLOYEE STOCK BENEFIT PLANS	9 Months Ended
	Sep. 30, 2013
EMPLOYEE STOCK BENEFIT PLANS	'
EMPLOYEE STOCK BENEFIT PLANS	'
	K.   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, restricted stock, 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. As of September 30, 2013, there were 2,989,993 shares remaining available for grant under the 2012 EIP.
	Summary of Stock-Based Compensation Expense
	Stock-based compensation expense recorded in the condensed consolidated statements of comprehensive income for the three and nine months ended September 30, 2013 and 2012, is as follows:
		Three Months Ended						Nine Months Ended
		September 30,						September 30,
		2013			2012			2013			2012
		(in thousands)
	Stock-based compensation expense allocation:
	Cost of product revenues	$	120		$	133		$	374		$	305
	Research and development	2,816			2,371			8,583			6,724
	Selling, general and administrative	5,029			4,248			15,147			12,215
	Total stock-based compensation	7,965			6,752			24,104			19,244
	Income tax effect	(2,993		)	(2,302		)	(9,058		)	(6,770		)
	After-tax effect of stock-based compensation expense	$	4,972		$	4,450		$	15,046		$	12,474
	Stock-based compensation expense for the three and nine months ended September 30, 2013, presented above, excludes $24.0 million of postcombination stock-based compensation expense resulting from the cash settlement of nonvested equity awards of Trius. The total was comprised of $12.4 million of research and development expense and $11.6 million of selling, general and administrative expense. See Note C., “Business Combinations and Acquisitions,” for additional information.
	General Option Information
	A summary of option activity for the nine months ended September 30, 2013, is as follows:
		Number of			Weighted
		shares			Average
					Exercise Price
	Outstanding as of December 31, 2012	8,025,194			$	27.31
	Granted	1,252,843			$	45.32
	Exercised	(1,310,085		)	$	20.92
	Canceled	(112,413		)	$	36.24
	Outstanding as of September 30, 2013	7,855,539			$	31.12
	Vested and exercisable as of September 30, 2013	4,685,736			$	25.1
	Weighted average grant-date fair value of options granted during the period	$	14.15
	RSU Information
	A summary of RSU activity, including PRSUs, for the nine months ended September 30, 2013, is as follows:
		Number of		Weighted
		Shares		Average Grant
				Date Fair Value
	Nonvested as of December 31, 2012	735,939		$	35.33
	Granted	443,745		$	44.15
	Vested	(271,724	)	$	32.35
	Forfeited	(23,722	)	$	37.75
	Nonvested as of September 30, 2013	884,238		$	40.61

INCOME_TAXES

INCOME TAXES	9 Months Ended
	Sep. 30, 2013
INCOME TAXES	'
INCOME TAXES	'
	L.   INCOME TAXES
	The following table reconciles the federal statutory tax rate to the effective tax rates for the three and nine months ended September 30, 2013 and 2012:
		Three Months Ended				Nine Months Ended
		September 30,				September 30,
		2013		2012		2013		2012
	Federal statutory tax rate applied to income before taxes	35	%	35	%	35	%	35	%
	Differential arising from:
	State	2.4	%	0.6	%	3.4	%	1.3	%
	Non-deductible expenses	(5.2	)%	0.5	%	(17.3	)%	0.6	%
	Domestic manufacturing deduction	1.5	%	(2.4	)%	9.8	%	(2.7	)%
	Contingent consideration	(4.7	)%	(0.4	)%	(15.8	)%	0.7	%
	2013 Federal research credit	16.3	%	—	%	54.5	%	—	%
	Prior year federal research credits	0.9	%	—	%	31.1	%	—	%
	Transaction costs	(7.0	)%	—	%	(19.4	)%	—	%
	Non-deductible loss on extinguishment of 2017 Notes	(24.4	)%	—	%	(67.5	)%	—	%
	Impact of reserve for uncertain tax positions	(0.1	)%	0.1	%	2.6	%	(6.7	)%
	Other	(1.4	)%	(0.4	)%	(5.3	)%	—	%
	Total	13.3	%	33	%	11.1	%	28.2	%
	As a result of the Company’s expected full year pre-tax loss for 2013, permanent items effecting the tax rate that reduce taxable income or reduce taxes payable are shown as an increase in the rate, as they increase the overall tax benefit for the three and nine months ended September 30, 2013. Permanent items that increase taxable income or increase the tax liability reduce the rate of tax benefit and are shown as negative items for the three and nine months ended September 30, 2013. For the three and nine months ended September 30, 2012, during which the Company was expecting full year pre-tax income and an overall tax provision, items that decrease the tax rate are shown as negative items, while items that increase the tax rate are shown as positive items.
	The decrease in the effective tax rate for the three and nine months ended September 30, 2013, as compared to the three and nine months ended September 30, 2012, is primarily due to the significant permanent book-to-tax differences in relation to the expected full year pre-tax loss for 2013. These permanent differences include non-deductible losses incurred in connection with the induced conversion of $221.2 million of the principal amount of the 2017 Notes in September 2013, and non-deductible transaction costs associated with the acquisitions of Trius and Optimer. The impact of these non-deductible expenses was partially offset by the benefit of the 2013 federal research credit as well as prior year research credits, including the 2012 federal research credit, which was retroactively extended to January 1, 2012 by the American Taxpayer Relief Act of 2012, enacted on January 2, 2013. The effective tax rate for the nine months ended September 30, 2012 also included the impact of the resolution of uncertain state tax positions in the second quarter of 2012, which resulted in an income tax benefit.
	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. 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.
	The Company acquired $192.8 million of federal NOLs in connection with the acquisition of Trius. These NOLs are subject to limitation under Internal Revenue Code, Section 382, which limits the amount of NOLs and credit carryforwards that may be utilized following an ownership change. The Company estimates that it will be able to utilize approximately $192.0 million of Trius NOLs in the future.
	The Company’s total uncertain tax positions were $38.8 million and $36.1 million as of September 30, 2013 and December 31, 2012, respectively. Of the total uncertain tax positions as of September 30, 2013, $15.9 million were included in other long-term liabilities within the condensed consolidated balance sheet and $22.9 million were offset against deferred tax assets.

SEGMENT_INFORMATION

SEGMENT INFORMATION	9 Months Ended
	Sep. 30, 2013
SEGMENT INFORMATION	'
SEGMENT INFORMATION	'
	M.   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 both the three months ended September 30, 2013 and 2012, the Company generated approximately 95% of revenues within the U.S. For both the nine months ended September 30, 2013 and 2012, the Company generated approximately 94% of revenues, within the U.S. As of September 30, 2013 and December 31, 2012, substantially all of the Company’s long-lived assets were held within the U.S.

LEGAL_PROCEEDINGS

LEGAL PROCEEDINGS	9 Months Ended
	Sep. 30, 2013
LEGAL PROCEEDINGS	'
LEGAL PROCEEDINGS	'
	N.   LEGAL PROCEEDINGS
	CUBICIN Patent Infringement Litigation
	In February 2012, the Company received a Paragraph IV Certification Notice Letter from Hospira, Inc., or Hospira, notifying Cubist that it had submitted an Abbreviated New Drug Application, or ANDA, to the U.S. Food and Drug Administration, or 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 a New Drug Application, or 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 and 8,129,342. Each of these patents is listed in the FDA’s list of “Approved Drug Products with Therapeutic Equivalence Evaluations” (commonly referred to as 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 court has scheduled the trial in these related actions to begin 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, Inc., on behalf of Agila Specialties Private Limited, collectively 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 October 2013, Cubist filed patent infringement lawsuits against Strides in response to its ANDA filing. The complaints, which were filed in the U.S. District Court for the District of Delaware and the U.S. District Court for the District of New Jersey, respectively allege infringement of U.S. Patent Nos. 6,468,967; 6,852,689; 8,058,238; and 8,129,342. The complaints seek: (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 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.
	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 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, or the DOJ, 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 us 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. 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. 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. These risks and uncertainties are discussed in more detail in Item 1A of Part II in this Quarterly Report on Form 10-Q under the heading “Risk Factors.”

SUBSEQUENT_EVENTS

SUBSEQUENT EVENTS	9 Months Ended
	Sep. 30, 2013
SUBSEQUENT EVENTS	'
SUBSEQUENT EVENTS	'
	O.   SUBSEQUENT EVENTS
	Acquisition of Optimer Pharmaceuticals
	On October 24, 2013, Cubist completed its acquisition of Optimer, a publicly-held biopharmaceutical company focused on commercializing innovative hospital specialty products, for cash consideration of $550.5 million, or $10.75 per share, plus one transferable CVR for each outstanding share of Optimer’s common stock, which entitles the holder to receive a cash payment of up to $5.00 per CVR upon achievement of certain sales milestones for a total maximum undiscounted potential CVR payout of $253.9 million. As a result of Cubist acquiring 100% of the outstanding shares of Optimer, Optimer became a wholly-owned subsidiary of Cubist. This transaction will be accounted for under the acquisition method of accounting for business combinations. All of the assets and liabilities of Optimer will be recorded at their respective fair values as of the acquisition date and consolidated with those of Cubist. Transaction costs will be expensed as incurred.
	Given the timing of the closing of the acquisition, the purchase accounting is incomplete at this time. As such, it is not practicable for the Company to disclose: (i) the allocation of purchase price to assets acquired and liabilities assumed; (ii) certain disclosures related to contingent consideration; and (iii) pro forma revenues and earnings of the combined entity. This information will be included in the Company’s 2013 Annual Report on Form 10-K to be filed with SEC.
	During the nine months ended September 30, 2013, the Company expensed $3.9 million of transaction costs in connection with Cubist’s acquisition of Optimer, which are included in selling, general and administrative expenses in the condensed consolidated statement of comprehensive income.

BASIS_OF_PRESENTATION_AND_ACCO1

BASIS OF PRESENTATION AND ACCOUNTING POLICIES (Policies)	9 Months Ended
	Sep. 30, 2013
BASIS OF PRESENTATION AND ACCOUNTING POLICIES	'
Basis of Presentation and Consolidation	'
	Basis of Presentation and Consolidation
	The accompanying condensed consolidated financial statements are unaudited and have been prepared by Cubist Pharmaceuticals, Inc. (“Cubist” or the “Company”) in accordance with accounting principles generally accepted in the United States of America, or GAAP, and pursuant to the instructions to Form 10-Q and Article 10 of Regulation S-X. The year-end condensed consolidated financial statements were derived from audited financial statements, but certain information and footnote disclosures required by GAAP normally included in the Company’s annual consolidated financial statements have been condensed or omitted. These interim condensed consolidated financial statements should be read in conjunction with the audited consolidated financial statements for the year ended December 31, 2012, which are contained in the Company’s Annual Report on Form 10-K filed with the Securities and Exchange Commission, or SEC, on February 27, 2013. The condensed consolidated financial statements, in the opinion of management, reflect all normal and recurring adjustments necessary for a fair statement of the Company’s financial position and results of operations.
	The accompanying condensed consolidated financial statements include the accounts of the Company 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 acquisition of Trius Therapeutics, Inc., or Trius, on September 11, 2013, were recorded at their fair values as of the date of acquisition. The operating results of Trius have been consolidated with those of Cubist from the date of acquisition. See Note C., “Business Combinations and Acquisitions,” for additional information. The results of operations for the interim periods are not necessarily indicative of the results of operations to be expected for any future period or the entire fiscal year. The accompanying condensed consolidated financial statements do not contemplate the impact of the Company’s acquisition of Optimer Pharmaceuticals, Inc., or Optimer, which was completed on October 24, 2013. See Note O., “Subsequent Events,” for additional information.
Use of Estimates	'
	Use of Estimates
	The preparation of financial statements in conformity with GAAP requires the extensive use of estimates and assumptions that affect the reported amounts of assets, liabilities, revenues, 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; accounting for 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 Level 1 and Level 2 or between Level 2 and Level 3. During the three and nine months ended September 30, 2013, there were no transfers between Level 1, Level 2 and Level 3.
	The carrying amounts of Cubist’s cash and cash equivalents, accounts receivable, 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 September 30, 2013 and December 31, 2012, and are carried at fair value.
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 as of September 30, 2013 and December 31, 2012, primarily represent amounts due to the Company from wholesalers, including AmerisourceBergen Drug Corporation, Cardinal Health, Inc. and McKesson Corporation. Cubist performs ongoing credit evaluations of its key wholesalers, distributors and other customers and generally does not require collateral. For the three and nine months ended September 30, 2013 and 2012, 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
		September 30,		December 31,
		2013		2012
	AmerisourceBergen Drug Corporation	20	%	22	%
	Cardinal Health, Inc.	17	%	18	%
	McKesson Corporation	20	%	20	%
		Percentage of Total				Percentage of Total
		Net Revenues for				Net Revenues for
		the Three Months Ended				the Nine Months Ended
		September 30,				September 30,
		2013		2012		2013		2012
	AmerisourceBergen Drug Corporation	18	%	20	%	19	%	20	%
	Cardinal Health, Inc.	17	%	18	%	17	%	19	%
	McKesson Corporation	18	%	18	%	18	%	18	%
IPR&D	'
	IPR&D
	IPR&D acquired in a business combination is capitalized on the Company’s condensed 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, 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 acquired IPR&D are expensed as incurred.
	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 fair 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 product candidates, Cubist could incur significant charges in the period in which the impairment occurs. The valuation techniques utilized in performing impairment tests incorporate significant assumptions and judgments to estimate the fair value. The use of different valuation techniques or different assumptions could result in materially different fair value estimates.
Revenue Recognition	'
	Revenue Recognition
	The Company’s principal sources of revenue during the reporting period were: (i) sales of CUBICIN® (daptomycin for injection) and ENTEREG® (alvimopan) in the United States, or U.S.; (ii) revenues derived from sales of CUBICIN 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) service revenues derived from Cubist’s co-promotion agreement with Optimer for the promotion and support of DIFICID® (fidaxomicin) in the U.S., which was terminated on October 24, 2013, as a result of the completion of Cubist’s acquisition of Optimer. See Note O., “Subsequent Events,” for additional information. 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.
	U.S. Product Revenues, net
	All revenues from product sales are recorded net of applicable provisions for returns, chargebacks, Medicaid program rebates, Medicare coverage gap discount program rebates, wholesaler management fees, volume-based rebates and discounts in the same period the related sales are recorded.
	Gross U.S. product revenues were offset by provisions for the three and nine months ended September 30, 2013 and 2012, as follows:
		Three Months Ended						Nine Months Ended
		September 30,						September 30,
		2013			2012			2013			2012
		(in thousands)
	Gross U.S. product revenues	$	277,999		$	250,881		$	796,217		$	716,906
	Provisions offsetting U.S. product revenues:
	Contractual adjustments	(13,249		)	(13,535		)	(43,281		)	(40,516		)
	Governmental rebates	(21,154		)	(18,992		)	(56,589		)	(54,001		)
	Total provisions offsetting product revenues	(34,403		)	(32,527		)	(99,870		)	(94,517		)
	U.S. product revenues, net	$	243,596		$	218,354		$	696,347		$	622,389
	Certain product sales qualify for rebates or discounts from standard list pricing due to government-sponsored programs or other contractual agreements. Contractual adjustments in the table above include provisions for returns, volume-based rebates, and pricing and early payment discounts extended to the Company’s external customers, as well as wholesaler distribution fees. Governmental rebates in the table above represent estimated amounts for Medicaid program rebates, Medicare coverage gap discount program rebates and chargebacks related to 340B/Public Health Service and Federal Supply Schedule drug pricing programs. Estimates and assumptions for reserves are analyzed quarterly. The Company reversed approximately $6.0 million and $14.1 million of revenue reserves, primarily consisting of Medicaid program rebates as a result of receiving claims information from certain state governments and additional data regarding the usage of CUBICIN by managed care organizations during the three and nine months ended September 30, 2013, respectively.
Basic and Diluted Net (Loss) Income Per Share	'
	Basic and Diluted Net (Loss) Income Per 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 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 J., “Debt,” and Note K., “Employee Stock Benefit Plans,” for additional information.
	The following table sets forth the computation of basic and diluted net (loss) income per common share:
		Three Months Ended						Nine Months Ended
		September 30,						September 30,
		2013			2012			2013			2012
		(in thousands, except share and per share amounts)
	Net (loss) income, basic	$	(33,895	)	$	40,321		$	(12,565	)	$	116,238
	Effect of dilutive securities:
	Interest on 2017 Notes, net of tax	—			1,853			—			5,469
	Debt issuance costs related to 2017 Notes, net of tax	—			245			—			723
	Debt discount amortization related to 2017 Notes, net of tax	—			2,296			—			6,659
	Interest on 2013 Notes, net of tax	—			128			—			—
	Debt issuance costs related to 2013 Notes, net of tax	—			17			—			—
	Debt discount amortization related to 2013 Notes, net of tax	—			316			—			—
	Net (loss) income, diluted	$	(33,895	)	$	45,176		$	(12,565	)	$	129,089
	Shares used in calculating basic net (loss) income per common share	67,841,665			64,048,673			66,122,521			63,521,491
	Effect of dilutive securities:
	Options to purchase shares of common stock and RSUs	—			2,262,445			—			2,305,428
	2017 Notes convertible into shares of common stock	—			15,424,155			—			15,424,155
	2013 Notes convertible into shares of common stock	—			1,121,639			—			—
	Shares used in calculating diluted net (loss) income per common share	67,841,665			82,856,912			66,122,521			81,251,074
	Net (loss) income per share, basic	$	(0.50	)	$	0.63		$	(0.19	)	$	1.83
	Net (loss) income per share, diluted	$	(0.50	)	$	0.55		$	(0.19	)	$	1.59
	Potential common shares excluded from the calculation of diluted net (loss) income per share, as their inclusion would have been antidilutive, were:
		Three Months Ended				Nine Months Ended
		September 30,				September 30,
		2013		2012		2013		2012
	Options to purchase shares of common stock and RSUs	8,739,777		2,059,361		8,739,777		2,535,235
	Warrants	9,705,442		—		9,705,442		—
	2020 Notes convertible into shares of common stock	5,459,311		—		5,459,311		—
	2018 Notes convertible into shares of common stock	4,246,131		—		4,246,131		—
	2017 Notes convertible into shares of common stock	7,842,943		—		7,842,943		—
	2013 Notes convertible into shares of common stock	—		—		—		2,521,856
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 did not recognize any 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 three and nine months ended September 30, 2013.
Subsequent Events	'
	Subsequent Events
	Cubist considers events or transactions that have occurred after the balance sheet date of September 30, 2013, but prior to the filing of the financial statements with the SEC on this Form 10-Q to provide additional evidence relative to certain estimates or to identify matters that require additional recognition or disclosure. On October 24, 2013, Cubist completed the acquisition of Optimer. See Note O., “Subsequent Events,” for additional information.
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 a net operating loss, or 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.

BASIS_OF_PRESENTATION_AND_ACCO2

BASIS OF PRESENTATION AND ACCOUNTING POLICIES (Tables)	9 Months Ended
	Sep. 30, 2013
BASIS OF PRESENTATION AND ACCOUNTING POLICIES	'
Concentration of risk	'
		Percentage of Total Accounts
		Receivable Balance as of
		September 30,		December 31,
		2013		2012
	AmerisourceBergen Drug Corporation	20	%	22	%
	Cardinal Health, Inc.	17	%	18	%
	McKesson Corporation	20	%	20	%
		Percentage of Total				Percentage of Total
		Net Revenues for				Net Revenues for
		the Three Months Ended				the Nine Months Ended
		September 30,				September 30,
		2013		2012		2013		2012
	AmerisourceBergen Drug Corporation	18	%	20	%	19	%	20	%
	Cardinal Health, Inc.	17	%	18	%	17	%	19	%
	McKesson Corporation	18	%	18	%	18	%	18	%
Schedule of gross U.S. product revenues offset by provisions	'
		Three Months Ended						Nine Months Ended
		September 30,						September 30,
		2013			2012			2013			2012
		(in thousands)
	Gross U.S. product revenues	$	277,999		$	250,881		$	796,217		$	716,906
	Provisions offsetting U.S. product revenues:
	Contractual adjustments	(13,249		)	(13,535		)	(43,281		)	(40,516		)
	Governmental rebates	(21,154		)	(18,992		)	(56,589		)	(54,001		)
	Total provisions offsetting product revenues	(34,403		)	(32,527		)	(99,870		)	(94,517		)
	U.S. product revenues, net	$	243,596		$	218,354		$	696,347		$	622,389
Summary of basic and diluted net (loss) income per common share	'
		Three Months Ended						Nine Months Ended
		September 30,						September 30,
		2013			2012			2013			2012
		(in thousands, except share and per share amounts)
	Net (loss) income, basic	$	(33,895	)	$	40,321		$	(12,565	)	$	116,238
	Effect of dilutive securities:
	Interest on 2017 Notes, net of tax	—			1,853			—			5,469
	Debt issuance costs related to 2017 Notes, net of tax	—			245			—			723
	Debt discount amortization related to 2017 Notes, net of tax	—			2,296			—			6,659
	Interest on 2013 Notes, net of tax	—			128			—			—
	Debt issuance costs related to 2013 Notes, net of tax	—			17			—			—
	Debt discount amortization related to 2013 Notes, net of tax	—			316			—			—
	Net (loss) income, diluted	$	(33,895	)	$	45,176		$	(12,565	)	$	129,089
	Shares used in calculating basic net (loss) income per common share	67,841,665			64,048,673			66,122,521			63,521,491
	Effect of dilutive securities:
	Options to purchase shares of common stock and RSUs	—			2,262,445			—			2,305,428
	2017 Notes convertible into shares of common stock	—			15,424,155			—			15,424,155
	2013 Notes convertible into shares of common stock	—			1,121,639			—			—
	Shares used in calculating diluted net (loss) income per common share	67,841,665			82,856,912			66,122,521			81,251,074
	Net (loss) income per share, basic	$	(0.50	)	$	0.63		$	(0.19	)	$	1.83
	Net (loss) income per share, diluted	$	(0.50	)	$	0.55		$	(0.19	)	$	1.59
Potential common shares excluded from calculation of diluted net (loss) income per share, as their inclusion would have been antidilutive	'
		Three Months Ended				Nine Months Ended
		September 30,				September 30,
		2013		2012		2013		2012
	Options to purchase shares of common stock and RSUs	8,739,777		2,059,361		8,739,777		2,535,235
	Warrants	9,705,442		—		9,705,442		—
	2020 Notes convertible into shares of common stock	5,459,311		—		5,459,311		—
	2018 Notes convertible into shares of common stock	4,246,131		—		4,246,131		—
	2017 Notes convertible into shares of common stock	7,842,943		—		7,842,943		—
	2013 Notes convertible into shares of common stock	—		—		—		2,521,856

BUSINESS_COMBINATIONS_AND_ACQU1

BUSINESS COMBINATIONS AND ACQUISITIONS (Tables)	9 Months Ended
	Sep. 30, 2013
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	$	694,426
	Contingent consideration (CVRs)	4,603
	Total consideration transferred	$	699,029
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	159,442
	Other assets acquired	5,522
	Total assets acquired	978,741
	Deferred tax liabilities	(249,353		)
	Other liabilities assumed	(30,359		)
	Total liabilities assumed	(279,712		)
	Total net assets acquired	$	699,029
Schedule of supplemental unaudited pro forma information	'
		Nine Months Ended
		September 30,
		2013			2012
		(in thousands)
	Total revenues, net	$	754,701		$	689,440
	Net (loss) income	(27,912		)	52,214

INVESTMENTS_Tables

INVESTMENTS (Tables)	9 Months Ended
	Sep. 30, 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 as of September 30, 2013
	Bank deposits	$	20,000	$	—	$	—		$	20,000
	U.S. Treasury securities	75,021		18		—			75,039
	Corporate and municipal notes	352,099		86		(55		)	352,130
	Total	$	447,120	$	104	$	(55	)	$	447,169
	Balance as of 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 marketable securities	'
		September 30, 2013				December 31, 2012
		Amortized		Fair		Amortized			Fair
		Cost		Value		Cost			Value
		(in thousands)
	Within 1 year	$	370,450	$	370,530	$	812,104		$	812,052
	1-2 years	76,670		76,639		3,171			3,167
	Total	$	447,120	$	447,169	$	815,275		$	815,219

FAIR_VALUE_MEASUREMENTS_Tables

FAIR VALUE MEASUREMENTS (Tables)	9 Months Ended
	Sep. 30, 2013
FAIR VALUE MEASUREMENTS	'
Assets and liabilities measured at fair value on a recurring basis	'
		September 30, 2013
		Fair Value Measurements Using
		Level 1			Level 2		Level 3		Total
		(in thousands)
	Assets
	Cash and cash equivalents: (1)
	Money market funds	$	146,595		$	—	$	—	$	146,595
	U.S. Treasury securities	59,999			—		—		59,999
	Corporate and municipal notes	—			170,217		—		170,217
	Short-term and long-term investments: (2)
	Bank deposits	—			20,000		—		20,000
	U.S. Treasury securities	75,039			—		—		75,039
	Corporate and municipal notes	—			352,130		—		352,130
	Total assets	$	281,633		$	542,347	$	—	$	823,980
	Liabilities
	Contingent consideration	$	—		$	—	$	161,372	$	161,372
	Total liabilities	$	—		$	—	$	161,372	$	161,372
	(1)   Excludes $161.7 million of cash as of September 30, 2013.
	(2)   Excludes certificates of deposit of $12.2 million recorded at cost as of September 30, 2013.
Quantitative information associated with fair value measurement of the Company's contingent consideration Level 3 inputs	'
		Contingent Consideration
		Trius		Adolor		Calixa
	Fair value as of September 30, 2013 (in thousands)	$4,879		$80,401		$76,092
	Valuation technique	Probability-adjusted discounted cash flow		Probability-adjusted discounted cash flow		Probability-adjusted discounted cash flow
	Unobservable input
	Probabilities of success - range (weighted average)	4% - 7%		29% - 54%		29% - 63%
		-6%		-43%		-48%
	Periods in which milestones are expected to be achieved	2016		2016 - 2020		2014 - 2018
	Discount rate	8.00%		5.3% / 16%		5.30%
Roll-forward of fair values of contingent consideration that are Level 3 measurements	'
		Contingent
		Consideration
		(in thousands)
	Beginning balance as of December 31, 2012	$	189,213
	Contingent consideration liability recorded upon acquisition of Trius	4,879
	Contingent consideration expense	7,280
	Contingent consideration milestone payment	(40,000		)
	Ending balance as of September 30, 2013	$	161,372

INVENTORY_Tables

INVENTORY (Tables)	9 Months Ended
	Sep. 30, 2013
INVENTORY	'
Schedule of inventory	'
		September 30,		December 31,
		2013		2012
		(in thousands)
	Raw materials	$	12,957	$	9,132
	Work-in-process	5,657		8,485
	Finished goods	36,465		24,330
	Inventory	55,079		41,947
	Included in other assets:
	Raw materials	30,436		34,091
	Work-in-process	2,702		1,733
	Finished goods	—		1,669
	Total	$	88,217	$	79,440

PROPERTY_AND_EQUIPMENT_NET_Tab

PROPERTY AND EQUIPMENT, NET (Tables)	9 Months Ended
	Sep. 30, 2013
PROPERTY AND EQUIPMENT, NET	'
Schedule of property and equipment, net	'
		September 30,			December 31,
		2013			2012
		(in thousands)
	Land and buildings	$	171,299		$	166,659
	Laboratory equipment	43,042			35,961
	Furniture and fixtures	3,908			3,351
	Computer hardware and software	23,490			20,903
	Construction-in-progress	2,358			3,120
		244,097			229,994
	Less: accumulated depreciation	(73,975		)	(63,529		)
	Property and equipment, net	$	170,122		$	166,465

GOODWILL_IPRANDD_AND_OTHER_INT1

GOODWILL IPRANDD AND OTHER INTANGIBLE ASSETS, NET (Tables)	9 Months Ended
	Sep. 30, 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		159,442
	Ending balance as of September 30, 2013		$	273,572
Schedule of carrying value of the Company's IPR&D assets	'
			September 30,			December 31,
			2013			2012
			(in thousands)
	Development and potential commercialization of:
	Tedizolid phosphate		$	659,000		$	—
	Bevenopran		78,700			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		$	931,700		$	272,700
Schedule of other intangible assets, net	'
				September 30,			December 31,
				2013			2012
				(in thousands)
	Patents			$	2,627		$	2,627
	Acquired technology rights			191,800			191,800
				194,427			194,427
	Less:	accumulated amortization — patents		(2,477		)	(2,431		)
		accumulated amortization — acquired technology rights		(54,539		)	(39,166		)
	Other intangible assets, net			$	137,411		$	152,830
Schedule of estimated aggregate amortization of intangible assets	'
			(in thousands)
	Remainder of 2013		$	5,182
	2014		20,729
	2015		20,729
	2016		19,449
	2017		18,210
	2018 and thereafter		53,112
	Total		$	137,411

ACCRUED_LIABILITIES_Tables

ACCRUED LIABILITIES (Tables)	9 Months Ended
	Sep. 30, 2013
ACCRUED LIABILITIES	'
Schedule of accrued liabilities	'
		September 30,		December 31,
		2013		2012
		(in thousands)
	Accrued royalties	$	42,700	$	72,103
	Accrued clinical trials	39,921		29,143
	Accrued Medicaid and Medicare rebates	14,707		20,565
	Accrued bonus	18,141		13,971
	Accrued benefits and incentive compensation	14,359		8,603
	Other accrued costs	30,816		19,248
	Accrued liabilities	$	160,644	$	163,633

DEBT_Tables

DEBT (Tables)	9 Months Ended
	Sep. 30, 2013
DEBT	'
Schedule of components of the Company's Convertible Senior Notes	'
		September 30,			December 31,
		2013			2012
		(in thousands)
	2020 Convertible Senior Notes
	Principal amount outstanding	$	450,000		$	—
	Unamortized discount	(114,323		)	—
	Net carrying amount	335,677			—
	2018 Convertible Senior Notes
	Principal amount outstanding	350,000			—
	Unamortized discount	(68,784		)	—
	Net carrying amount	281,216			—
	2017 Convertible Senior Notes
	Principal amount outstanding	228,822			450,000
	Unamortized discount	(36,176		)	(82,189		)
	Net carrying amount	192,646			367,811
	Total Convertible Senior Notes
	Principal amount outstanding	1,028,822			450,000
	Unamortized discount	(219,283		)	(82,189		)
	Net carrying amount	$	809,539		$	367,811

EMPLOYEE_STOCK_BENEFIT_PLANS_T

EMPLOYEE STOCK BENEFIT PLANS (Tables)	9 Months Ended
	Sep. 30, 2013
EMPLOYEE STOCK BENEFIT PLANS	'
Schedule of stock-based compensation expense	'
		Three Months Ended						Nine Months Ended
		September 30,						September 30,
		2013			2012			2013			2012
		(in thousands)
	Stock-based compensation expense allocation:
	Cost of product revenues	$	120		$	133		$	374		$	305
	Research and development	2,816			2,371			8,583			6,724
	Selling, general and administrative	5,029			4,248			15,147			12,215
	Total stock-based compensation	7,965			6,752			24,104			19,244
	Income tax effect	(2,993		)	(2,302		)	(9,058		)	(6,770		)
	After-tax effect of stock-based compensation expense	$	4,972		$	4,450		$	15,046		$	12,474
Schedule of stock option activity	'
		Number of			Weighted
		shares			Average
					Exercise Price
	Outstanding as of December 31, 2012	8,025,194			$	27.31
	Granted	1,252,843			$	45.32
	Exercised	(1,310,085		)	$	20.92
	Canceled	(112,413		)	$	36.24
	Outstanding as of September 30, 2013	7,855,539			$	31.12
	Vested and exercisable as of September 30, 2013	4,685,736			$	25.1
	Weighted average grant-date fair value of options granted during the period	$	14.15
Schedule of RSU activity, including PRSUs	'
		Number of		Weighted
		Shares		Average Grant
				Date Fair Value
	Nonvested as of December 31, 2012	735,939		$	35.33
	Granted	443,745		$	44.15
	Vested	(271,724	)	$	32.35
	Forfeited	(23,722	)	$	37.75
	Nonvested as of September 30, 2013	884,238		$	40.61

INCOME_TAXES_Tables

INCOME TAXES (Tables)	9 Months Ended
	Sep. 30, 2013
INCOME TAXES	'
Schedule of the reconciliation of the federal statutory tax rate to the effective tax rates	'
		Three Months Ended				Nine Months Ended
		September 30,				September 30,
		2013		2012		2013		2012
	Federal statutory tax rate applied to income before taxes	35	%	35	%	35	%	35	%
	Differential arising from:
	State	2.4	%	0.6	%	3.4	%	1.3	%
	Non-deductible expenses	(5.2	)%	0.5	%	(17.3	)%	0.6	%
	Domestic manufacturing deduction	1.5	%	(2.4	)%	9.8	%	(2.7	)%
	Contingent consideration	(4.7	)%	(0.4	)%	(15.8	)%	0.7	%
	2013 Federal research credit	16.3	%	—	%	54.5	%	—	%
	Prior year federal research credits	0.9	%	—	%	31.1	%	—	%
	Transaction costs	(7.0	)%	—	%	(19.4	)%	—	%
	Non-deductible loss on extinguishment of 2017 Notes	(24.4	)%	—	%	(67.5	)%	—	%
	Impact of reserve for uncertain tax positions	(0.1	)%	0.1	%	2.6	%	(6.7	)%
	Other	(1.4	)%	(0.4	)%	(5.3	)%	—	%
	Total	13.3	%	33	%	11.1	%	28.2	%

BASIS_OF_PRESENTATION_AND_ACCO3

BASIS OF PRESENTATION AND ACCOUNTING POLICIES (Details) (USD $)

Sep. 30, 2013

Sep. 30, 2013

Dec. 31, 2012

Sep. 30, 2013

Dec. 31, 2012

Sep. 30, 2013

Dec. 31, 2012

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Accounts receivable

Accounts receivable

Accounts receivable

Accounts receivable

Accounts receivable

Accounts receivable

Revenues

Revenues

Revenues

Revenues

Revenues

Revenues

Revenues

Revenues

Revenues

Revenues

Revenues

Revenues

AmerisourceBergen Drug Corporation

AmerisourceBergen Drug Corporation

Cardinal Health, Inc.

Cardinal Health, Inc.

McKesson Corporation

McKesson Corporation

AmerisourceBergen Drug Corporation

AmerisourceBergen Drug Corporation

AmerisourceBergen Drug Corporation

AmerisourceBergen Drug Corporation

Cardinal Health, Inc.

Cardinal Health, Inc.

Cardinal Health, Inc.

Cardinal Health, Inc.

McKesson Corporation

McKesson Corporation

McKesson Corporation

McKesson Corporation

Concentration of risk

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'

Benchmark percentage Concentration of risk

'

20.00%

22.00%

17.00%

18.00%

20.00%

20.00%

18.00%

20.00%

19.00%

20.00%

17.00%

18.00%

17.00%

19.00%

18.00%

18.00%

18.00%

18.00%

Fair Value Measurements

'

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Assets transferred out of Level 1 to Level 2

$0

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'

'

Assets transferred out of Level 2 to Level 1

0

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'

'

Liabilities transferred out of Level 1 to Level 2

0

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'

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'

'

'

Liabilities transferred out of Level 2 to Level 1

0

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'

'

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'

'

'

Assets transferred out of Level 2 to Level 3

0

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'

'

Assets transferred out of Level 3 to Level 2

0

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'

Liabilities transferred out of Level 2 to Level 3

0

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'

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'

Liabilities transferred out of Level 3 to Level 2

$0

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'

'

BASIS_OF_PRESENTATION_AND_ACCO4

BASIS OF PRESENTATION AND ACCOUNTING POLICIES (Details 2) (USD $)	3 Months Ended		9 Months Ended
	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012
Gross U.S. product revenues offset by provisions	'	'	'	'
Gross U.S. product revenues	$277,999,000	$250,881,000	$796,217,000	$716,906,000
Provisions offsetting U.S. product revenues:	'	'	'	'
Contractual adjustments	-13,249,000	-13,535,000	-43,281,000	-40,516,000
Governmental rebates	-21,154,000	-18,992,000	-56,589,000	-54,001,000
Total provisions offsetting product revenues	-34,403,000	-32,527,000	-99,870,000	-94,517,000
U.S. product revenues, net	243,596,000	218,354,000	696,347,000	622,389,000
Reduction in provision for revenue reserves	$6,000,000	'	$14,100,000	'

BASIS_OF_PRESENTATION_AND_ACCO5

BASIS OF PRESENTATION AND ACCOUNTING POLICIES (Details 3) (USD $)	3 Months Ended		9 Months Ended
In Thousands, except Share data, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012
Basic and diluted net (loss) income per share	'	'	'	'
Net (loss) income, basic	($33,895)	$40,321	($12,565)	$116,238
Effect of dilutive securities:	'	'	'	'
Net (loss) income, diluted	-33,895	45,176	-12,565	129,089
Reconciliation of basic and diluted shares	'	'	'	'
Shares used in calculating basic net (loss) income per common share	67,841,665	64,048,673	66,122,521	63,521,491
Options to purchase shares of common stock and RSUs (in shares)	'	2,262,445	'	2,305,428
Shares used in calculating diluted net (loss) income per common share	67,841,665	82,856,912	66,122,521	81,251,074
Net (loss) income per share, basic (in dollars per share)	($0.50)	$0.63	($0.19)	$1.83
Net (loss) income per share, diluted (in dollars per share)	($0.50)	$0.55	($0.19)	$1.59
2.25% Convertible subordinated notes due June 2013 (2013 Notes)	'	'	'	'
Computation of basic and diluted net income (loss) per common share	'	'	'	'
Notes stated interest rate percentage	2.25%	'	2.25%	'
Effect of dilutive securities:	'	'	'	'
Interest on convertible notes, net of tax	'	128	'	'
Debt issuance costs, net of tax	'	17	'	'
Debt discount amortization, net of tax	'	316	'	'
Reconciliation of basic and diluted shares	'	'	'	'
Notes convertible into common stock (in shares)	'	1,121,639	'	'
2.50% convertible senior notes due November 2017 (2017 Notes)	'	'	'	'
Computation of basic and diluted net income (loss) per common share	'	'	'	'
Notes stated interest rate percentage	2.50%	'	2.50%	'
Effect of dilutive securities:	'	'	'	'
Interest on convertible notes, net of tax	'	1,853	'	5,469
Debt issuance costs, net of tax	'	245	'	723
Debt discount amortization, net of tax	'	$2,296	'	$6,659
Reconciliation of basic and diluted shares	'	'	'	'
Notes convertible into common stock (in shares)	'	15,424,155	'	15,424,155
1.125% convertible senior notes due 2018 (2018 Notes)	'	'	'	'
Computation of basic and diluted net income (loss) 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 income (loss) per common share	'	'	'	'
Notes stated interest rate percentage	1.88%	'	1.88%	'

BASIS_OF_PRESENTATION_AND_ACCO6

BASIS OF PRESENTATION AND ACCOUNTING POLICIES (Details 4)	3 Months Ended		9 Months Ended
	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012
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)	8,739,777	2,059,361	8,739,777	2,535,235
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	'	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	'	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	'	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	'	7,842,943	'
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)	'	'	'	2,521,856

BUSINESS_AGREEMENTS_Details

BUSINESS AGREEMENTS (Details) (USD $)	1 Months Ended
In Millions, unless otherwise specified	Sep. 30, 2013	Jun. 30, 2013	Mar. 31, 2013	Sep. 30, 2013	Sep. 30, 2013
	Dong-A ST Co., Ltd.	Amended and restated collaboration and license agreement with Hydra Biosciences, Inc.	Astellas Pharma Inc.	Bayer Pharma AG	Bayer Pharma AG
	License Agreements		License Agreements	Agreement for exclusive rights to commercialize tedizolid phosphate	Bayer
	Trius			Trius	Agreement for exclusive rights to commercialize tedizolid phosphate
					Trius
Licensing and Collaboration Agreements	'	'	'	'	'
Remaining milestone payments	$11.50	'	'	'	'
Minimum period after the date of the first commercial sale over which royalties on annual net worldwide sales would be paid	'12 years	'	'	'	'
Upfront, non-refundable payment	'	15	'	'	'
Payment for license agreement	'	'	25	'	'
Payments made 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 development, regulatory, and commercial milestones	'	'	'	$69.10	'

BUSINESS_COMBINATIONS_AND_ACQU2

BUSINESS COMBINATIONS AND ACQUISITIONS (Details) (USD $)

3 Months Ended

9 Months Ended

3 Months Ended

9 Months Ended

3 Months Ended

9 Months Ended

1 Months Ended

3 Months Ended

9 Months Ended

0 Months Ended

1 Months Ended

3 Months Ended

9 Months Ended

1 Months Ended

3 Months Ended

9 Months Ended

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Dec. 31, 2012

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2012

Sep. 11, 2013

Sep. 11, 2013

Sep. 30, 2013

Sep. 30, 2013

Sep. 11, 2013

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2013

Tedizolid phosphate

Research and development expense

Research and development expense

Research and development expense

Research and development expense

Selling, general and administrative expense

Selling, general and administrative expense

Selling, general and administrative expense

Selling, general and administrative expense

Trius Therapeutics, Inc.

Trius Therapeutics, Inc.

Trius Therapeutics, Inc.

Trius Therapeutics, Inc.

Trius Therapeutics, Inc.

Trius Therapeutics, Inc.

Trius Therapeutics, Inc.

Trius Therapeutics, Inc.

Trius Therapeutics, Inc.

Trius Therapeutics, Inc.

Trius Therapeutics, Inc.

Trius Therapeutics, Inc.

Trius Therapeutics, Inc.

Trius Therapeutics, Inc.

Trius Therapeutics, Inc.

right

Tedizolid phosphate

Minimum

Maximum

Maximum

Research and development expense

Research and development expense

Research and development expense

Selling, general and administrative expense

Selling, general and administrative expense

Selling, general and administrative expense

BUSINESS COMBINATIONS AND ACQUISITIONS

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Percentage of issued and outstanding shares purchased

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100.00%

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

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$13.50

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Number of contingent value rights receivable by stockholders of acquiree

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1

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

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$2

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Total Acquisition-Date Fair Value

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Cash transferred, including transaction costs

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$694,426,000

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Contingent consideration (CVRs)

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4,603,000

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Total consideration transferred

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'

'

'

'

'

'

'

699,029,000

'

'

'

'

'

'

'

'

'

'

Transaction costs paid on behalf of acquiree

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

13,700,000

'

'

'

'

'

'

'

'

'

'

Charges for stock-based compensation

7,965,000

6,752,000

24,104,000

19,244,000

'

'

2,816,000

2,371,000

8,583,000

6,724,000

5,029,000

4,248,000

15,147,000

12,215,000

24,000,000

24,000,000

24,000,000

'

'

'

'

'

'

12,400,000

12,400,000

12,400,000

11,600,000

11,600,000

11,600,000

Undiscounted contingent consideration

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

0

108,400,000

'

'

'

'

'

'

'

Estimated fair values of the assets acquired and liabilities assumed

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Cash

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

22,697,000

'

'

'

'

'

'

'

'

'

'

Investments

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

39,513,000

'

'

'

'

'

'

'

'

'

'

IPR&D

931,700,000

'

931,700,000

'

272,700,000

659,000,000

'

'

'

'

'

'

'

'

'

'

'

'

659,000,000

'

'

'

'

'

'

'

'

'

'

Deferred tax assets

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

92,567,000

'

'

'

'

'

'

'

'

'

'

Goodwill

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

159,442,000

'

'

'

'

'

'

'

'

'

'

Other assets acquired

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

5,522,000

'

'

'

'

'

'

'

'

'

'

Total assets acquired

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

978,741,000

'

'

'

'

'

'

'

'

'

'

Deferred tax liabilities

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

-249,353,000

'

'

'

'

'

'

'

'

'

'

Other liabilities assumed

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

-30,359,000

'

'

'

'

'

'

'

'

'

'

Total liabilities assumed

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

-279,712,000

'

'

'

'

'

'

'

'

'

'

Total net assets acquired

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

699,029,000

'

'

'

'

'

'

'

'

'

'

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

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

8.00%

'

'

9.50%

'

'

'

'

'

'

'

'

'

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

'

'

'

'

'

'

'

'

'

'

'

'

'

'

4,800,000

4,800,000

4,800,000

'

'

'

'

'

'

'

'

'

'

'

'

Transaction costs

'

'

'

'

'

'

'

'

'

'

'

'

'

'

10,200,000

10,200,000

10,200,000

'

'

'

'

'

'

'

'

'

'

'

'

Supplemental unaudited pro forma information

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Total revenues, net

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

754,701,000

689,440,000

'

'

'

'

'

'

'

'

'

'

'

Net (loss) income

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

($27,912,000)

$52,214,000

'

'

'

'

'

'

'

'

'

'

'

BUSINESS_COMBINATIONS_AND_ACQU3

BUSINESS COMBINATIONS AND ACQUISITIONS (Details 2) (USD $)	3 Months Ended		9 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012
Non-recurring adjustments to pro forma information	'	'	'	'
Net income	($33,895)	$40,321	($12,565)	$116,238
Transaction costs	'	'	'	'
Non-recurring adjustments to pro forma information	'	'	'	'
Net income	'	'	-24,900	24,900
Compensation expense related to severance and retention agreements	'	'	'	'
Non-recurring adjustments to pro forma information	'	'	'	'
Net income	'	'	-2,100	2,100
Trius Therapeutics, Inc. | Transaction costs	'	'	'	'
Non-recurring adjustments to pro forma information	'	'	'	'
Net income	'	'	-24,900	24,900
Trius Therapeutics, Inc. | Stock-based compensation expense related to the acceleration of vesting of previously unvested awards	'	'	'	'
Non-recurring adjustments to pro forma information	'	'	'	'
Net income	'	'	($24,000)	$24,000

INVESTMENTS_Details

INVESTMENTS (Details) (USD $)	Sep. 30, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified
Available-for-sale investments	'	'
Amortized Cost	$447,120	$815,275
Unrealized Gains	104	162
Unrealized Losses	-55	-218
Fair Value	447,169	815,219
Bank deposits	'	'
Available-for-sale investments	'	'
Amortized Cost	20,000	61,000
Fair Value	20,000	61,000
U.S. Treasury securities	'	'
Available-for-sale investments	'	'
Amortized Cost	75,021	114,041
Unrealized Gains	18	4
Unrealized Losses	'	-3
Fair Value	75,039	114,042
Corporate and municipal notes	'	'
Available-for-sale investments	'	'
Amortized Cost	352,099	640,234
Unrealized Gains	86	158
Unrealized Losses	-55	-215
Fair Value	$352,130	$640,177

INVESTMENTS_Details_2

INVESTMENTS (Details 2) (USD $)	9 Months Ended				1 Months Ended
	Sep. 30, 2013	Dec. 31, 2012	Sep. 30, 2013	Sep. 16, 2013	Feb. 28, 2013	Sep. 30, 2013	Sep. 30, 2013	Dec. 31, 2012
			Optimer Pharmaceuticals, Inc.	Option agreement	Option agreement	Option agreement	Excluded portion	Excluded portion
				Non-voting senior preferred stock	Adynxx	Adynxx
Amortized Cost	'	'	'	'	'	'	'	'
Within 1 year, Amortized Cost	$370,450,000	$812,104,000	'	'	'	'	'	'
1-2 years, Amortized Cost	76,670,000	3,171,000	'	'	'	'	'	'
Amortized Cost	447,120,000	815,275,000	'	'	'	'	'	'
Fair Value	'	'	'	'	'	'	'	'
Within 1 year, Fair Value	370,530,000	812,052,000	'	'	'	'	'	'
1-2 years, Fair Value	76,639,000	3,167,000	'	'	'	'	'	'
Fair Value	447,169,000	815,219,000	'	'	'	'	'	'
Certificates of deposit	'	'	'	'	'	'	12,200,000	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 is exercisable	'	'	'	'	'60 days	'	'	'
Additional payment to be made on exercise of option	'	'	'	'	40,000,000	'	'	'
Amount of payment which represents the maximum exposure to any potential losses associated with this VIE, at cost, subject to impairment testing	'	'	'	'	'	20,000,000	'	'
Carrying value of the investments included in prepaid expenses and other current assets	'	'	'	25,000,000	'	20,000,000	'	'
Amount agreed to be provided to acquiree per quarter to fund their operations in exchange for non-voting senior preferred stock	'	'	25,000,000	'	'	'	'	'
Maximum amount agreed to be provided to acquiree to fund their operations in exchange for non-voting senior preferred stock	'	'	$75,000,000	'	'	'	'	'

FAIR_VALUE_MEASUREMENTS_Detail

FAIR VALUE MEASUREMENTS (Details) (USD $)	Sep. 30, 2013	Dec. 31, 2012
Excluded portion	'	'
Assets	'	'
Cash	$161,700,000	'
Certificate of deposit excluded and recorded at cost	12,200,000	60,100,000
Recurring Basis | Level 1	'	'
Assets	'	'
Total assets	281,633,000	'
Recurring Basis | Level 1 | Money market funds	'	'
Assets	'	'
Cash and cash equivalents:	146,595,000	'
Recurring Basis | Level 1 | U.S. Treasury securities	'	'
Assets	'	'
Cash and cash equivalents:	59,999,000	'
Short-term and long-term investments:	75,039,000	'
Recurring Basis | Level 2	'	'
Assets	'	'
Total assets	542,347,000	'
Recurring Basis | Level 2 | Bank deposits	'	'
Assets	'	'
Short-term and long-term investments:	20,000,000	'
Recurring Basis | Level 2 | Corporate and municipal notes	'	'
Assets	'	'
Cash and cash equivalents:	170,217,000	'
Short-term and long-term investments:	352,130,000	'
Recurring Basis | Level 3	'	'
Liabilities	'	'
Contingent consideration	161,372,000	'
Total liabilities	161,372,000	'
Recurring Basis | Total Fair Value	'	'
Assets	'	'
Total assets	823,980,000	'
Liabilities	'	'
Contingent consideration	161,372,000	'
Total liabilities	161,372,000	'
Recurring Basis | Total Fair Value | Money market funds	'	'
Assets	'	'
Cash and cash equivalents:	146,595,000	'
Recurring Basis | Total Fair Value | Bank deposits	'	'
Assets	'	'
Short-term and long-term investments:	20,000,000	'
Recurring Basis | Total Fair Value | U.S. Treasury securities	'	'
Assets	'	'
Cash and cash equivalents:	59,999,000	'
Short-term and long-term investments:	75,039,000	'
Recurring Basis | Total Fair Value | Corporate and municipal notes	'	'
Assets	'	'
Cash and cash equivalents:	170,217,000	'
Short-term and long-term investments:	$352,130,000	'

FAIR_VALUE_MEASUREMENTS_Detail1

FAIR VALUE MEASUREMENTS (Details 2) (USD $)

1 Months Ended

9 Months Ended

1 Months Ended

9 Months Ended

9 Months Ended

Dec. 31, 2011

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2013

Dec. 31, 2012

Aug. 31, 2013

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2013

Dec. 31, 2012

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2013

AnnualPayment

Trius Therapeutics, Inc.

Trius Therapeutics, Inc.

Trius Therapeutics, Inc.

Trius Therapeutics, Inc.

Adolor

Adolor

Adolor

Adolor

Adolor

Calixa Therapeutics Inc.

Calixa Therapeutics Inc.

Calixa Therapeutics Inc.

Calixa Therapeutics Inc.

Calixa Therapeutics Inc.

Calixa Therapeutics Inc.

Calixa Therapeutics Inc.

Level 2

Level 2

Level 2

Contingent Consideration

Contingent Consideration

Minimum

Maximum

Weighted Average

Minimum

Maximum

Weighted Average

Bevenopran (formerly known as CB-5945)

Bevenopran (formerly known as CB-5945)

Minimum

Maximum

Weighted Average

Ceftolozane/tazobactam (formerly known as CXA-201)

Ceftolozane/tazobactam (formerly known as CXA-201)

2020 Convertible Senior Notes

2018 Convertible Senior Notes

2017 Convertible Senior Notes

Level 3

Level 3

Trius Therapeutics, Inc.

Level 3 Disclosures

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Contingent consideration

'

'

'

$4,879,000

'

'

'

'

'

'

$80,401,000

$77,000,000

'

$76,092,000

'

'

'

$76,092,000

$112,200,000

'

'

'

'

'

Probability of success (as a percent)

'

'

'

'

4.00%

7.00%

6.00%

29.00%

54.00%

43.00%

'

'

'

'

29.00%

63.00%

48.00%

'

'

'

'

'

'

'

Discount rate (as a percent)

'

'

'

8.00%

'

'

'

5.30%

16.00%

'

'

'

'

5.30%

'

'

'

'

'

'

'

'

'

'

Contingent Consideration

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Undiscounted contingent consideration

'

'

'

'

0

108,400,000

'

0

233,800,000

'

'

'

'

180,000,000

'

'

'

'

'

'

'

'

'

'

Payment for contingent consideration

'

15,746,000

12,592,000

'

'

'

'

'

'

'

'

'

40,000,000

'

'

'

'

'

'

'

'

'

'

'

Reconciliation of fair value using Level 3 inputs, liabilities

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Balance at the beginning of the period

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

189,213,000

'

Contingent consideration liability recorded upon acquisition

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

4,879,000

Contingent consideration expense

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

7,280,000

'

Contingent consideration milestone payment

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

-40,000,000

'

Balance at the end of the period

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

161,372,000

'

Other Fair Value Measurements

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Fair value of notes

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

480,800,000

379,300,000

526,200,000

'

'

Number of remaining annual payments under termination agreement

6

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Aggregate payments due Glaxo

22,500,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

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

'

$14,100,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

INVENTORY_Details

INVENTORY (Details) (USD $)	Sep. 30, 2013	Dec. 31, 2012	Sep. 30, 2013	Sep. 30, 2013
In Thousands, unless otherwise specified			ENTEREG	API
INVENTORY	'	'	'	'
Raw materials	$12,957	$9,132	'	'
Work-in-process	5,657	8,485	'	'
Finished goods	36,465	24,330	'	'
Inventory	55,079	41,947	'	'
Included in other assets:	'	'	'	'
Raw materials	30,436	34,091	'	'
Work-in-process	2,702	1,733	'	'
Finished goods	'	1,669	'	'
Total	$88,217	$79,440	'	'
INVENTORY	'	'	'	'
Period in which inventory is expected to be sold	'	'	'1 year	'
Shelf-life	'	'	'3 years	'60 months
Period over which the entity expects to consume substantially all of the inventory	'	'	'	'7 years

PROPERTY_AND_EQUIPMENT_NET_Det

PROPERTY AND EQUIPMENT, NET (Details) (USD $)	3 Months Ended		9 Months Ended
	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012	Dec. 31, 2012
Property and equipment, net	'	'	'	'	'
Property and equipment, gross	$244,097,000	'	$244,097,000	'	$229,994,000
Less: accumulated depreciation	-73,975,000	'	-73,975,000	'	-63,529,000
Property and equipment, net	170,122,000	'	170,122,000	'	166,465,000
Depreciation expense	3,500,000	3,100,000	10,400,000	9,200,000	'
Land and buildings	'	'	'	'	'
Property and equipment, net	'	'	'	'	'
Property and equipment, gross	171,299,000	'	171,299,000	'	166,659,000
Laboratory equipment	'	'	'	'	'
Property and equipment, net	'	'	'	'	'
Property and equipment, gross	43,042,000	'	43,042,000	'	35,961,000
Furniture and fixtures	'	'	'	'	'
Property and equipment, net	'	'	'	'	'
Property and equipment, gross	3,908,000	'	3,908,000	'	3,351,000
Computer hardware and software	'	'	'	'	'
Property and equipment, net	'	'	'	'	'
Property and equipment, gross	23,490,000	'	23,490,000	'	20,903,000
Construction-in-progress	'	'	'	'	'
Property and equipment, net	'	'	'	'	'
Property and equipment, gross	$2,358,000	'	$2,358,000	'	$3,120,000

GOODWILL_IPRANDD_AND_OTHER_INT2

GOODWILL IPRANDD AND OTHER INTANGIBLE ASSETS, NET (Details) (USD $)	9 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2013
Goodwill	'
Balance at the beginning of the period	$114,130
Goodwill acquired	159,442
Balance at the end of the period	273,572
Accumulated impairment losses	0
Trius	'
Goodwill	'
Balance at the end of the period	$159,400

GOODWILL_IPRANDD_AND_OTHER_INT3

GOODWILL IPRANDD AND OTHER INTANGIBLE ASSETS, NET (Details 2) (USD $)	3 Months Ended		9 Months Ended
	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012	Dec. 31, 2012
Other intangible assets, net	'	'	'	'	'
Total IPR&D	$931,700,000	'	$931,700,000	'	$272,700,000
Finite-lived intangible assets	'	'	'	'	'
Intangible assets, gross	194,427,000	'	194,427,000	'	194,427,000
Other intangible assets, net	137,411,000	'	137,411,000	'	152,830,000
Amortization expense	5,200,000	5,200,000	15,400,000	15,700,000	'
Estimated aggregate amortization of intangible assets	'	'	'	'	'
Remainder of 2013	5,182,000	'	5,182,000	'	'
2014	20,729,000	'	20,729,000	'	'
2015	20,729,000	'	20,729,000	'	'
2016	19,449,000	'	19,449,000	'	'
2017	18,210,000	'	18,210,000	'	'
2018 and thereafter	53,112,000	'	53,112,000	'	'
Total	137,411,000	'	137,411,000	'	152,830,000
Patents	'	'	'	'	'
Finite-lived intangible assets	'	'	'	'	'
Intangible assets, gross	2,627,000	'	2,627,000	'	2,627,000
Less: accumulated amortization	-2,477,000	'	-2,477,000	'	-2,431,000
Acquired technology rights	'	'	'	'	'
Finite-lived intangible assets	'	'	'	'	'
Intangible assets, gross	191,800,000	'	191,800,000	'	191,800,000
Less: accumulated amortization	-54,539,000	'	-54,539,000	'	-39,166,000
Tedizolid phosphate	'	'	'	'	'
Other intangible assets, net	'	'	'	'	'
Total IPR&D	659,000,000	'	659,000,000	'	'
Bevenopran (formerly known as CB-5945)	'	'	'	'	'
Other intangible assets, net	'	'	'	'	'
Total IPR&D	78,700,000	'	78,700,000	'	78,700,000
Ceftolozane/tazobactam (formerly known as CXA-201) for HABP and VABP	'	'	'	'	'
Other intangible assets, net	'	'	'	'	'
Total IPR&D	174,000,000	'	174,000,000	'	174,000,000
Ceftolozane/tazobactam (formerly known as CXA-201) for cUTI and cIAI	'	'	'	'	'
Other intangible assets, net	'	'	'	'	'
Total IPR&D	$20,000,000	'	$20,000,000	'	$20,000,000

ACCRUED_LIABILITIES_Details

ACCRUED LIABILITIES (Details) (USD $)	Sep. 30, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified
ACCRUED LIABILITIES	'	'
Accrued royalties	$42,700	$72,103
Accrued clinical trials	39,921	29,143
Accrued Medicaid and Medicare rebates	14,707	20,565
Accrued bonus	18,141	13,971
Accrued benefits and incentive compensation	14,359	8,603
Other accrued costs	30,816	19,248
Accrued liabilities	$160,644	$163,633

DEBT_Details

DEBT (Details) (USD $)	1 Months Ended		3 Months Ended	9 Months Ended
	Sep. 30, 2013	Oct. 31, 2010	Sep. 30, 2013	Sep. 30, 2013	Dec. 31, 2012
Debt	'	'	'	'	'
Principal amount outstanding	$1,028,822,000	'	$1,028,822,000	$1,028,822,000	$450,000,000
Unamortized discount	-219,283,000	'	-219,283,000	-219,283,000	-82,189,000
Net carrying amount	809,539,000	'	809,539,000	809,539,000	367,811,000
Equity component of convertible debt issuance, net of tax and issuance costs	'	'	'	113,053,000	'
Principal amount of the 2017 Notes converted	221,200,000	'	'	'	'
Convertible Bond Hedge	'	'	'	'	'
Common stock covered under convertible bond hedge (in shares)	9,705,442	'	9,705,442	9,705,442	'
Exercise price (in dollars per unit)	$82.43	'	'	'	'
Purchase of convertible bond hedge	179,390,000	'	'	179,390,000	'
Warrant Transactions	'	'	'	'	'
Number of common stock called by warrants (in shares)	9,705,442	'	9,705,442	9,705,442	'
Exercise price (in dollars per share)	$96.43	'	$96.43	$96.43	'
Number of trading days over which warrants are exercisable	'80 days	'	'	'	'
Amount received on warrants sold	121,675,000	'	'	121,675,000	'
2018 Convertible Senior Notes and 2020 Convertible Senior Notes	'	'	'	'	'
Debt	'	'	'	'	'
Aggregate principal amount of notes issued	800,000,000	'	'	'	'
Number of note series	2	'	'	'	'
Net proceeds after debt issuance cost	775,600,000	'	'	'	'
Conversion rate of common stock	0.0121318	'	'	'	'
Initial conversion price of shares (in dollars per share)	$82.43	'	$82.43	$82.43	'
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%	'	'	'	'
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	'	1,000	1,000	'
Issuance costs incurred	24,400,000	'	'	'	'
Equity component of convertible debt issuance, net of tax and issuance costs	5,600,000	'	'	'	'
Debt issuance costs allocated to the liability components	18,800,000	'	'	'	'
2018 Convertible Senior Notes and 2020 Convertible Senior Notes | Minimum	'	'	'	'	'
Debt	'	'	'	'	'
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	'20 days	'	'	'	'
2018 Convertible Senior Notes and 2020 Convertible Senior Notes | Maximum	'	'	'	'	'
Debt	'	'	'	'	'
Convertibility of debt, trading price of debt test, percentage of closing price of stock used in calculation	98.00%	'	'	'	'
2020 Convertible Senior Notes	'	'	'	'	'
Debt	'	'	'	'	'
Principal amount outstanding	450,000,000	'	450,000,000	450,000,000	'
Unamortized discount	-114,323,000	'	-114,323,000	-114,323,000	'
Net carrying amount	335,677,000	'	335,677,000	335,677,000	'
Aggregate principal amount of notes issued	450,000,000	'	'	'	'
Notes stated interest rate percentage	1.88%	'	1.88%	1.88%	'
Expected life of debt discount	'7 years	'	'	'	'
Carrying value of equity component	70,500,000	'	70,500,000	70,500,000	'
Effective interest rate on liability component (as a percent)	6.40%	'	'	'	'
2018 Convertible Senior Notes	'	'	'	'	'
Debt	'	'	'	'	'
Principal amount outstanding	350,000,000	'	350,000,000	350,000,000	'
Unamortized discount	-68,784,000	'	-68,784,000	-68,784,000	'
Net carrying amount	281,216,000	'	281,216,000	281,216,000	'
Aggregate principal amount of notes issued	350,000,000	'	'	'	'
Number of note series	1	'	'	'	'
Notes stated interest rate percentage	1.13%	'	1.13%	1.13%	'
Expected life of debt discount	'5 years	'	'	'	'
Carrying value of equity component	42,600,000	'	42,600,000	42,600,000	'
Effective interest rate on liability component (as a percent)	5.70%	'	'	'	'
2017 Convertible Senior Notes	'	'	'	'	'
Debt	'	'	'	'	'
Principal amount outstanding	228,822,000	'	228,822,000	228,822,000	450,000,000
Unamortized discount	-36,176,000	'	-36,176,000	-36,176,000	-82,189,000
Net carrying amount	192,646,000	'	192,646,000	192,646,000	367,811,000
Aggregate principal amount of notes issued	'	450,000,000	'	'	'
Net proceeds after debt issuance cost	'	436,000,000	'	'	'
Conversion rate of common stock	0.0342759	'	'	0.0342759	'
Initial conversion price of shares (in dollars per share)	$29.18	'	$29.18	$29.18	'
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%	'
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	'	1,000	1,000	'
Notes stated interest rate percentage	2.50%	'	2.50%	2.50%	'
Expected life of debt discount	'	'	'	'7 years	'
Effective interest rate on liability component (as a percent)	'	'	'	7.00%	'
If-converted value in excess of the principal amount of debt	'	'	'	269,600,000	'
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	0	'	'	'	'
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	'	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	'	'
2017 Convertible Senior Notes | Minimum	'	'	'	'	'
Debt	'	'	'	'	'
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	'	'	'	'20 days	'
2017 Convertible Senior Notes | Maximum	'	'	'	'	'
Debt	'	'	'	'	'
Convertibility of debt, trading price of debt test, percentage of closing price of stock used in calculation	'	'	'	98.00%	'

DEBT_Details_2

DEBT (Details 2) (Senior secured revolving credit facility, USD $)	1 Months Ended				1 Months Ended			1 Months Ended
In Millions, unless otherwise specified	Nov. 30, 2012	Sep. 30, 2013	Dec. 31, 2012	Sep. 03, 2013	Sep. 30, 2013	Sep. 03, 2013	Sep. 03, 2013	Sep. 30, 2013	Sep. 03, 2013	Sep. 03, 2013
				Maximum	Eurodollar rate	Eurodollar rate	Eurodollar rate	Base rate	Base rate	Base 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	'	'	'	'	'	'
Basis spread on variable rate (as a percent)	'	'	'	'	'	2.25%	3.00%	'	1.25%	2.00%
Outstanding credit facility	'	$0	$0	'	'	'	'	'	'	'
Variable rate basis	'	'	'	'	'Eurodollar rate	'	'	'Base rate	'	'

EMPLOYEE_STOCK_BENEFIT_PLANS_D

EMPLOYEE STOCK BENEFIT PLANS (Details) (2012 Equity Incentive Plan)	Sep. 30, 2013
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	2,989,993

EMPLOYEE_STOCK_BENEFIT_PLANS_D1

EMPLOYEE STOCK BENEFIT PLANS (Details 2) (USD $)

3 Months Ended

9 Months Ended

1 Months Ended

3 Months Ended

9 Months Ended

3 Months Ended

9 Months Ended

3 Months Ended

9 Months Ended

1 Months Ended

3 Months Ended

9 Months Ended

3 Months Ended

9 Months Ended

1 Months Ended

3 Months Ended

9 Months Ended

In Thousands, unless otherwise specified

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2013

Trius Therapeutics, Inc.

Trius Therapeutics, Inc.

Trius Therapeutics, Inc.

Cost of product revenues

Cost of product revenues

Cost of product revenues

Cost of product revenues

Research and development

Research and development

Research and development

Research and development

Research and development

Research and development

Research and development

Selling, general and administrative

Selling, general and administrative

Selling, general and administrative

Selling, general and administrative

Selling, general and administrative

Selling, general and administrative

Selling, general and administrative

Trius Therapeutics, Inc.

Trius Therapeutics, Inc.

Trius Therapeutics, Inc.

Trius Therapeutics, Inc.

Trius Therapeutics, Inc.

Trius Therapeutics, Inc.

Summary of Stock-based Compensation Expense

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Total stock-based compensation

$7,965

$6,752

$24,104

$19,244

$24,000

$24,000

$24,000

$120

$133

$374

$305

$2,816

$2,371

$8,583

$6,724

$12,400

$12,400

$12,400

$5,029

$4,248

$15,147

$12,215

$11,600

$11,600

$11,600

Income tax effect

-2,993

-2,302

-9,058

-6,770

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

After-tax effect of stock-based compensation expense

$4,972

$4,450

$15,046

$12,474

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

EMPLOYEE_STOCK_BENEFIT_PLANS_D2

EMPLOYEE STOCK BENEFIT PLANS (Details 3) (USD $)	9 Months Ended
	Sep. 30, 2013
Stock options	'
Number of options	'
Outstanding as of beginning of the period (in shares)	8,025,194
Granted (in shares)	1,252,843
Exercised (in shares)	-1,310,085
Canceled (in shares)	-112,413
Outstanding as of end of the period (in shares)	7,855,539
Vested and exercisable as of end of the period (in shares)	4,685,736
Weighted Average Exercise Price	'
Outstanding as of beginning of the period (in dollars per share)	$27.31
Granted (in dollars per share)	$45.32
Exercised (in dollars per share)	$20.92
Canceled (in dollars per share)	$36.24
Outstanding as of end of the period (in dollars per share)	$31.12
Vested and exercisable as of end of the period (in dollars per share)	$25.10
Weighted average grant-date fair value of options granted during the period (in dollars per share)	$14.15
Restricted stock units	'
Number of restricted stock units	'
Nonvested as of beginning of the period (in shares)	735,939
Granted (in shares)	443,745
Vested (in shares)	-271,724
Forfeited (in shares)	-23,722
Nonvested as of end of the period (in shares)	884,238
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)	$44.15
Vested (in dollars per share)	$32.35
Forfeited (in dollars per share)	$37.75
Nonvested stock as of end of the period (in dollars per share)	$40.61

INCOME_TAXES_Details

INCOME TAXES (Details) (USD $)	1 Months Ended	3 Months Ended		9 Months Ended
In Millions, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012
Effective Tax Rate	'	'	'	'	'
Federal statutory rate applied to income before taxes (as a percent)	'	35.00%	35.00%	35.00%	35.00%
Differential arising from:	'	'	'	'	'
State (as a percent)	'	2.40%	0.60%	3.40%	1.30%
Non-deductible expenses (as a percent)	'	-5.20%	0.50%	-17.30%	0.60%
Domestic manufacturing deduction (as a percent)	'	1.50%	-2.40%	9.80%	-2.70%
Contingent consideration (as a percent)	'	-4.70%	-0.40%	-15.80%	0.70%
2013 Federal research credit (as a percent)	'	16.30%	'	54.50%	'
Prior year federal research credits (as a percent)	'	0.90%	'	31.10%	'
Non-deductible transaction costs (as a percent)	'	-7.00%	'	-19.40%	'
Non-deductible loss on extinguishment of 2017 Notes (as a percent)	'	-24.40%	'	-67.50%	'
Impact of reserve for uncertain tax positions (as a percent)	'	-0.10%	0.10%	2.60%	-6.70%
Other (as a percent)	'	-1.40%	-0.40%	-5.30%	'
Total (as a percent)	'	13.30%	33.00%	11.10%	28.20%
Principal amount of the 2017 Notes converted	$221.20	'	'	'	'
Federal | Trius Therapeutics, Inc.	'	'	'	'	'
Operating loss carryforwards	'	'	'	'	'
NOL carryforwards	192.8	192.8	'	192.8	'
NOL carryforwards to be utilized in future	$192	192	'	192	'

INCOME_TAXES_Details_2

INCOME TAXES (Details 2) (USD $)	Sep. 30, 2013	Dec. 31, 2012
In Millions, unless otherwise specified
INCOME TAXES	'	'
Uncertain tax positions	$38.80	$36.10
Uncertain tax positions included in other long-term liabilities	15.9	'
Uncertain tax positions offset against deferred tax assets	$22.90	'

SEGMENT_INFORMATION_Details

SEGMENT INFORMATION (Details)	3 Months Ended		9 Months Ended
	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012
			Segment
SEGMENT INFORMATION	'	'	'	'
Number of business segments	'	'	1	'
Approximate percentage of revenues generated within the U. S.	95.00%	95.00%	94.00%	94.00%

LEGAL_PROCEEDINGS_Details

LEGAL PROCEEDINGS (Details) (USD $)	9 Months Ended
In Millions, unless otherwise specified	Sep. 30, 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

SUBSEQUENT_EVENTS_Details

SUBSEQUENT EVENTS (Details) (Optimer Pharmaceuticals, Inc., USD $)	Sep. 30, 2013	Oct. 24, 2013	Oct. 24, 2013
		Subsequent event	Subsequent event
		right	Maximum
Subsequent events	'	'	'
Cash consideration	'	$550,500,000	'
Purchase price of outstanding common stock of acquiree (in dollars per share)	'	$10.75	'
Number of transferable contingent value rights receivable by stockholders of acquiree	'	1	'
Maximum additional cash payment per share (in dollars per share)	'	$5	'
Undiscounted contingent consideration	'	'	253,900,000
Percentage of outstanding shares acquired	'	100.00%	'
Transaction costs	$3,900,000	'	'