Innoviva (INVA) 10-K 3 Mar 14 2013 FY Annual report Financial data

Document_and_Entity_Informatio

Document and Entity Information (USD $)	12 Months Ended
	Dec. 31, 2013	Feb. 14, 2014	Jun. 30, 2013
Document and Entity Information	'	'	'
Entity Registrant Name	'THERAVANCE INC	'	'
Entity Central Index Key	'0001080014	'	'
Document Type	'10-K	'	'
Document Period End Date	31-Dec-13	'	'
Amendment Flag	'false	'	'
Current Fiscal Year End Date	'--12-31	'	'
Entity Well-known Seasoned Issuer	'Yes	'	'
Entity Voluntary Filers	'No	'	'
Entity Current Reporting Status	'Yes	'	'
Entity Filer Category	'Large Accelerated Filer	'	'
Entity Public Float	'	'	$1,657,233,711
Entity Common Stock, Shares Outstanding	'	111,976,127	'
Document Fiscal Year Focus	'2013	'	'
Document Fiscal Period Focus	'FY	'	'

Consolidated_Balance_Sheets

Consolidated Balance Sheets (USD $)	Dec. 31, 2013	Dec. 31, 2012
Current assets:	'	'
Cash and cash equivalents	$143,510,000	$94,849,000
Short-term investments	321,615,000	153,640,000
Accounts receivable, net of allowances of $89 and $0 at December 31, 2013 and 2012	199,000	0
Receivables from collaborative arrangements (including amounts from a related party of $2,247 and $123 at December 31, 2013 and 2012)	3,181,000	1,064,000
Prepaid expenses and other current assets	4,287,000	4,066,000
Inventories	10,406,000	7,514,000
Total current assets	483,198,000	261,133,000
Marketable securities	55,374,000	95,194,000
Restricted cash	833,000	833,000
Property and equipment, net	10,238,000	9,154,000
Intangible assets, net	124,257,000	0
Other assets	7,355,000	2,268,000
Total assets	681,255,000	368,582,000
Current liabilities:	'	'
Accounts payable	7,583,000	5,377,000
Payable to a related party	40,000,000	0
Accrued personnel-related expenses	10,881,000	9,002,000
Accrued clinical and development expenses	9,714,000	6,550,000
Accrued interest on convertible subordinated notes	2,800,000	2,372,000
Other accrued liabilities	4,137,000	2,072,000
Deferred revenue	9,289,000	4,593,000
Total current liabilities	84,404,000	29,966,000
Convertible subordinated notes	287,500,000	172,500,000
Deferred rent	4,774,000	5,074,000
Deferred revenue	5,455,000	6,014,000
Commitments and contingencies (Notes 3, 10 and 12)	'	'
Stockholders' equity	'	'
Preferred stock, $0.01 par value, 230 shares authorized, no shares issued and outstanding	'	'
Additional paid-in capital	1,803,048,000	1,488,447,000
Accumulated other comprehensive income	162,000	99,000
Accumulated deficit	-1,505,203,000	-1,334,502,000
Total stockholders' equity	299,122,000	155,028,000
Total liabilities and stockholders' equity	681,255,000	368,582,000
Common stock	'	'
Stockholders' equity	'	'
Common stock	1,115,000	984,000
Class A common stock	'	'
Stockholders' equity	'	'
Common stock	$0	$0

Consolidated_Balance_Sheets_Pa

Consolidated Balance Sheets (Parenthetical) (USD $)	Dec. 31, 2013	Dec. 31, 2012
In Thousands, except Per Share data, unless otherwise specified
Account receivable, allowance	$89	$0
Receivable from related party	$2,247	$123
Preferred stock, par value (in dollars per share)	$0.01	$0.01
Preferred stock, shares authorized	500	500
Preferred stock, shares issued	0	0
Common stock	'	'
Common stock, par value (in dollars per share)	$0.01	$0.01
Common stock, authorized shares	200,000	200,000
Common stock, outstanding shares	111,516	98,379
Class A common stock	'	'
Common stock, par value (in dollars per share)	$0.01	$0.01
Common stock, authorized shares	30,000	30,000
Common stock, outstanding shares	0	0

Consolidated_Statements_of_Ope

Consolidated Statements of Operations (USD $)	12 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Consolidated Statements of Operations	'	'	'
Royalty revenue from a related party, net of intangible assets amortization of $743 in 2013 and $0 in 2012 and 2011	$1,202	$0	$0
Net revenue from collaborative arrangements (including amounts from a related party of $3,330 in 2013, $5,613 in 2012, and $9,658 in 2011)	3,556	135,758	24,512
Total net revenue	4,758	135,758	24,512
Operating expenses:	'	'	'
Research and development	125,181	117,898	103,568
Selling, general and administrative	48,440	30,859	30,681
Total operating expenses	173,621	148,757	134,249
Loss from operations	-168,863	-12,999	-109,737
Other income (expense), net	6,732	0	0
Interest income	778	460	415
Interest expense	-9,348	-6,003	-6,022
Net loss	($170,701)	($18,542)	($115,344)
Basic and diluted net loss per share (in dollars per share)	($1.67)	($0.20)	($1.41)
Shares used to compute basic and diluted net loss per share (in shares)	102,425	90,909	82,051

Consolidated_Statements_of_Ope1

Consolidated Statements of Operations (Parenthetical) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Consolidated Statements of Operations	'	'	'
Amortization of intangible assets	$743	$0	$0
Revenue from a related party	$3,330	$5,613	$9,658

Consolidated_Statements_of_Com

Consolidated Statements of Comprehensive Loss (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Consolidated Statements of Comprehensive Loss	'	'	'
Net loss	($170,701)	($18,542)	($115,344)
Other comprehensive income (loss):	'	'	'
Net unrealized gain (loss) on available-for-sale securities, net of tax	63	83	-17
Comprehensive loss	($170,638)	($18,459)	($115,361)

Consolidated_Statements_of_Sto

Consolidated Statements of Stockholders' Equity (Net Capital Deficiency) (USD $)	Total	Common Stock	Class A Common Stock	Common Stock	Common Stock	Additional Paid-In Capital	Accumulated Other Comprehensive Income	Accumulated Deficit
In Thousands, except Share data, unless otherwise specified	USD ($)			USD ($)	Class A Common Stock	USD ($)	USD ($)	USD ($)
					USD ($)
Balance at Dec. 31, 2010	($22,420)	'	'	$710	$94	$1,177,359	$33	($1,200,616)
Balance (in shares) at Dec. 31, 2010	'	'	'	70,950,000	9,402,000	'	'	'
Increase (Decrease) in Stockholders' Equity	'	'	'	'	'	'	'	'
Exercise of stock options, and issuance of common stock in settlement of restricted stock units, stock awards and purchase plan	12,195	'	'	46	0	12,149	0	0
Exercise of stock options, and issuance of common stock in settlement of restricted stock units, stock awards and purchase plan (in shares)	'	'	'	4,617,000	0	'	'	'
Issuance of common stock in private placement to a related party	13,618	'	'	5	0	13,613	0	0
Issuance of common stock in private placement to a related party, net of expenses (in shares)	'	'	'	574,000	0	'	'	'
Conversion of convertible subordinated notes due 2015	0	'	'	'	'	0	0	0
Conversion of Class A common stock	'	'	'	94	-94	'	'	'
Conversion of Class A common stock (in shares)	'	'	'	9,402,000	-9,402,000	'	'	'
Stock-based compensation	24,916	'	'	0	0	24,916	0	0
Net loss	-115,344	'	'	0	0	0	0	-115,344
Net unrealized gain (loss) on marketable securities	-17	'	'	0	0	0	-17	0
Balance at Dec. 31, 2011	-87,052	'	'	855	0	1,228,037	16	-1,315,960
Balance (in shares) at Dec. 31, 2011	'	'	'	85,543,000	0	'	'	'
Increase (Decrease) in Stockholders' Equity	'	'	'	'	'	'	'	'
Exercise of stock options, and issuance of common stock in settlement of restricted stock units, stock awards and purchase plan	7,081	'	'	22	0	7,059	0	0
Exercise of stock options, and issuance of common stock in settlement of restricted stock units, stock awards and purchase plan (in shares)	'	'	'	2,151,000	0	'	'	'
Issuance of common stock in private placement to a related party	229,296	'	'	107	0	229,189	0	0
Issuance of common stock in private placement to a related party, net of expenses (in shares)	'	'	'	10,685,000	0	'	'	'
Stock-based compensation	24,162	'	'	0	0	24,162	0	0
Net loss	-18,542	'	'	0	0	0	0	-18,542
Net unrealized gain (loss) on marketable securities	83	'	'	0	0	0	83	0
Balance at Dec. 31, 2012	155,028	'	'	984	0	1,488,447	99	-1,334,502
Balance (in shares) at Dec. 31, 2012	'	98,379,000	0	98,379,000	0	'	'	'
Increase (Decrease) in Stockholders' Equity	'	'	'	'	'	'	'	'
Exercise of stock options, and issuance of common stock in settlement of restricted stock units, stock awards and purchase plan	26,991	'	'	29	0	26,962	0	0
Exercise of stock options, and issuance of common stock in settlement of restricted stock units, stock awards and purchase plan (in shares)	'	'	'	2,964,000	0	'	'	'
Issuance of common stock in private placement to a related party	126,030	'	'	35	0	125,995	0	0
Issuance of common stock in private placement to a related party, net of expenses (in shares)	'	'	'	3,505,000	0	'	'	'
Conversion of convertible subordinated notes due 2015	171,231	'	'	67	0	171,164	0	0
Conversion of convertible subordinated notes due 2015 (in shares)	'	'	'	6,668,000	0	'	'	'
Stock-based compensation	25,858	'	'	0	0	25,858	0	0
Capped call options associated with convertible subordinated notes due 2023	-35,378	'	'	0	0	-35,378	0	0
Net loss	-170,701	'	'	0	0	0	0	-170,701
Net unrealized gain (loss) on marketable securities	63	'	'	0	0	0	63	0
Balance at Dec. 31, 2013	$299,122	'	'	$1,115	$0	$1,803,048	$162	($1,505,203)
Balance (in shares) at Dec. 31, 2013	'	111,516,000	0	111,516,000	0	'	'	'

Consolidated_Statements_of_Sto1

Consolidated Statements of Stockholders' Equity (Net Capital Deficiency) (Parenthetical) (USD $)	12 Months Ended
In Millions, unless otherwise specified	Dec. 31, 2012
Consolidated Statements of Stockholders' Equity (Net Capital Deficiency)	'
Issuance of common stock in private placement to a related party, expenses	$0.40

Consolidated_Statements_of_Cas

Consolidated Statements of Cash Flows (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Cash flows from operating activities	'	'	'
Net loss	($170,701)	($18,542)	($115,344)
Adjustments to reconcile net loss to net cash used in operating activities:	'	'	'
Depreciation and amortization	8,203	7,326	7,583
Stock-based compensation	25,687	23,783	24,916
Change in fair value of capped-call derivative assets	1,422	0	0
Other non-cash items	17	187	18
Changes in operating assets and liabilities:	'	'	'
Accounts receivables	702	0	0
Receivables from collaborative arrangements	-2,117	-841	-29
Prepaid expenses and other current assets	36	-441	2,288
Inventories	-3,100	-4,822	0
Other assets	-578	0	0
Accounts payable	1,613	-1,480	3,310
Accrued personnel-related expenses, accrued clinical and development expenses, and other accrued liabilities	5,850	-1,829	5,124
Accrued interest on convertible subordinated notes	428	0	0
Deferred rent expense	-299	-747	2,429
Deferred revenue	3,235	-130,107	-18,633
Net cash used in operating activities	-129,602	-127,513	-88,338
Cash flows from investing activities	'	'	'
Purchases of property and equipment	-2,734	-2,590	-3,628
Purchases of available-for-sale securities	-410,407	-330,484	-301,563
Maturities of available-for-sale securities	255,861	224,902	231,476
Sales of available-for-sale securities	22,600	49,729	17,321
Increase in intangible assets	-85,000	0	0
Release of restricted cash	0	60	0
Issuances of notes receivable	0	-140	-140
Payments received on notes receivable	100	240	715
Net cash used in investing activities	-219,580	-58,283	-55,819
Cash flows from financing activities	'	'	'
Payments on note payable and capital leases	0	-69	-206
Proceeds from issuances of common stock, net	153,021	236,377	25,808
Purchase of capped-call options	-36,800	0	0
Proceeds from issuances of convertible subordinated notes, net of debt issuance costs	281,622	-441	0
Net cash provided by financing activities	397,843	235,867	25,602
Net increase (decrease) in cash and cash equivalents	48,661	50,071	-118,555
Cash and cash equivalents at beginning of period	94,849	44,778	163,333
Cash and cash equivalents at end of period	143,510	94,849	44,778
Supplemental Disclosure of Cash Flow Information	'	'	'
Cash paid for interest	7,970	5,177	5,195
Supplemental Non-cash Financing Activities	'	'	'
Conversion of convertible subordinated notes into common stock	$172,499	$0	$0

Description_of_Operations_and_

Description of Operations and Summary of Significant Accounting Policies	12 Months Ended
	Dec. 31, 2013
Description of Operations and Summary of Significant Accounting Policies	'
Description of Operations and Summary of Significant Accounting Policies	'
	1. Description of Operations and Summary of Significant Accounting Policies
	Description of Operations
	Theravance, Inc. (Theravance, the Company, the Registrant or we and other similar pronouns) is a biopharmaceutical company with a pipeline of internally discovered product candidates and strategic collaborations with pharmaceutical companies. Theravance is focused on the discovery, development and commercialization of small molecule medicines across a number of therapeutic areas including respiratory disease, bacterial infections, and central nervous system (CNS)/pain.
	Business Separation
	In April 2013, Theravance announced that its Board of Directors approved plans to separate its businesses into two independent publicly traded companies. The company to be spun-off, Theravance Biopharma, Inc. (Theravance Biopharma), filed an initial Form 10 with the SEC on August 1, 2013 and filed amendments of its Form 10 with the SEC on September 27, 2013, October 29, 2013 and November 22, 2013. After the spin-off, Theravance will be responsible for all development and commercial activities under the LABA collaboration and the Strategic Alliance agreements with Glaxo Group Limited (GSK). Theravance will be eligible to receive the associated potential royalty revenues from FF/VI (RELVAR®/BREO® ELLIPTA®), UMEC/VI (ANORO™ ELLIPTA™) and potentially VI monotherapy and 15% of the potential royalty revenues from UMEC/VI/FF, MABA, and MABA/FF and other products that may be developed under the LABA collaboration and Strategic Alliance agreements. Theravance Biopharma will be a biopharmaceutical company focused on discovery, development and commercialization of small-molecule medicines in areas of significant unmet medical need. The result will be two independent, publicly traded companies with different business models enabling investors to align their investment philosophies with the strategic opportunities and financial objectives of the two independent companies. The consolidated financial statements do not reflect any adjustments resulting from the planned business separation.
	Principles of Consolidation
	The consolidated financial statements include the accounts of Theravance and its wholly owned subsidiaries. All intercompany balances and transactions have been eliminated in consolidation.
	Our consolidated financial statements are denominated in U.S. dollars. Accordingly, changes in exchange rates between the applicable foreign currency and the U.S. dollar will affect the translation of our foreign subsidiary's financial results into U.S. dollars for purposes of reporting our consolidated financial results. Monetary and non-monetary assets and liabilities are remeasured into U.S. dollars at the applicable period end exchange rate. Operating expenses are remeasured at average exchange rates in effect during each period, except for those expenses related to non-monetary assets which are remeasured at historical exchange rates. Gains or losses from remeasurement of foreign currency financial statements into U.S. dollars are included in our consolidated statements of operations and were insignificant for all periods presented, as was the effect of exchange rate changes on cash and cash equivalents.
	Use of Management's Estimates
	The preparation of consolidated financial statements in conformity with U.S. Generally Accepted Accounting Principles ("GAAP") requires management to make estimates and assumptions that affect the amounts reported in the consolidated financial statements and accompanying notes. Actual results could differ materially from those estimates. On an ongoing basis, management evaluates its significant accounting policies and estimates. We base our estimates on historical experience and other relevant assumptions that we believe to be reasonable under the circumstances. These estimates also form the basis for making judgments about the carrying values of assets and liabilities when these values are not readily apparent from other sources.
	Segment Reporting
	We have determined that we operate in a single segment, which is the discovery (research), development and commercialization of human therapeutics. Revenues are generated primarily from our collaborative arrangements with GSK, located in Great Britain, Astellas Pharma Inc. ("Astellas") (through January 2012), located in Japan, and Merck (which agreement terminated in December 2013), located in the United States.
	All property and equipment is maintained in the United States.
	Cash and Cash Equivalents
	We consider all highly liquid investments purchased with a maturity of three months or less on the date of purchase to be cash equivalents. Cash equivalents are carried at cost, which approximates fair value.
	Under certain lease agreements and letters of credit, we have pledged cash and cash equivalents as collateral. Restricted cash related to such agreements was $0.8 million as of December 31, 2013 and 2012.
	Investments in Marketable Securities
	We invest in short-term investments and marketable securities, primarily corporate notes, government, government agency, and municipal bonds. We classify our marketable securities as available-for-sale securities and report them at fair value in cash equivalents, short-term investments or marketable securities on the consolidated balance sheets with related unrealized gains and losses included as a component of stockholders' equity. The amortized cost of debt securities is adjusted for amortization of premiums and accretion of discounts to maturity, which is included in interest income on the consolidated statements of operations. Realized gains and losses and declines in value judged to be other-than-temporary, if any, on available-for-sale securities are included in interest income. The cost of securities sold is based on the specific identification method. Interest and dividends on securities classified as available-for-sale are included in interest income.
	We regularly review all of our investments for other-than-temporary declines in estimated fair value. Our review includes the consideration of the cause of the impairment, including the creditworthiness of the security issuers, the number of securities in an unrealized loss position, the severity and duration of the unrealized losses, whether we have the intent to sell the securities and whether it is more likely than not that we will be required to sell the securities before the recovery of their amortized cost basis. When we determine that the decline in estimated fair value of an investment is below the amortized cost basis and the decline is other-than-temporary, we reduce the carrying value of the security and record a loss for the amount of such decline.
	Fair Value of Financial Instruments
	Financial instruments include cash equivalents, marketable securities, accounts receivable, related party receivables, accounts payable, accrued liabilities and convertible subordinated notes. Marketable securities are carried at estimated fair value. The carrying value of cash equivalents, accounts receivable, receivables from related party, accounts payable and accrued liabilities approximate their estimated fair value due to the relatively short-term nature of these instruments. The fair value of the convertible subordinated notes is described in Note 9, "Long-Term Debt."
	Accounts Receivable
	Trade accounts receivable are recorded net of allowances for wholesaler chargebacks related to government rebate programs, cash discounts for prompt payment and sales returns. Estimates for wholesaler chargebacks for government rebates, cash discounts and sales returns are based on contractual terms, historical trends and our expectations regarding the utilization rates for these programs. When appropriate, we record an allowance for doubtful accounts based upon our assessment of collectability. For the year ended December 31, 2013, we did not have any write-offs of accounts receivable. We perform ongoing credit evaluations of our customers and generally do not require collateral.
	Concentration of Credit and Other Risks
	We invest in a variety of financial instruments and, by our policy, limit the amount of credit exposure with any one issuer, industry or geographic area for investments other than instruments backed by the U.S. federal government.
	Our accounts receivable at December 31, 2013, represent amounts due to us from distributors. The following table summarizes accounts receivable, net balances at December 31, 2013 by distributor:
	Distributor	Accounts Receivable		Percentage of Total
		(In thousands)		Accounts Receivable
				Balance
	McKesson Corporation	$	132		66	%
	AmerisourceBergen Drug Corporation		66		33
	Other		1		1
	Total	$	199		100	%
	We depend on a single-source supplier of the API in VIBATIV® and one supplier to provide fill-finish services related to the manufacturing of VIBATIV®. If any of our suppliers were to limit or terminate production or otherwise fail to meet the quality or delivery requirements needed to supply VIBATIV® at levels to meet market demand, we could experience a loss of revenue, which could materially and adversely impact our results of operations.
	Inventories
	Inventories consist of raw materials, work-in-process and finished goods related to the production of VIBATIV® (telavancin). Raw materials include VIBATIV® API and other raw materials. Work-in-process and finished goods include third party manufacturing costs and labor and indirect costs we incur in the production process. Included in inventories are raw materials and work-in-process that may be used as clinical products, which are charged to research and development (R&D) expense when consumed. In addition, under certain commercialization agreements, we may sell VIBATIV® packaged in unlabeled vials that are recorded in work-in-process. Inventories are stated at the lower of cost or market value. We determine the cost of inventory using the average-cost method for validation batches. We analyze our inventory levels quarterly and write down any inventory that is expected to become obsolete, that has a cost basis in excess of its expected net realizable value or for inventory quantities in excess of expected requirements.
	Property and Equipment
	Property, equipment and leasehold improvements are stated at cost and depreciated using the straight-line method as follows:
	Leasehold improvements	Shorter of remaining lease terms or useful life
	Equipment, furniture and fixtures	5 - 7 years
	Software and computer equipment	3 years
	Capitalized Software
	We capitalize certain costs related to direct material and service costs for software obtained for internal use. Capitalized software costs are depreciated over 3 years.
	Impairment of Long-Lived Assets
	Long-lived assets include property and equipment. The carrying value of long-lived assets is reviewed for impairment whenever events or changes in circumstances indicate that the asset may not be recoverable. An impairment loss is recognized when the total of estimated future cash flows expected to result from the use of the asset and its eventual disposition is less than its carrying amount.
	Bonus Accruals
	We have short-term bonus programs for eligible employees. Bonuses are determined based on various criteria, including the achievement of corporate, departmental and individual goals. Bonus accruals are estimated based on various factors, including target bonus percentages per level of employee and probability of achieving the goals upon which bonuses are based.
	In 2011, we granted special long-term retention and incentive cash bonus awards to certain employees. The awards have dual triggers of vesting based upon the achievement of certain performance conditions over a six-year timeframe from 2011 through December 31, 2016 and continued employment. As of December 31, 2013, we determined that the achievement of the requisite performance conditions was not probable and, as a result, no compensation expense has been recognized.
	Deferred Rent
	Deferred rent consists of the difference between cash payments and the recognition of rent expense on a straight-line basis for the buildings we occupy. Rent expense is being recognized ratably over the life of the leases. Because our facility operating leases provide for rent increases over the terms of the leases, average annual rent expense during the first 1.5 years of the leases exceeded our actual cash rent payments. Also included in deferred rent are lease incentives of $2.6 million as of December 31, 2013, which is being recognized ratably over the life of the leases.
	Revenue Recognition
	Revenue is recognized when the four basic criteria of revenue recognition are met: (1) persuasive evidence of an arrangement exists; (2) delivery has occurred or services have been rendered; (3) the fee is fixed or determinable; and (4) collectability is reasonably assured. Determination of criteria (3) and (4) are based on management's judgments regarding the nature of the fee charged for products or services delivered and the collectability of those fees. Where the revenue recognition criteria are not met, we defer the recognition of revenue by recording deferred revenue until such time that all criteria are met.
	Collaborative Arrangements and Multiple-Element Arrangements
	Revenue from nonrefundable, up-front license or technology access payments under license and collaborative arrangements that are not dependent on any future performance by us is recognized when such amounts are earned. If we have continuing obligations to perform under the arrangement, such fees are recognized over the estimated period of continuing performance obligation.
	We account for multiple element arrangements, such as license and development agreements in which a customer may purchase several deliverables, in accordance with FASB ASC Subtopic 605-25, "Multiple Element Arrangements." For new or materially amended multiple element arrangements, we identify the deliverables at the inception of the arrangement and each deliverable within a multiple deliverable revenue arrangement is accounted for as a separate unit of accounting if both of the following criteria are met: (1) the delivered item or items have value to the customer on a standalone basis and (2) for an arrangement that includes a general right of return relative to the delivered item(s), delivery or performance of the undelivered item(s) is considered probable and substantially in our control. We allocate revenue to each non-contingent element based on the relative selling price of each element. When applying the relative selling price method, we determine the selling price for each deliverable using vendor-specific objective evidence ("VSOE") of selling price, if it exists, or third-party evidence ("TPE") of selling price, if it exists. If neither VSOE nor TPE of selling price exist for a deliverable, we use the best estimated selling price for that deliverable. Revenue allocated to each element is then recognized based on when the basic four revenue recognition criteria are met for each element.
	For multiple-element arrangements entered into prior to January 1, 2011, we determined the deliverables under our collaborative arrangements did not meet the criteria to be considered separate accounting units for the purposes of revenue recognition. As a result, we recognized revenue from non-refundable, upfront fees and development contingent payments ratably over the term of its performance under the agreements. These upfront or contingent payments received, pending recognition as revenue, are recorded as deferred revenue and are classified as a short-term or long-term liability on the consolidated balance sheets and amortized over the estimated period of performance. We periodically review the estimated performance periods of our contracts based on the progress of our programs.
	Where a portion of non-refundable upfront fees or other payments received are allocated to continuing performance obligations under the terms of a collaborative arrangement, they are recorded as deferred revenue and recognized as revenue or as an accrued liability and recognized as a reduction of research and development expenses ratably over the term of our estimated performance period under the agreement. We determine the estimated performance periods, and they are periodically reviewed based on the progress of the related program. The effect of any change made to an estimated performance period and, therefore revenue recognized, would occur on a prospective basis in the period that the change was made.
	Under certain collaborative arrangements, we have been reimbursed for a portion of our research and development expenses. These reimbursements have been reflected as a reduction of research and development expense in our consolidated statements of operations, as we do not consider performing research and development services to be a part of our ongoing and central operations. Therefore, the reimbursement of research and developmental services and any amounts allocated to our research and development services are recorded as a reduction of research and development expense.
	Amounts deferred under a collaborative arrangement in which the performance obligations are terminated will result in an immediate recognition of any remaining deferred revenue and accrued liability in the period that termination occurred, provided that all performance obligations have been satisfied.
	We account for contingent payments in accordance with FASB Subtopic ASC 605-28 "Revenue Recognition—Milestone Method." We recognize revenue from milestone payments when (i) the milestone event is substantive and its achievability was not reasonably assured at the inception of the agreement and (ii) we do not have ongoing performance obligations related to the achievement of the milestone. Milestone payments are considered substantive if all of the following conditions are met: the milestone payment (a) is commensurate with either our performance to achieve the milestone or the enhancement of the value of the delivered item or items as a result of a specific outcome resulting from our performance to achieve the milestone, (b) relates solely to past performance, and (c) is reasonable relative to all of the deliverables and payment terms (including other potential milestone consideration) within the arrangement. See Note 3, "Collaborative Arrangements," for analysis of each milestone event deemed to be substantive or non-substantive.
	In accordance with FASB Subtopic ASC 808-10, "Collaborative Arrangements," and pursuant to our agreement with Astellas, we recognized as revenue the net impact of transactions with Astellas related to VIBATIV® inventories including revenue specifically attributable to any sales, and cost of inventories either transferred or expensed as unrealizable.
	Product Revenues
	We sell VIBATIV® in the U.S. through a limited number of distributors, and title and risk of loss transfer upon receipt by these distributors. Healthcare providers order VIBATIV® through these distributors. For all product shipped in 2013, we are deferring the recognition of revenue until the product is sold through to healthcare providers, the end customers, due to the inherent uncertainties in estimating normal channel inventory at the distributors, and during which period we also provided extended payment terms and expanded return rights that allow distributors to return the product. As of December 31, 2013, we had deferred revenue of $0.9 million related to VIBATIV® shipments included in current liabilities in the consolidated balance sheet.
Product sales are recorded net of estimated government-mandated rebates and chargebacks, distribution fees, estimated product returns and other deductions. We reflect such reductions in revenue as either an allowance to the related account receivable from the distributor, or as an accrued liability, depending on the nature of the sales deduction. Sales deductions are based on management's estimates that consider payer mix in target markets, industry benchmarks and experience to date. We monitor inventory levels in the distribution channel, as well as sales of VIBATIV® by distributors to healthcare providers, using product-specific data provided by the distributors. Product return allowances are based on amounts owed or to be claimed on related sales. These estimates take into consideration the terms of our agreements with customers, historical product returns of VIBATIV® experienced by Astellas, rebates or discounts taken, estimated levels of inventory in the distribution channel, the shelf life of the product, and specific known market events, such as competitive pricing and new product introductions. We update our estimates and assumptions each quarter and if actual future results vary from our estimates, we may adjust these estimates, which could have an effect on product sales and earnings in the period of adjustment.
Sales Discounts:    We offer cash discounts to our customers, generally 2% of the sales price, as an incentive for prompt payment. We expect our customers to comply with the prompt payment terms to earn the cash discount. We account for cash discounts by reducing accounts receivable by the full amount and recognizing the discount as a reduction of revenue in the same period the related revenue is recognized.
Chargebacks and Government Rebates:    For VIBATIV® sales in the U.S., we estimate reductions to product sales for qualifying federal and state government programs including discounted pricing offered to Public Health Service (PHS) as well as government-managed Medicaid programs. Our reduction for PHS is based on actual chargebacks that distributors have claimed for reduced pricing offered to such health care providers. Our accrual for Medicaid is based upon statutorily-defined discounts, estimated payer mix, expected sales to qualified healthcare providers, and our expectation about future utilization. The Medicaid accrual and government rebates that are invoiced directly to us are recorded in other accrued liabilities on the consolidated balance sheet. For qualified programs that can purchase our products through distributors at a lower contractual government price, the distributors charge back to us the difference between their acquisition cost and the lower contractual government price, which we record as an allowance against accounts receivable.
Distribution Fees and Product Returns:    We have written contracts with our distributors that include terms for distribution-related fees. We record distribution-related fees based on a percentage of the product sales price. We offer our distributors a right to return product purchased directly from us, which is principally based upon the product's expiration date. Additionally, we have granted more expansive return rights to our distributors following our product launch of VIBATIV®. We will generally accept returns for expired product during the six months prior to and twelve months after the product expiration date on product that had been sold to our distributors. Product returned is generally not resalable given the nature of our products and method of administration. We have developed estimates for VIBATIV® product returns based upon historical VIBATIV® sales from our former collaborative partner, Astellas. We record distribution fees and product returns as an allowance against accounts receivable.
Allowance for Doubtful Accounts:    We maintain a policy to record allowances for potentially doubtful accounts for estimated losses resulting from the inability of our customers to make required payments. As of December 31, 2013, there was no allowance for doubtful accounts.
Royalties:    We recognize royalty revenue on licensee net sales of our products in the period in which the royalties are earned and reported to us and collectability is reasonably assured.
Intangible Assets
We capitalize fees paid to licensors related to agreements for approved products or commercialized products. We capitalize these fees as finite-lived intangible assets and amortize these intangible assets on a straight-line basis over their estimated useful lives once we begin recognizing the related royalty revenue. Consistent with our policy for classification of costs under the research and development collaborative arrangements, the amortization of these intangible assets will be recognized as a reduction of royalty revenue. We review our intangible assets for impairment when events or changes in circumstances indicate that the carrying amount of such assets may not be recoverable. The recoverability of finite-lived intangible assets is measured by comparing the asset's carrying amount to the expected undiscounted future cash flows that the asset is expected to generate. The determination of recoverability typically requires various estimates and assumptions, including estimating the useful life over which cash flows will occur, their amount, and the asset's residual value, if any. We derive the required cash flow estimates from near-term forecasted product sales and long-term projected sales in the corresponding market.
Research and Development Costs
Research and development costs are expensed in the period that services are rendered or goods are received. Research and development costs consist of salaries and benefits, laboratory supplies and facility costs, as well as fees paid to third parties that conduct certain research and development activities on behalf of us, net of certain external research and development costs reimbursed under our collaborative arrangements.
Preclinical Study and Clinical Study Expenses
A substantial portion of our preclinical studies and all of our clinical studies have been performed by third-party contract research organizations (CROs). Some CROs bill monthly for services performed, while others bill based upon milestones achieved. We review the activities performed under the significant contracts each quarter. For preclinical studies, the significant factors used in estimating accruals include the percentage of work completed to date and contract milestones achieved. For clinical study expenses, the significant factors used in estimating accruals include the number of patients enrolled and percentage of work completed to date. Vendor confirmations are obtained for contracts with longer duration when necessary to validate our estimate of expenses. Our estimates are highly dependent upon the timeliness and accuracy of the data provided by our CROs regarding the status of each program and total program spending and adjustments are made when deemed necessary.
Advertising Expenses
We expense the costs of advertising, including promotional expenses, as incurred. Advertising expenses were not significant in 2013 and were $0 in 2012 and 2011.
Fair Value of Stock-Based Compensation Awards
We use the Black-Scholes-Merton option pricing model to estimate the fair value of options granted under our equity incentive plans and rights to acquire stock granted under our employee stock purchase plan (ESPP). The Black-Scholes-Merton option valuation model requires the use of assumptions, including the expected term of the award and the expected stock price volatility. We use the "simplified" method as described in Staff Accounting Bulletin No. 107, "Share-Based Payment," for the expected option term because the usage of its historical option exercise data is limited due to post-IPO exercise restrictions. Beginning April 1, 2011, we used our historical volatility to estimate expected stock price volatility. Prior to April 1, 2011, we used peer company price volatility to estimate expected stock price volatility due to our limited historical common stock price volatility since our initial public offering in 2004.
Restricted Stock Units (RSUs) and Restricted Stock Awards (RSAs) are measured based on the fair market values of the underlying stock on the dates of grant.
Stock-based compensation expense was calculated based on awards ultimately expected to vest and was reduced for estimated forfeitures at the time of grant and revised, if necessary, in subsequent periods if actual forfeitures differed from those estimates. Our estimated annual forfeiture rates for stock options, RSUs and RSAs are based on our historical forfeiture experience.
The estimated fair value of stock options, RSUs and RSAs is expensed on a straight-line basis over the expected term of the grant and the estimated fair value of performance-contingent RSUs and RSAs is expensed using an accelerated method over the term of the award once we have determined that it is probable that performance milestones will be achieved. Compensation expense for RSUs and RSAs that contain performance conditions is based on the grant date fair value of the award. Compensation expense is recorded over the requisite service period based on management's best estimate as to whether it is probable that the shares awarded are expected to vest. We assess the probability of the performance milestones being met on a continuous basis.
Compensation expense for purchases under the ESPP is recognized based on the fair value of the common stock on the date of offering, less the purchase discount percentage provided for in the plan.
We have not recognized, and do not expect to recognize in the near future, any income tax benefit related to employee stock-based compensation expense as a result of the full valuation allowance on our deferred tax assets including deferred tax assets related to our net operating loss carryforwards.
Other Income (Expense), net
In May 2013, we entered into a royalty participation agreement with Elan Corporation, plc ("Elan"). The closing of the transaction was subject to closing conditions, including the approval of the transaction by Elan's shareholders. Elan's shareholders did not approve the transaction at an Extraordinary General Meeting. Subsequently, we terminated the agreement and, as a result, Elan paid us a $10.0 million termination fee in June 2013, which is reflected in other income on the consolidated statements of operations. Other expense is comprised of third party expenses related to the aforementioned royalty participation agreement and the change in the estimated fair value of the capped-call instruments related to our convertible subordinated notes issued in January 2013, which is reflected in other expense.
Income Taxes
We utilize the asset and liability method of accounting for income taxes. Under this method, deferred tax assets and liabilities are determined based on differences between financial reporting and tax basis of assets and liabilities and are measured using enacted tax rates and laws that will be in effect when the differences are expected to reverse. A valuation allowance is provided when it is more likely than not that some portion or all of a deferred tax asset will not be realized.
None of our currently unrecognized tax benefits would affect our effective income tax rate if recognized, due to the valuation allowance that currently offsets our deferred tax assets. We do not anticipate the total amount of unrecognized income tax benefits relating to uncertain tax positions existing at December 31, 2013 will significantly increase or decrease in the next 12 months.
We assess all material positions taken in any income tax return, including all significant uncertain positions, in all tax years that are still subject to assessment or challenge by relevant taxing authorities. Assessing an uncertain tax position begins with the initial determination of the position's sustainability and is measured at the largest amount of benefit that is greater than 50% likely to be realized upon ultimate settlement. As of each balance sheet date, unresolved uncertain tax positions must be reassessed, and we will determine whether: the factors underlying the sustainability assertion have changed and whether the amount of the recognized tax benefit is still appropriate.
The recognition and measurement of tax benefits requires significant judgment. Judgments concerning the recognition and measurement of a tax benefit might change as new information becomes available.
Comprehensive Loss
Comprehensive loss is comprised of net loss and other comprehensive income (loss). Other comprehensive income (loss) consists of changes in unrealized gains and losses on our available-for-sale securities, net of tax.
Related Parties
Transactions with GSK are described in Note 3, "Collaborative Arrangements".
Robert V. Gunderson, Jr. is a director of the Company. We have engaged Gunderson Dettmer Stough Villeneuve Franklin & Hachigian, LLP, of which Mr. Gunderson is a partner, as our primary legal counsel. Fees incurred in the ordinary course of business were $3.2 million in 2013, $1.2 million in 2012, and $0.3 million in 2011.

Net_Loss_per_Share

Net Loss per Share	12 Months Ended
	Dec. 31, 2013
Net Loss per Share	'
Net Loss per Share	'
	2. Net Loss per Share
	Basic net loss per share is computed by dividing net loss by the weighted-average number of shares of common stock outstanding, less RSAs subject to forfeiture. Diluted net loss per share is computed by dividing net loss by the weighted-average number of shares of common stock outstanding, less RSAs subject to forfeiture, plus all additional common shares that would have been outstanding, assuming dilutive potential common shares had been issued for other dilutive securities.
	For the years ended December 31, 2013, 2012 and 2011, diluted and basic net loss per share were identical since potential common shares were excluded from the calculation, as their effect was anti-dilutive.
	The computations for basic and diluted net loss per share were as follows:
		Year Ended December 31,
	(In thousands, except for per share data)	2013			2012			2011
	Numerator:
	Net loss	$	(170,701	)	$	(18,542	)	$	(115,344	)
	Denominator:
	Weighted-average shares of stock outstanding		104,789			93,410			84,493
	Less: unvested RSAs		(2,364	)		(2,501	)		(2,442	)
	Weighted-average shares used to compute basic and diluted net loss per share		102,425			90,909			82,051
	Net loss per share:
	Basic and diluted net loss per share	$	(1.67	)	$	(0.20	)	$	(1.41	)
	Anti-dilutive Securities
	The following common equivalent shares were not included in the computation of diluted net loss per share because their effect was anti-dilutive:
		Year Ended December 31,
	(In thousands)	2013			2012			2011
	Shares issuable under Equity Incentive Plans and ESPP		4,095			5,367			5,464
	Shares issuable upon the conversion of convertible subordinated notes		2,780			6,668			6,668
	Total anti-dilutive securities		6,875			12,035			12,132

Collaborative_Arrangements

Collaborative Arrangements	12 Months Ended
	Dec. 31, 2013
Collaborative Arrangements	'
Collaborative Arrangements	'
	3. Collaborative Arrangements
	Revenues from Collaborative Arrangements
	We recognized total net revenue as follows:
		Year Ended December 31,
	(In thousands)	2013			2012			2011
	GSK	$	4,532		$	5,613		$	9,658
	Astellas		—			125,788			14,854
	Other		226			4,357			—
	Total net revenue	$	4,758		$	135,758		$	24,512
	GSK
	LABA Collaboration
	In November 2002, we entered into our long-acting beta2 agonist (LABA) collaboration with GSK to develop and commercialize once-daily LABA products for the treatment of chronic obstructive pulmonary disease (COPD) and asthma. For the treatment of COPD, the collaboration has developed two combination products: (1) RELVAR®/BREO® ELLIPTA® (FF/VI), a once-daily combination medicine consisting of a LABA, vilanterol (VI), and an inhaled corticosteroid (ICS), fluticasone furoate (FF) and (2) ANORO™ ELLIPTA™ (UMEC/VI), a once-daily medicine combining a long-acting muscarinic antagonist (LAMA), umeclidinium bromide (UMEC), with a LABA, VI. For the treatment of asthma, RELVAR® ELLIPTA® is approved in multiple regions outside of North America and the collaboration is further developing FF/VI for the U.S.
	In the event that a product containing VI is successfully developed and commercialized, we will be obligated to make milestone payments to GSK, which could total as much as $220.0 million if both a single-agent and a combination product or two different combination products are launched in multiple regions of the world. Of these potential payments to GSK for registrational and launch-related milestone fees, we have paid a total of $85.0 million and accrued a liability of $40.0 million as of December 31, 2013 and recorded an additional $15.0 million payment in January 2014. These milestone fees paid or owed to GSK were capitalized as finite-lived intangible assets, which are being amortized over their estimated useful life. We estimate the remaining potential milestone payments of $80.0 million could be payable by the end of 2014.
	Total milestone fees paid of $85.0 million as of December 31, 2013 resulted from the following:
	•
	In May 2013, the U.S. Food and Drug Administration (FDA) approved BREO® ELLIPTA® as an inhaled long-term, once-daily maintenance treatment of airflow obstruction in patients with COPD, including chronic bronchitis and/or emphysema. It is also indicated to reduce exacerbations of COPD in patients with a history of exacerbations.
	•
	In September 2013, the Japanese Ministry of Health, Labour and Welfare (MHLW) approved RELVAR® ELLIPTA® for the treatment of bronchial asthma in cases where concurrent use of inhaled corticosteroid and long-acting inhaled beta2 agonist is required.
	•
	In October 2013, BREO® ELLIPTA® was launched in the U.S. for the treatment of COPD.
	•
	In November 2013, the European Commission granted marketing authorization for RELVAR® ELLIPTA® for the regular treatment of asthma and the systematic treatment of COPD.
	Total milestone fees accrued as liabilities of $40.0 million as of December 31, 2013 resulted from the following:
	•
	In December 2013, RELVAR® ELLIPTA® was launched in Japan for the treatment of bronchial asthma.
	•
	In December 2013, the U.S. FDA approved ANORO™ ELLIPTA™ as a combination anticholinergic/long-acting beta2-adrenergic agonist (LABA) indicated for the long-term, once-daily, maintenance treatment of airflow obstruction in patients with chronic obstructive pulmonary disease (COPD), including chronic bronchitis and/or emphysema.
	Total milestone fees recorded of $15.0 million in January 2014 resulted from the following:
	•
	In January 2014, RELVAR® ELLIPTA® was launched in the European Union.
	We are entitled to receive annual royalties from GSK on sales of RELVAR®/BREO® ELLIPTA® as follows: 15% on the first $3.0 billion of annual global net sales and 5% for all annual global net sales above $3.0 billion. Sales of single-agent LABA medicines and combination medicines would be combined for the purposes of this royalty calculation. For other products combined with a LABA from the LABA collaboration, such as ANORO™ ELLIPTA™, royalties are upward tiering and range from 6.5% to 10%.
	2004 Strategic Alliance
	In March 2004, we entered into our strategic alliance with GSK (the Strategic Alliance agreement and the LABA collaboration are together referred to herein as the GSK Agreements). Under this alliance, GSK received an option to license exclusive development and commercialization rights to product candidates from certain of our discovery programs on pre-determined terms and on an exclusive, worldwide basis. Upon GSK's decision to license a program, GSK is responsible for funding all future development, manufacturing and commercialization activities for product candidates in that program. In addition, GSK is obligated to use diligent efforts to develop and commercialize product candidates from any program that it licenses. If the program is successfully advanced through development by GSK, we are entitled to receive clinical, regulatory and commercial milestone payments and royalties on any sales of medicines developed from the program. If GSK chooses not to license a program, we retain all rights to the program and may continue the program alone or with a third party. GSK has no further option rights on any of our research or development programs under the strategic alliance.
	In 2005, GSK licensed our bifunctional muscarinic antagonist-beta2 agonist (MABA) program for the treatment of COPD, and in October 2011, we and GSK expanded the MABA program by adding six additional Theravance-discovered preclinical MABA compounds (the "Additional MABAs"). GSK's development, commercialization, milestone and royalty obligations under the strategic alliance remain the same with respect to GSK961081 ('081), the lead compound in the MABA program. GSK is obligated to use diligent efforts to develop and commercialize at least one MABA within the MABA program, but may terminate progression of any or all Additional MABAs at any time and return them to us, at which point we may develop and commercialize such Additional MABAs alone or with a third party. Both GSK and we have agreed not to conduct any MABA clinical studies outside of the strategic alliance so long as GSK is in possession of the Additional MABAs. If a single-agent MABA medicine containing '081 is successfully developed and commercialized, we are entitled to receive royalties from GSK of between 10% and 20% of annual global net sales up to $3.5 billion, and 7.5% for all annual global net sales above $3.5 billion. If a MABA medicine containing '081 is commercialized as a combination product, such as '081/FF, the royalty rate is 70% of the rate applicable to sales of the single-agent MABA medicine. For single-agent MABA medicines containing an Additional MABA, we are entitled to receive royalties from GSK of between 10% and 15% of annual global net sales up to $3.5 billion, and 10% for all annual global net sales above $3.5 billion. For combination products containing an Additional MABA, such as a MABA/ICS combination, the royalty rate is 50% of the rate applicable to sales of the single-agent MABA medicine. If a MABA medicine containing '081 is successfully developed and commercialized in multiple regions of the world, we could earn total contingent payments of up to $125.0 million for a single-agent medicine and up to $250.0 million for both a single-agent and a combination medicine. If a MABA medicine containing an Additional MABA is successfully developed and commercialized in multiple regions of the world, we could earn total contingent payments of up to $129.0 million.
	Agreements Entered into with GSK in Connection with the Spin-Off
	In conjunction with the planned spin-off of Theravance Biopharma, on March 3, 2014, we, Theravance Biopharma and GSK entered into a series of agreements clarifying how the companies will implement the spin-off and operate following the spin-off. We, Theravance Biopharma and GSK entered into a three-way master agreement providing for GSK's consent to the spin-off provided certain conditions are met. In addition, we and GSK also entered into amendments of our LABA collaboration and Strategic Alliance agreements, and Theravance Biopharma and GSK entered into a governance agreement, a registration rights agreement and an extension agreement. The three-way master agreement is currently effective, but will terminate if the spin-off is not effected by June 30, 2014, and the other agreements will become effective upon the spin-off, provided that the spin-off is effected on or before June 30, 2014.
	The amendments to the GSK Agreements do not change the economics or royalty rates. The amendments to the GSK Agreements do provide that GSK's diligent efforts obligations regarding commercialization matters under both agreements will change upon regulatory approval in either the United States or the European Union of UMEC/VI/FF or a MABA in combination with FF. Upon such regulatory approval, GSK's diligent efforts obligations as to commercialization matters under the GSK Agreements will have the objective of focusing on the best interests of patients and maximizing the net value of the overall portfolio of products under the collaboration agreement and strategic alliance agreement. Since GSK's commercialization efforts following such regulatory approval will be guided by a portfolio approach across products in which we will retain our full interests upon the spin-off and also products in which we will have retained only a portion of our interests upon the planned spin-off transaction, GSK's commercialization efforts may have the effect of reducing the overall value of our remaining interests in the GSK Agreements after the spin-off.
	Purchases of Common Stock under the Company's Governance Agreement and Common Stock Purchase Agreements with GSK
	Prior to 2013, affiliates of GSK purchased an aggregate of 26,411,103 shares of our common stock. In 2013, GSK purchased 3,504,970 shares of our common stock pursuant to its periodic "top-up" rights under our Amended and Restated Governance Agreement, dated as of June 4, 2004, as amended, among us, GSK and certain GSK affiliates, for a total investment of $126.0 million.
	GSK Contingent Payments and Revenue
	The potential future contingent payments receivable related to the MABA program of $363.0 million are not deemed substantive milestones due to the fact that the achievement of the event underlying the payment predominantly relates to GSK's performance of future development, manufacturing and commercialization activities for product candidates after licensing the program.
	Net revenue recognized from GSK under the LABA collaboration and strategic alliance agreements was as follows:
		Year Ended December 31,
	(In thousands)	2013			2012			2011
	Royalty revenue	$	1,945		$	—		$	—
	Amortization of intangible assets		(743	)		—			—
	Net royalty revenue		1,202			—			—
	LABA collaboration(1)		1,815			3,629			4,718
	Strategic alliance agreement		—			—			1,858
	Strategic alliance—MABA program license(2)		1,515			1,984			3,082
	Total net revenue from GSK	$	4,532		$	5,613		$	9,658
	-1
	We revised the estimated performance period for the LABA program based on its progress in the fourth quarter of 2011, resulting in an increase to net loss of $0.4 million for the year ended December 31, 2011. Deferred revenue under this agreement was fully recognized in 2013.
	-2
	We revised the estimated performance period for the MABA program based on its progress as follows: (i) in the fourth quarter of 2011, resulting in an increase to net loss of $0.2 million for the year ended December 31, 2011, (ii) in the fourth quarter of 2012, resulting in an increase to net loss of $0.1 million for the year ended December 31, 2012 and (iii) in the fourth quarter of 2013, resulting in an increase to net loss of $0.1 million for the year ended December 31, 2013. We do not expect that these revisions will have a material impact on future revenue recognized under this program.
	Merck
	Research Collaboration and License Agreement
	In October 2012, we entered into a research collaboration and license agreement (the "Research Collaboration and License Agreement") with Merck, known as MSD outside the United States and Canada, to discover, develop and commercialize novel small molecule therapeutics directed towards a target being investigated for the treatment of hypertension and heart failure. Under the agreement, we granted Merck a worldwide, exclusive license to our therapeutic candidates. We received a $5.0 million upfront payment in November 2012. Also, we received funding for research and were eligible for potential future contingent payments totaling up to $148.0 million for the first indication and royalties on worldwide annual net sales of any products derived from the collaboration. The initial research term was twelve months, with optional extensions by mutual agreement. Merck had the right to terminate the agreement at any time and provided Theravance with notice of termination in September 2013. The agreement was terminated in December 2013.
	Under the Research Collaboration and License Agreement, the significant deliverables were determined to be the license, research services and committee participation. We determined that the license represents a separate unit of accounting because the license has standalone value. The license, which includes rights to our underlying technologies for our therapeutic candidates, permit Merck to perform all efforts necessary to use our technologies to bring a therapeutic candidate through development and, upon regulatory approval, commercialization. We based the best estimate of selling price on potential future cash flows under the arrangement over the estimated development period. We determined that the research services represent a separate unit of accounting and based the best estimate of selling price on the nature and timing of the services to be performed. We determined that the committee participation represents a separate unit of accounting as Merck could negotiate for and/or acquire these services from other third-parties and based the best estimate of selling price on the nature and timing of the services to be performed.
	The $5.0 million upfront payment received in November 2012 was allocated to the three units of accounting based on the relative selling price method as follows: $4.4 million to the license, $0.4 million to the research services and $0.2 million to the committee participation. We recognized revenue of $4.4 million from the license in 2012 as the technical transfer activities were complete and the associated unit of accounting was deemed delivered. The amount of the upfront payment allocated to the research services was deferred and is being recognized as a reduction of research and development expense as the underlying services are performed, since the nature of the research services is more appropriately characterized as research and development expense consistent with the research reimbursements being received. The amount of the upfront payment allocated to the committee participation was deferred and recognized as revenue over the estimated performance period.
	Due to the notice of termination, we revised the estimated performance period resulting in an increase in revenue of $206,000 in 2013. Revenue recognized from Merck under the collaboration agreement was $226,000 in 2013.
	Clinigen Group
	Commercialization Agreement
In March 2013, we entered into a commercialization agreement (the "Clinigen Commercialization Agreement") with Clinigen Group plc (Clinigen) to commercialize VIBATIV® for the treatment of hospital acquired nosocomial pneumonia, including ventilator-associated pneumonia, known or suspected to be caused by methicillin resistant Staphylococcus aureus (MRSA) when other alternatives are not suitable. Under the agreement, we granted Clinigen exclusive commercialization rights in the European Union and certain other European countries (including Switzerland and Norway). We received a $5.0 million upfront payment in March 2013. Also, we are eligible to receive tiered royalty payments on net sales of VIBATIV®, ranging from 20% to 30%. We are responsible, either directly or through our vendors or contractors, for supplying at Clinigen's expense both API and finished drug product for Clinigen's commercialization activities. The agreement has a term of at least 15 years, with an option to extend exercisable by Clinigen. However, Clinigen may terminate the agreement at any time after it has initiated commercialization upon 12 months' advance notice.
Under the Clinigen Commercialization Agreement, the significant deliverables were determined to be the license, committee participation and manufacturing supply. We determined that the license represents a separate unit of accounting as the license, which includes rights to our underlying technologies for VIBATIV®, has standalone value because the rights conveyed permit Clinigen to perform all efforts necessary to use our technologies to bring the compound through commercialization. We based the best estimate of selling price for the license on potential future cash flows under the arrangement over the estimated commercialization period. We determined that the committee participation represents a separate unit of accounting as Clinigen could negotiate for and/or acquire these services from other third parties, and we based the best estimate of selling price on the nature and timing of the services to be performed. We based the best estimate of selling price for the manufacturing supply on a fully burdened cost to purchase and transfer the underlying API and finished goods from our third party contract manufacturer.
The $5.0 million upfront payment received in 2013 was allocated to two units of accounting based on the relative selling price method as follows: $4.9 million to the license and $0.1 million to the committee participation. We did not recognize any revenue from the license and committee participation as the technical transfer activities were not completed as of December 31, 2013 and the associated units of accounting were not delivered. The amount of the upfront payment allocated to the committee participation was deferred and will be recognized as revenue over the estimated performance period. Amounts received under a future separate supply agreement for API and finished goods, which will be manufactured by our third party contract manufacturers, will be recognized as revenue to the extent of future API and finished goods inventory sales.
R-Pharm CJSC
Development and Commercialization Agreements
In October 2012, we entered into two development and commercialization agreements with R-Pharm CJSC (R-Pharm): one to develop and commercialize VIBATIV® (the "VIBATIV® Development and Commercialization Agreement") and the other to develop and commercialize TD-1792 (the "TD-1792 Development and Commercialization Agreement"), one of our investigational glycopeptide-cephalosporin heterodimer antibiotics for the treatment of Gram-positive infections. Under each agreement, we granted R-Pharm exclusive development and commercialization rights in Russia, Ukraine, other member countries of the Commonwealth of Independent States, and Georgia. We received $1.1 million in upfront payments for each agreement. Also, we are eligible to receive potential future contingent payments totaling up to $10.0 million for both agreements and royalties on net sales by R-Pharm of 15% from TD-1792 and 25% from VIBATIV®. The contingent payments are not deemed substantive milestones due to the fact that the achievement of the event underlying the payment predominantly relates to R-Pharm's performance of future development and commercialization activities.
TD-1792
Under the TD-1792 Development and Commercialization Agreement, the significant deliverables were determined to be the license, committee participation and a contingent obligation to supply R-Pharm with API compound at R-Pharm's expense, either directly or through our contract manufacturer. We determined that the license represents a separate unit of accounting as the license, which includes rights to our underlying technologies for TD-1792, has standalone value because the rights conveyed permit R-Pharm to perform all efforts necessary to use our technologies to bring the compounds through development and, upon regulatory approval, commercialization. Also, we determined that the committee participation represents a separate unit of accounting as R-Pharm could negotiate for and/or acquire these services from other third parties, and we based the best estimate of selling price on the nature and timing of the services to be performed. In March 2013, we entered into a supply agreement for TD-1792 API compound under which we will sell our existing API compound to R-Pharm. Upon execution of this supply agreement, we determined that the supply agreement represents a separate unit of accounting under the development and commercialization arrangement and based the best estimate of selling price for the supply agreement on our fully burdened cost to manufacture the underlying API.
The $1.1 million upfront payment for the TD-1792 agreement was allocated to two units of accounting based on the relative selling price method as follows: $0.9 million to the license and $0.1 million to the committee participation. The amount allocated to the license was deferred and will be recognized as revenue upon completion of technical transfer for the underlying license. The amount allocated to committee participation was deferred and is being recognized as revenue over the estimated performance period.
Amounts to be received under the supply agreement described above will be recognized as revenue to the extent R-Pharm purchases API compound from us.
VIBATIV®
Under the VIBATIV® Development and Commercialization Agreement, the significant deliverables were determined to be the license, committee participation and a contingent obligation to supply R-Pharm with API compound at R-Pharm's expense, subject to entering into a future supply agreement. We determined that the license represents a separate unit of accounting as the license, which includes rights to our underlying technologies for VIBATIV®, has standalone value because the rights conveyed permit R-Pharm to perform all efforts necessary to use our technologies to bring the compounds through development and, upon regulatory approval, commercialization. We based the best estimate of selling price for the license on potential future cash flows under the arrangement over the estimated performance period. We determined that the committee participation represents a separate unit of accounting as R-Pharm could negotiate for and/or acquire these services from other third parties, and we based the best estimate of selling price on the nature and timing of the services to be performed.
The $1.1 million upfront payment for the VIBATIV® agreement was allocated to two units of accounting based on the relative selling price method as follows: $1.0 million to the license and $33,000 to the committee participation. The amount allocated to the license was deferred and will be recognized as revenue upon completion of technical transfer. The amount allocated to committee participation was deferred and is being recognized as revenue over the estimated performance period.
Alfa Wassermann
Development and Collaboration Arrangement
In October 2012, we entered into a development and collaboration arrangement with Alfa Wassermann società per azioni (S.p.A.) ("Alfa Wassermann") for velusetrag under which the parties agreed to collaborate in the execution of a two-part Phase 2 program to test the efficacy, safety and tolerability of velusetrag in the treatment of patients with gastroparesis (a medical condition consisting of a paresis (partial paralysis) of the stomach, resulting in food remaining in the stomach for a longer time than normal). Alfa Wassermann has an exclusive option to develop and commercialize velusetrag in the European Union, Russia, China, Mexico and certain other countries, while we retain full rights to velusetrag in the United States, Canada, Japan and certain other countries. We are entitled to receive funding for the Phase 2a study and a subsequent Phase 2b study if the parties agree to proceed. If Alfa Wassermann exercises its license option at the completion of the Phase 2 program, then we are entitled to receive a $10.0 million option fee. If velusetrag is successfully developed and commercialized, we are entitled to receive potential future contingent payments totaling up to $53.5 million, and royalties on net sales by Alfa Wassermann ranging from the low teens to 20%.
Former Collaborative Arrangement with Astellas
License, Development and Commercialization Agreement
In November 2005, we entered into a global collaboration arrangement with Astellas for the license, development and commercialization of VIBATIV®. Under this agreement, Astellas paid us non-refundable cash payments totaling $191.0 million. In January 2012, Astellas exercised its right to terminate the collaboration agreement. The rights previously granted to Astellas ceased upon termination of the agreement, and Astellas stopped all promotional sales efforts. Pursuant to the terms of the agreement, Astellas is entitled to a ten-year, 2% royalty on future net sales of VIBATIV®. As such, we recognized as revenue $125.8 million of deferred revenue related to Astellas in 2012, and we are no longer eligible to receive any further milestone payments from Astellas.
Net revenue recognized from Astellas under the former collaborative arrangement was as follows:
	Year Ended December 31,
(In thousands)	2013			2012			2011
Recognition of deferred revenue	$	—		$	125,819		$	—
Amortization of deferred revenue		—			—			12,975
Royalties from net sales of VIBATIV®		—			—			2,422
Proceeds from VIBATIV® delivered to Astellas		—			—			1,171
Cost of VIBATIV® delivered to Astellas		—			—			(1,177	)
Cost of unrealizable VIBATIV® inventories		—			—			(537	)
Astellas-labeled product sales allowance		—			(31	)		—
Total net revenue from Astellas	$	—		$	125,788		$	14,854
Reimbursement of R&D Costs
Under the GSK, Merck, Alfa Wasserman, R-Pharm and Astellas collaboration arrangements, we are entitled to reimbursement of certain R&D costs. Our policy is to account for the reimbursement payments by its collaboration partners as reductions to R&D expense.
The following table summarizes the reductions to R&D expenses related to the reimbursement payments:
	Year Ended December 31,
(In thousands)	2013			2012			2011
GSK	$	473		$	168		$	449
Merck		4,937			756			—
Alfa Wasserman		1,500			185			—
R-Pharm		86			—			—
Astellas		—			—			390
Total reduction to R&D expense	$	6,996		$	1,109		$	839

AvailableforSale_Securities

Available-for-Sale Securities	12 Months Ended
	Dec. 31, 2013
Available-for-Sale Securities	'
Available-for-Sale Securities	'
	4. Available-for-Sale Securities
	The classification of available-for-sale securities in the consolidated balance sheets is as follows:
	(In thousands)	December 31,		December 31,
		2013		2012
	Cash and cash equivalents	$	125,009	$	86,298
	Short-term investments		321,615		153,640
	Marketable securities		55,374		95,194
	Restricted cash		833		833
	Total	$	502,831	$	335,965
	The estimated fair value of available-for-sale securities is based on quoted market prices for these or similar investments that were based on prices obtained from a commercial pricing service. Available-for-sale securities are summarized below:
		December 31, 2013
	(In thousands)	Amortized		Gross		Gross			Estimated
		Cost		Unrealized		Unrealized			Fair Value
				Gains		Losses
	U.S. government securities	$	42,104	$	55	$	(1	)	$	42,158
	U.S. government agencies		141,278		61		(8	)		141,331
	U.S. corporate notes		94,923		54		—			94,977
	U.S. commercial paper		102,021		2		(1	)		102,022
	Money market funds		122,343		—		—			122,343
	Total	$	502,669	$	172	$	(10	)	$	502,831
		December 31, 2012
	(In thousands)	Amortized		Gross		Gross			Estimated
		Cost		Unrealized		Unrealized			Fair Value
				Gains		Losses
	U.S. government securities	$	27,197	$	10	$	(2	)	$	27,205
	U.S. government agencies		115,397		85		(16	)		115,466
	U.S. corporate notes		91,544		32		(10	)		91,566
	U.S. commercial paper		23,082		—		—			23,082
	Money market funds		78,646		—		—			78,646
	Total	$	335,866	$	127	$	(28	)	$	335,965
	At December 31, 2013, all of the available-for-sale securities had contractual maturities within two years and the average duration of marketable securities was approximately seven months. We do not intend to sell the investments that are in an unrealized loss position, and it is unlikely that we will be required to sell the investments before recovery of their amortized cost basis, which may be maturity. We have determined that the gross unrealized losses on our marketable securities at December 31, 2013 were temporary in nature. All marketable securities with unrealized losses at December 31, 2013 have been in a loss position for less than twelve months.
	During 2013, 2012, and 2011, we sold available-for-sale securities totaling $22.6 million, $49.7 million and $17.3 million, and the related realized gains and losses were not significant in any of those periods.

Fair_Value_Measurements

Fair Value Measurements	12 Months Ended
	Dec. 31, 2013
Fair Value Measurements	'
Fair Value Measurements	'
	5. Fair Value Measurements
	We define fair value as the exchange price that would be received for an asset or paid to transfer a liability (an exit price) in the principal or most advantageous market for the asset or liability in an orderly transaction between market participants on the measurement date.
	Our valuation techniques are based on observable and unobservable inputs. Observable inputs reflect readily obtainable data from independent sources, while unobservable inputs reflect our market assumptions. We classify these inputs into the following hierarchy:
	Level 1—Quoted prices for identical instruments in active markets.
	Level 2—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—Unobservable inputs and little, if any, market activity for the assets.
	Our available-for-sale securities are measured at fair value on a recurring basis and our convertible subordinated notes are not measured at fair value on a recurring basis. The estimated fair values were as follows:
		Estimated Fair Value Measurements at
		Reporting Date Using:
		Quoted Prices		Significant		Significant
		in Active		Other		Unobservable
		Markets for		Observable		Inputs
		Identical		Inputs
		Assets
	Types of Instruments	Level 1		Level 2		Level 3		Total
	(In thousands)
	Assets at December 31, 2013:
	U.S. government securities	$	42,158	$	—	$	—	$	42,158
	U.S. government agency securities		98,236		43,095		—		141,331
	U.S. corporate notes		61,591		33,386		—		94,977
	U.S. commercial paper		3,499		98,523		—		102,022
	Money market funds		122,343		—		—		122,343
	Total assets measured at estimated fair value	$	327,827	$	175,004	$	—	$	502,831
	Liabilities at December 31, 2013:
	Convertible subordinated notes due 2023	$	—	$	408,250	$	—	$	408,250
		Estimated Fair Value Measurements at
		Reporting Date Using:
		Quoted Prices		Significant		Significant
		in Active		Other		Unobservable
		Markets for		Observable		Inputs
		Identical		Inputs
		Assets
	Types of Instruments	Level 1		Level 2		Level 3		Total
	(In thousands)
	Assets at December 31, 2012:
	U.S. government securities	$	27,205	$	—	$	—	$	27,205
	U.S. government agency securities		56,969		58,497		—		115,466
	U.S. corporate notes		40,472		51,094		—		91,566
	U.S. commercial paper		—		23,082		—		23,082
	Money market funds		78,646		—		—		78,646
	Total assets measured at estimated fair value	$	203,292	$	132,673	$	—	$	335,965
	Liabilities at December 31, 2012:
	Convertible subordinated notes due 2015	$	—	$	194,050	$	—	$	194,050
	At December 31, 2013, securities with a total fair value of $6.8 million were measured using Level 1 inputs in comparison to December 31, 2012, at which time the securities had a fair value of $7.0 million and were measured using Level 2 inputs. The transfer to Level 1 from Level 2 was primarily the result of increased trading volume of the securities at and around December 31, 2013, compared to December 31, 2012.
	At December 31, 2013, securities with a total fair value of $2.9 million were measured using Level 2 inputs in comparison to December 31, 2012, at which time the securities had a fair value of $2.9 million and were measured using Level 1 inputs. The transfer to Level 2 from Level 1 was primarily the result of decreased trading volume of the securities at and around December 31, 2013, compared to December 31, 2012.
	At December 31, 2012, there were no transfers from Level 1 to Level 2 or from Level 2 to Level 1 in comparison to December 31, 2011.

Inventories

Inventories	12 Months Ended
	Dec. 31, 2013
Inventories	'
Inventories	'
	6. Inventories
	Inventories are as follows:
		December 31,
	(In thousands)	2013		2012
	Raw materials	$	5,138	$	5,668
	Work-in-process		360		1,846
	Finished goods		4,908		—
	Total inventories	$	10,406	$	7,514

Property_and_Equipment

Property and Equipment	12 Months Ended
	Dec. 31, 2013
Property and Equipment	'
Property and Equipment	'
	7. Property and Equipment
	Property and equipment consists of the following:
		December 31,
	(In thousands)	2013			2012
	Computer equipment	$	3,084		$	3,027
	Software		5,391			5,073
	Furniture and fixtures		3,890			3,829
	Laboratory equipment		31,910			29,229
	Leasehold improvements		17,769			17,416
			62,044			58,574
	Less accumulated depreciation and amortization		(51,806	)		(49,420	)
	Property and equipment, net	$	10,238		$	9,154
	Depreciation expense was $2.7 million in 2013, $3.3 million in 2012, and $3.8 million in 2011. The change in accumulated depreciation is net of asset retirements. In 2012, we recognized a write-off of $0.2 million related to assets that could no longer be used in operations.

Intangible_Assets

Intangible Assets	12 Months Ended
	Dec. 31, 2013
Intangible Assets	'
Intangible Assets	'
	8. Intangible Assets
	Intangible assets, which consist of registrational and launch-related milestone fees paid or owed to GSK, were as follows:
		December 31, 2013
	(In thousands)	Weighted		Gross		Accumulated			Net Carrying
		Average		Carrying		Amortization			Value
		Remaining		Value
		Amortization
		Period
		(Years)
	FDA approval and launch of BREO® ELLIPTA® in the U.S.		15.7	$	60,000	$	(632	)	$	59,368
	MHLW approval and launch of RELVAR® ELLIPTA® in Japan		14.9		20,000		(111	)		19,889
	European Commission approval of RELVAR® ELLIPTA®		15		15,000		—			15,000
	FDA approval of ANOROTM ELLIPTATM in the U.S.		15.2		30,000		—			30,000
	Total intangible assets			$	125,000	$	(743	)	$	124,257
	Additional information regarding these milestone fees is included in Note 3 "Collaborative Arrangements." Amortization expense for the BREO® ELLIPTA® intangible asset for the U.S. region and the RELVAR® ELLIPTA® intangible asset for the Japan region began in the fourth quarter of 2013 and is recorded as a reduction in revenue from collaborative arrangements. Estimated annual amortization expense of intangible assets is $7.1 million for 2014, $8.1 million for each of the years from 2015 to 2018 and $84.7 million thereafter.

LongTerm_Debt

Long-Term Debt	12 Months Ended
	Dec. 31, 2013
Long-Term Debt	'
Long-Term Debt	'
	9. Long-Term Debt
	Long-term debt is as follows:
		December 31,
	(In thousands)	2013		2012
	Convertible Subordinated Notes Due 2015	$	—	$	172,500
	Convertible Subordinated Notes Due 2023		287,500		—
	Total long-term debt	$	287,500	$	172,500
	Convertible Subordinated Notes Due 2015
	In January 2008, we completed an underwritten public offering of $172.5 million aggregate principal amount of unsecured 3% Convertible Subordinated Notes due January 15, 2015 (2015 Notes). The financing raised proceeds, net of issuance costs, of $166.7 million. On June 4, 2013, we called for the redemption of all outstanding 2015 Notes, $172.5 million principal amount, pursuant to the redemption right in the indenture governing the 2015 Notes. Any 2015 Notes outstanding on July 5, 2013 were to be redeemed in cash for 100% of the principal amount, plus accrued and unpaid interest to, but excluding, the redemption date. The 2015 Notes were convertible at any time prior to 5:00 p.m. Eastern time on July 3, 2013 into shares of our common stock at a conversion rate of 38.6548 shares per $1,000 principal amount (equivalent to a conversion price of approximately $25.87 per share). All of the convertible subordinated notes, $172.5 million principal amount, were converted into 6,667,932 of our common stock between June 30, 2013 and July 3, 2013 and none were redeemed for cash. As a result of the conversion, unamortized debt issuance costs of $1.3 million was reclassified from other long-term assets to additional paid-in capital in the third quarter of 2013.
	Amortization of the debt issuance costs ceased upon the conversion of the 2015 Notes. Amortization expense was $0.4 million in 2013 and $0.8 million in 2012 and 2011.
	Convertible Subordinated Notes Due 2023
	In January 2013, we completed an underwritten public offering of $287.5 million aggregate principal amount of unsecured convertible subordinated notes, which will mature on January 15, 2023. The financing raised proceeds, net of issuance costs, of approximately $281.2 million, less $36.8 million to purchase two privately-negotiated capped call option transactions in connection with the issuance of the notes. The notes bear interest at the rate of 2.125% per year, that is payable semi-annually in arrears, in cash on January 15 and July 15 of each year, beginning on July 15, 2013. The issuance costs, which are included in other long-term assets, are being amortized over the life of the notes. Unamortized issuance costs totaled $5.8 million as of December 31, 2013. Amortization expense was $0.5 million in 2013.
	The notes are convertible, at the option of the holder, into shares of our common stock at an initial conversion rate of 35.9903 shares per $1,000 principal amount of the notes, subject to adjustment in certain circumstances, which represents an initial conversion price of approximately $27.79 per share. Holders of the notes will be able to require us to repurchase some or all of their notes upon the occurrence of a fundamental change at 100% of the principal amount of the notes being repurchased plus accrued and unpaid interest. We may not redeem the notes prior to their stated maturity date.
	In connection with the offering of the notes, we entered into two privately-negotiated capped call option transactions with a single counterparty. The capped call option transaction is an integrated instrument consisting of a call option on our common stock purchased by us with a strike price equal to the conversion price of $27.79 per share for the underlying number of shares and a cap price of $38.00 per share. The cap component is economically equivalent to a call option sold by us for the underlying number of shares with a strike price of $38.00 per share. As an integrated instrument, the settlement of the capped call coincides with the due date of the convertible debt. At settlement, we will receive from our hedge counterparty a number of our common shares that will range from zero, if the stock price is below $27.79 per share, to a maximum of 2,779,659 shares, if the stock price is above $38.00 per share. However, if the market price of our common stock, as measured under the terms of the capped call transactions, exceeds $38.00 per share, there is no incremental anti-dilutive benefit from the capped call. The aggregate cost of the capped call options was $36.8 million.
	The terms of the capped call option agreements include a provision under which we would have been required to make cash payments to the counterparty if the debt offering did not close. As a result of this provision, the capped calls were recorded as derivative assets between the trade dates and the date of the closing of the debt offering, at which time the cash settlement provision was no longer applicable. Upon the closing of the debt offering, the capped call transactions met the criteria for classification as an equity instrument, and we reclassified the carrying value of the capped call derivative assets to stockholders' equity. The change in fair value between the trade dates and the date at which the capped call derivative assets were reclassified to stockholders' equity was $1.4 million, which was recorded as other income (expense), net, in our consolidated statement of operations in 2013.

StockBased_Compensation

Stock-Based Compensation	12 Months Ended
	Dec. 31, 2013
Stock-Based Compensation	'
Stock-Based Compensation	'
	10. Stock-Based Compensation
	Equity Incentive Plans
	In May 2012, we adopted the 2012 Equity Incentive Plan (2012 Plan). The number of shares of our common stock available for issuance under the 2012 Plan is equal to 6,500,000 shares plus up to 12,667,411 additional shares that may be added to the 2012 Plan in connection with the forfeiture, repurchase, cash settlement or termination of awards outstanding under the 2004 Equity Incentive Plan (2004 Plan), the 2008 New Employee Equity Incentive Plan, the 1997 Stock Plan and the Long-Term Stock Option Plan (collectively, the "Prior Plans") as of December 31, 2011. While a maximum of 12,667,411 shares could be added to the 2012 Plan from the Prior Plans, this assumes that all the awards outstanding on December 31, 2011 will be forfeited, repurchased, cash settled or terminated. Therefore, the actual number that may be added to the 2012 Plan share reserve will likely be lower. No additional awards have been or will be made after May 15, 2012 under the 2004 Plan. Stock options and stock appreciation rights (SARs) will reduce the 2012 Plan reserve by one share for every share granted, and stock awards other than options and SARs granted will reduce the 2012 Plan share reserve by 1.45 shares for every share granted. The 2012 Plan share reserve was also reduced by the number of stock awards granted under the 2004 Plan on or after January 1, 2012, using the same ratios described. As of December 31, 2013, total shares remaining available for issuance under the 2012 Plan were 3,152,390.
	The 2012 Plan provides for the grant of incentive stock options, nonstatutory stock options, restricted stock awards, stock unit awards and SARs to employees, non-employee directors and consultants. Stock options may be granted with an exercise price not less than the fair market value of the common stock on the grant date. Stock options granted to employees generally have a maximum term of 10 years and vest over a four year period from the date of grant; 25% vest at the end of one year, and 75% vest monthly over the remaining three years. We may grant options with different vesting terms from time to time. Unless an employee's termination of service is due to disability or death, upon termination of service, any unexercised vested options will be forfeited at the end of three months or the expiration of the option, whichever is earlier.
	Employee Stock Purchase Plan
	Under the 2004 Employee Stock Purchase Plan (ESPP), our non-officer employees may purchase common stock through payroll deductions at a price equal to 85 percent of the lower of the fair market value of the stock at the beginning of the offering period or at the end of each applicable purchase period. The ESPP provides for consecutive and overlapping offering periods of 24 months in duration, with each offering period composed of four consecutive six-month purchase periods. The purchase periods end on either May 15th or November 15th. ESPP contributions are limited to a maximum of 15 percent of an employee's eligible compensation.
	Our ESPP plan also includes a feature that provides for a new offering period to begin when the fair market value of our common stock on any purchase date during an offering period falls below the fair market value of our common stock on the first day of such offering period. This feature is called a reset. We had resets for new twenty-four month offering periods starting on May 16, 2008, November 16, 2008, May 16, 2010, November 16, 2011, May 16, 2012 and November 16, 2012. We applied modification accounting to determine the incremental fair value associated with the ESPP resets and recognized the related incremental stock- based compensation expense.
	As of December 31, 2013, a total of 2,025,000 shares of common stock were approved and authorized for issuance under the ESPP. Through December 31, 2013, we had issued 1,740,861 shares under the ESPP at an average price of $11.29 per share. As of December 31, 2013, total shares remaining available for issuance under the ESPP were 284,139. As a result of our announcement that our Board of Directors had approved plans to separate our businesses into two independent publicly traded companies, all monies remaining after the purchase on November 15, 2013 were refunded to employees. It was also determined that ESPP shares relating to purchase periods ending after November 15, 2013 were not probable of vesting. Therefore, $0.8 million of compensation expense relating to purchase periods ending after November 15, 2013 was reversed in the fourth quarter of 2013, and any remaining unamortized compensation expense relating to these purchase periods will not be recognized. ESPP was suspended after the November 15, 2013 purchase period.
	Performance-Contingent RSAs
	Over the past three years, the Compensation Committee of the Company's Board of Directors (the "Compensation Committee") has approved grants of performance-contingent RSAs to senior management and a non-executive officer. Generally, these awards have dual triggers of vesting based upon the achievement of certain performance goals by a pre-specified date, as well as a requirement for continued employment. When the performance goals are deemed achieved for these types of awards, time-based vesting and, as a result, recognition of stock-based compensation expense commence.
	Included in these performance-contingent RSAs is the grant of 1,290,000 special long-term retention and incentive performance-contingent RSAs to senior management approved by the Compensation Committee in 2011. The awards have dual triggers of vesting based upon the achievement of certain performance conditions over a six-year timeframe from 2011 through December 31, 2016 and continued employment. The maximum potential expense associated with this program is $28.2 million related to stock-based compensation expense, which would be recognized in increments based on achievement of the performance conditions. As of December 31, 2013, we determined that the achievement of the requisite performance conditions was not probable and, as a result, no compensation expense has been recognized. If sufficient performance conditions are achieved in 2014, then we would recognize up to $6.7 million in stock-based compensation expense associated with these RSAs.
	Performance-Contingent RSUs
	The Compensation Committee of the Company's Board of Directors has approved grants of performance-contingent RSUs to employees. These awards have dual triggers of vesting based upon the successful achievement of certain corporate operating milestones in specified timelines, as well as a requirement for continued employment. When the performance goals are deemed to be probable of achievement for these types of awards, time-based vesting and, as a result, recognition of stock-based compensation expense commences.
	Director Compensation Program
	Our non-employee directors receive compensation for services provided as a director. Each member of our Board who is not an employee receives an annual retainer as well as a fee for each board and committee meeting attended. Commencing on April 27, 2011, chairpersons of the various committees of the Board, the Audit Committee, the Compensation Committee, Nominating/Corporate Governance Committee and the Science and Technology Advisory Committee receive a fixed retainer. The lead independent director also receives a fixed retainer.
	Each of our independent directors receives periodic automatic grants of equity awards under a program implemented under the 2004 Plan. These grants are non-discretionary. Only our independent directors or affiliates of such directors are eligible to receive automatic grants under the 2004 Plan. Under the program, as amended in July 2010, each individual who first becomes an independent director will, on the date such individual joins the Board, automatically be granted (i) a one-time grant of RSUs covering 6,000 shares of our common stock and (ii) a one-time nonstatutory stock option grant covering 6,000 shares of our common stock.
	These initial equity grants vest monthly over the director's first two years of service. In addition, on the date of joining the Board, the new director will also receive the standard annual equity awards (if joining on the date of the Company's Annual Meeting of Stockholders) or pro-rated annual equity awards (if joining on any other date). The pro-ration is based upon the number of months of service the new board member will provide during the 12-month period ending on the one-year anniversary of the most recent annual meeting of stockholders. Annually, upon his or her re-election to the Board at the Annual Meeting of Stockholders, each independent director is automatically granted both an RSU covering 6,000 shares of our common stock and a nonstatutory stock option covering 6,000 shares of our common stock. These standard annual equity awards vest monthly over the twelve month period of service following the date of grant. In addition, all automatic equity awards vest in full if the Company is subject to a change in control or the Board member dies while in service.
	Stock-Based Compensation Expense
	Stock-based compensation expense is included in the consolidated statements of operations as follows:
		Year Ended December 31,
	(In thousands)	2013			2012		2011
	Research and development	$	16,017		$	13,667	$	13,422
	Selling, general and administrative		9,670			10,116		11,494
	Total stock-based compensation expense	$	25,687		$	23,783	$	24,916
	Stock-based compensation expense included in the consolidated statements of operations by award type is as follows:
		Year Ended December 31,
	(In thousands)	2013			2012		2011
	Employee stock options	$	4,132		$	3,417	$	4,528
	Employee RSUs		10,174			10,803		10,876
	Employee RSAs		9,723			7,602		5,498
	Employee performance RSUs		61			743		2,414
	Employee performance RSAs		1,061			366		—
	Non-employee options and RSUs		—			—		307
	ESPP		536			852		1,293
	Total stock-based compensation expense	$	25,687		$	23,783	$	24,916
	Total stock-based compensation expense capitalized to inventory was $0.2 million for 2013, $0.4 million for 2012, and $0 for 2011.
	As of December 31, 2013, the unrecognized stock-based compensation cost, net of expected forfeitures, and the estimated weighted-average amortization period, using the straight-line attribution method, was as follows:
	(In thousands, except amortization period)	Unrecognized			Weighted-average
		Compensation			amortization
		Cost			period (years)
	Stock options	$	16, 916			3.1
	RSUs		15,473			2.4
	RSAs		23,296			2.5
	Performance RSUs		4			0.1
	Performance RSAs		627			2.9
	Total unrecognized stock-based compensation expense	$	56,316
	Compensation Awards
	The following table summarizes equity award activity under the 2012 Plan and Prior Plans and related information:
	(In thousands, except per share data)	Number of			Weighted-		Number of			Weighted-		Number of			Weighted-
		Shares			average		Shares			average		Shares			average
		Subject to			Exercise Price		Subject to			Fair Value		Outstanding			Fair Value
		Outstanding			of		Outstanding			per		Subject to			per
		Options			Outstanding		RSUs			Share at		Vesting or			Share at
					Options					Grant		Performance			Grant
												Conditions
												with
												Vesting
	Balance at December 31, 2010		7,654		$	16.91		1,897		$	12.45		33		$	26.1
	Granted		629			21.98		471			24.96		2,483			24.61
	Exercised		(1,265	)		8.87		—			—		—			—
	Released RSUs/RSAs		—			—		(797	)		13.89		(74	)		24.96
	Forfeited		(127	)		29.15		(29	)		15.35		—			—
	Balance at December 31, 2011		6,891			18.62		1,542			15.47		2,442			24.62
Granted		335			21.91		528			18.45		447			18.11
Exercised		(947	)		7.98		—			—		—			—
Released RSUs/RSAs		—			—		(752	)		14.19		(388	)		24.77
Forfeited		(159	)		24.43		(78	)		18.48		—			—
Balance at December 31, 2012		6,120			20.3		1,240			17.32		2,501			23.43
Granted		820			35.54		572			23.47		510			23.25
Exercised		(1,977	)		14.04		—			—		—			—
Released RSUs/RSAs		—			—		(630	)		15.38		(452	)		21.64
Forfeited		(139	)		25.69		(67	)		18.14		(194	)		24.37
Balance at December 31, 2013		4,824			25.3		1,115			21.53		2,365			23.66
As of December 31, 2013, the aggregate intrinsic value of the options outstanding was $51.2 million and the aggregate intrinsic value of the options exercisable was $45.3 million.
The total intrinsic value of the options exercised was $41.4 million in 2013, $15.2 million in 2012, and $17.1 million in 2011. The total estimated fair value of options vested was $3.7 million in 2013, $4.1 million in 2012, and $6.4 million in 2011.
Valuation Assumptions
We based the range of weighted-average estimated values of employee stock option grants and rights granted under the employee stock purchase plan, as well as the weighted-average assumptions used in calculating these values, on estimates at the date of grant, as follows:
	Year Ended December 31,
	2013		2012		2011
Employee stock options
Risk-free interest rate	0.76% - 2.02%		0.74% - 1.17%		1.10% - 2.57%
Expected life (in years)	6-May		6-May		6-May
Volatility	58% - 60%		55% - 60%		49% - 55%
Dividend yield	—%		—%		—%
Weighted-average estimated fair value of stock options granted	$19.96		$11.50		$11.11
Employee stock purchase plan issuances
Risk-free interest rate	0.09% - 0.26%		0.14% - 0.29%		0.05% - 0.54%
Expected life (in years)	0.5 - 2		0.5 - 2		0.5 - 2
Volatility	56% - 61%		51% - 64%		48% - 59%
Dividend yield	—%		—%		—%
Weighted-average estimated fair value of ESPP issuances	$16.44		$8.07		$9.46
Range of Stock Option Exercise Prices
As of December 31, 2013, all outstanding options to purchase our common stock are summarized in the following table (in thousands, except years and per share data):
	Options Outstanding								Options Exercisable
Range of Exercise Prices	Number			Weighted-		Weighted-			Options		Weighted-			Weighted-
	Outstanding			average		average			Exercisable		average			average
				Remaining		Exercise					Remaining			Exercise
				Contractual		Prices					Contractual			Price
				Life in Years							Life in Years
$3.10 - $9.69		280			0.5	$	8.99			280		0.5		$	8.99
$9.70 - $16.00		557			3.1		14.77			551		3.1			14.8
$16.01 - $19.80		936			3.8		18.26			785		3.1			18.24
$19.81 - $24.71		467			6.7		22.08			271		5.6			22
$24.72 - $29.70		987			3.2		28.23			939		2.9			28.31
$29.71 - $35.00		916			3.6		33.34			893		3.4			33.39
$35.01 - $41.53		681			9.7		37.46			8		3.1			35.46
Total		4,824			4.5		25.3			3,727		3.1			23.51
Stockholders' Equity
In 2013, approximately 2.0 million awards were exercised at a weighted-average exercise price of $14.04 per share, for total cash proceeds of approximately $27.7 million.

Income_Taxes

Income Taxes	12 Months Ended
	Dec. 31, 2013
Income Taxes	'
Income Taxes	'
	11. Income Taxes
	Due to ongoing operating losses and the inability to recognize any income tax benefit, there is no provision for income taxes for any periods presented.
	Deferred income taxes reflect the net tax effects of temporary differences between the carrying amounts of assets and liabilities for financial reporting purposes and the amounts used for income tax purposes. Significant components of our deferred tax assets are as follows:
		December 31,
	(In thousands)	2013			2012
	Deferred tax assets:
	Net operating loss carryforwards	$	479,000		$	411,000
	Deferred revenues		6,000			4,000
	Capitalized research and development expenditures		30,000			35,000
	Research and development tax credit carryforwards		44,000			38,000
	Other		32,000			33,000
	Total deferred tax assets		591,000			521,000
	Valuation allowance		(591,000	)		(521,000	)
	Net deferred tax assets	$	—		$	—
	The differences between the U.S. federal statutory income tax rate to our effective tax rate are as follows:
		Year Ended December 31,
		2013			2012			2011
	U.S. federal statutory income tax rate		34	%		34	%		34	%
	Federal and state research credits		3.63			(4.21	)		1.67
	Non-deductible executive compensation		(0.07	)		(13.24	)		—
	Stock-based compensation		0.28			(1.36	)		(0.32	)
	Expiration of net operating loss		—			(1.81	)		(0.42	)
	Other		(2.51	)		(2.09	)		0.75
	Change in valuation allowance		(35.33	)		(11.29	)		(35.68	)
	Effective tax rate		(0.00	)%		(0.00	)%		(0.00	)%
	Realization of deferred tax assets is dependent on future taxable income, if any, the timing and the amount of which are uncertain. Accordingly, the deferred tax assets have been fully offset by a valuation allowance. The valuation allowance increased by $70.1 million in 2013, $3.0 million in 2012 and $50.0 million in 2011.
	As of December 31, 2013, we had federal net operating loss carryforwards of approximately $1,412.0 million, which will expire from 2018 through 2033, and federal research and development tax credit carryforwards of approximately $52.7 million, which will expire from 2018 through 2033. We also had state net operating loss carryforwards of approximately $890.9 million expiring in the years 2014 through 2033 and state research tax credits of approximately $57.9 million, which do not expire.
	The net operating loss deferred tax asset balances as of December 31, 2013 and 2012 do not include excess tax benefits from stock option exercises. Stockholders' equity will be credited if and when such excess tax benefits are ultimately realized.
	Utilization of net operating loss and tax credit carryforwards may be subject to a substantial annual limitation due to ownership change limitations provided by the Internal Revenue Code and similar state provisions. Annual limitations may result in expiration of net operating loss and tax credit carryforwards before some or all of such amounts have been utilized.
	Our policy is to recognize interest and/or penalties related to income tax matters in income tax expense. As of December 31, 2013 and 2012, we had no accrued interest or penalties due to our net operating losses available to offset any tax adjustment.
	We conducted an analysis through 2013 to determine whether an ownership change had occurred since inception. The analysis indicated that two ownership changes occurred in prior years. However, notwithstanding the applicable annual limitations, no portion of the net operating loss or credit carryforwards are expected to expire before becoming available to reduce federal and state income tax liabilities.
	Uncertain Tax Positions
	A reconciliation of the beginning and ending balances of the total amounts of unrecognized tax benefits are as follows (in thousands):
	Unrecognized tax benefits as of December 31, 2010	$	42,600
	Gross decrease for tax positions for prior years		—
	Gross increase in tax positions for current year		4,300
	Unrecognized tax benefits as of December 31, 2011		46,900
	Gross decrease for tax positions for prior years		—
	Gross increase in tax positions for current year		5,600
	Unrecognized tax benefits as of December 31, 2012		52,500
	Gross decrease for tax positions for prior years		(565	)
	Gross increase in tax positions for current year		5,485
	Unrecognized tax benefits as of December 31, 2013	$	57,420
	If we eventually are able to recognize these uncertain positions, most of the $57.4 million of the unrecognized benefit would reduce our effective tax rate, except for excess tax benefits related to stock-based payments. We currently have a full valuation allowance against our deferred tax assets, which would impact the timing of the effective tax rate benefit should any of these uncertain positions be favorably settled in the future. We do not believe it is reasonably possible that our unrecognized tax benefits will significantly change within the next twelve months.
	We are subject to taxation in the U.S. and various state jurisdictions. The tax years 1996 and forward remain open to examination by the federal and most state tax authorities due to net operating loss and overall credit carryforward positions.

Commitments_and_Contingencies

Commitments and Contingencies	12 Months Ended
	Dec. 31, 2013
Commitments and Contingencies	'
Commitments and Contingencies	'
	12. Commitments and Contingencies
	Operating Leases and Subleases
	We lease approximately 150,000 square feet of office and laboratory space in two buildings in South San Francisco, California, under a non-cancelable operating lease that ends in May 2020. We may extend the terms of this lease for two additional five-year periods. Future minimum lease payments under this lease, exclusive of executory costs, at December 31, 2013, were as follows:
	(In thousands)
	Years ending December 31:
	2014	$	4,859
	2015		5,770
	2016		5,943
	2017		6,121
	2018		6,305
	Thereafter		9,253
	Total	$	38,251
	Expenses and income associated with operating leases were as follows:
		Year Ended December 31,
	(In thousands)	2013		2012			2011
	Rent expense	$	5,972	$	5,720		$	6,702
	Sublease income	$	—	$	(160	)	$	(637	)
	Purchase Obligations
	As of December 31, 2013, we had outstanding purchase obligations on commercially reasonable terms, primarily for services under contract research, development and clinical and commercial supply agreements totaling $0.8 million.
	Special Long-Term Retention and Incentive Equity Awards Program
	In 2011, we granted special long-term retention and incentive cash bonus awards to certain employees. The awards have dual triggers of vesting based upon the achievement of certain performance conditions over a six-year timeframe from 2011 through December 31, 2016 and continued employment. The maximum potential cash bonus expense associated with this program is $38.2 million, which would be recognized in increments based on the probable achievement of the performance conditions. As of December 31, 2013, we determined that the achievement of the requisite performance conditions was not probable and, as a result, no bonus expense has been recognized. If sufficient performance conditions are probable of being achieved in 2014, then we could recognize up to $9.5 million cash bonus expense in 2014.
	Guarantees and Indemnifications
	We indemnify our officers and directors for certain events or occurrences, subject to certain limits. We believe the fair value of these indemnification agreements is minimal. Accordingly, we have not recognized any liabilities relating to these agreements as of December 31, 2013.

Subsequent_Events

Subsequent Events	12 Months Ended
	Dec. 31, 2013
Subsequent Events	'
Subsequent Events	'
	13. Subsequent Events
	Sale of Stock
	On February 14, 2014, we entered into an agreement with GSK pursuant to which GSK agreed to purchase through an affiliate, in a private placement, 342,229 shares of our common stock at $37.55 per share, for an aggregate purchase price of approximately $12.9 million, pursuant to its rights under our governance agreement with GSK dated June 4, 2004, as amended.

SCHEDULE_II_VALUATION_AND_QUAL

SCHEDULE II - VALUATION AND QUALIFYING ACCOUNTS	12 Months Ended
	Dec. 31, 2013
VALUATION AND QUALIFYING ACCOUNTS	'
VALUATION AND QUALIFYING ACCOUNTS	'
	SCHEDULE II
	VALUATION AND QUALIFYING ACCOUNTS
	For the Year Ended December 31, 2013
	(In thousands)
				Additions
								Deductions
								From
								Allowance
	Description	Balance at		Charged to		Charged to		Accounts		Balance at
		Beginning		Costs and		Other				End of Year
		of Year		Expenses		Accounts(1)
	Year Ended December 31, 2013
	Accounts Receivable Allowances	$	—	$	—	$	89	$	—	$	89
		$	—	$	—	$	89	$	—	$	89
	-1
	Allowances are for sales returns, cash discounts and government chargebacks.

Description_of_Operations_and_1

Description of Operations and Summary of Significant Accounting Policies (Policies)	12 Months Ended
	Dec. 31, 2013
Description of Operations and Summary of Significant Accounting Policies	'
Principles of Consolidation	'
	Principles of Consolidation
	The consolidated financial statements include the accounts of Theravance and its wholly owned subsidiaries. All intercompany balances and transactions have been eliminated in consolidation.
	Our consolidated financial statements are denominated in U.S. dollars. Accordingly, changes in exchange rates between the applicable foreign currency and the U.S. dollar will affect the translation of our foreign subsidiary's financial results into U.S. dollars for purposes of reporting our consolidated financial results. Monetary and non-monetary assets and liabilities are remeasured into U.S. dollars at the applicable period end exchange rate. Operating expenses are remeasured at average exchange rates in effect during each period, except for those expenses related to non-monetary assets which are remeasured at historical exchange rates. Gains or losses from remeasurement of foreign currency financial statements into U.S. dollars are included in our consolidated statements of operations and were insignificant for all periods presented, as was the effect of exchange rate changes on cash and cash equivalents.
Use of Management's Estimates	'
	Use of Management's Estimates
	The preparation of consolidated financial statements in conformity with U.S. Generally Accepted Accounting Principles ("GAAP") requires management to make estimates and assumptions that affect the amounts reported in the consolidated financial statements and accompanying notes. Actual results could differ materially from those estimates. On an ongoing basis, management evaluates its significant accounting policies and estimates. We base our estimates on historical experience and other relevant assumptions that we believe to be reasonable under the circumstances. These estimates also form the basis for making judgments about the carrying values of assets and liabilities when these values are not readily apparent from other sources.
Segment Reporting	'
	Segment Reporting
	We have determined that we operate in a single segment, which is the discovery (research), development and commercialization of human therapeutics. Revenues are generated primarily from our collaborative arrangements with GSK, located in Great Britain, Astellas Pharma Inc. ("Astellas") (through January 2012), located in Japan, and Merck (which agreement terminated in December 2013), located in the United States.
	All property and equipment is maintained in the United States.
Cash and Cash Equivalents	'
	Cash and Cash Equivalents
	We consider all highly liquid investments purchased with a maturity of three months or less on the date of purchase to be cash equivalents. Cash equivalents are carried at cost, which approximates fair value.
	Under certain lease agreements and letters of credit, we have pledged cash and cash equivalents as collateral. Restricted cash related to such agreements was $0.8 million as of December 31, 2013 and 2012.
Investments in Marketable Securities	'
	Investments in Marketable Securities
	We invest in short-term investments and marketable securities, primarily corporate notes, government, government agency, and municipal bonds. We classify our marketable securities as available-for-sale securities and report them at fair value in cash equivalents, short-term investments or marketable securities on the consolidated balance sheets with related unrealized gains and losses included as a component of stockholders' equity. The amortized cost of debt securities is adjusted for amortization of premiums and accretion of discounts to maturity, which is included in interest income on the consolidated statements of operations. Realized gains and losses and declines in value judged to be other-than-temporary, if any, on available-for-sale securities are included in interest income. The cost of securities sold is based on the specific identification method. Interest and dividends on securities classified as available-for-sale are included in interest income.
	We regularly review all of our investments for other-than-temporary declines in estimated fair value. Our review includes the consideration of the cause of the impairment, including the creditworthiness of the security issuers, the number of securities in an unrealized loss position, the severity and duration of the unrealized losses, whether we have the intent to sell the securities and whether it is more likely than not that we will be required to sell the securities before the recovery of their amortized cost basis. When we determine that the decline in estimated fair value of an investment is below the amortized cost basis and the decline is other-than-temporary, we reduce the carrying value of the security and record a loss for the amount of such decline.
Fair Value of Financial Instruments	'
	Fair Value of Financial Instruments
	Financial instruments include cash equivalents, marketable securities, accounts receivable, related party receivables, accounts payable, accrued liabilities and convertible subordinated notes. Marketable securities are carried at estimated fair value. The carrying value of cash equivalents, accounts receivable, receivables from related party, accounts payable and accrued liabilities approximate their estimated fair value due to the relatively short-term nature of these instruments. The fair value of the convertible subordinated notes is described in Note 9, "Long-Term Debt."
Accounts Receivable	'
	Accounts Receivable
	Trade accounts receivable are recorded net of allowances for wholesaler chargebacks related to government rebate programs, cash discounts for prompt payment and sales returns. Estimates for wholesaler chargebacks for government rebates, cash discounts and sales returns are based on contractual terms, historical trends and our expectations regarding the utilization rates for these programs. When appropriate, we record an allowance for doubtful accounts based upon our assessment of collectability. For the year ended December 31, 2013, we did not have any write-offs of accounts receivable. We perform ongoing credit evaluations of our customers and generally do not require collateral.
Concentration of Credit and Other Risks	'
	Concentration of Credit and Other Risks
	We invest in a variety of financial instruments and, by our policy, limit the amount of credit exposure with any one issuer, industry or geographic area for investments other than instruments backed by the U.S. federal government.
	Our accounts receivable at December 31, 2013, represent amounts due to us from distributors. The following table summarizes accounts receivable, net balances at December 31, 2013 by distributor:
	Distributor	Accounts Receivable		Percentage of Total
		(In thousands)		Accounts Receivable
				Balance
	McKesson Corporation	$	132		66	%
	AmerisourceBergen Drug Corporation		66		33
	Other		1		1
	Total	$	199		100	%
	We depend on a single-source supplier of the API in VIBATIV® and one supplier to provide fill-finish services related to the manufacturing of VIBATIV®. If any of our suppliers were to limit or terminate production or otherwise fail to meet the quality or delivery requirements needed to supply VIBATIV® at levels to meet market demand, we could experience a loss of revenue, which could materially and adversely impact our results of operations.
Inventories	'
	Inventories
	Inventories consist of raw materials, work-in-process and finished goods related to the production of VIBATIV® (telavancin). Raw materials include VIBATIV® API and other raw materials. Work-in-process and finished goods include third party manufacturing costs and labor and indirect costs we incur in the production process. Included in inventories are raw materials and work-in-process that may be used as clinical products, which are charged to research and development (R&D) expense when consumed. In addition, under certain commercialization agreements, we may sell VIBATIV® packaged in unlabeled vials that are recorded in work-in-process. Inventories are stated at the lower of cost or market value. We determine the cost of inventory using the average-cost method for validation batches. We analyze our inventory levels quarterly and write down any inventory that is expected to become obsolete, that has a cost basis in excess of its expected net realizable value or for inventory quantities in excess of expected requirements.
Property and Equipment	'
	Property and Equipment
	Property, equipment and leasehold improvements are stated at cost and depreciated using the straight-line method as follows:
	Leasehold improvements	Shorter of remaining lease terms or useful life
	Equipment, furniture and fixtures	5 - 7 years
	Software and computer equipment	3 years
Capitalized Software	'
	Capitalized Software
	We capitalize certain costs related to direct material and service costs for software obtained for internal use. Capitalized software costs are depreciated over 3 years.
Impairment of Long-Lived Assets	'
	Impairment of Long-Lived Assets
	Long-lived assets include property and equipment. The carrying value of long-lived assets is reviewed for impairment whenever events or changes in circumstances indicate that the asset may not be recoverable. An impairment loss is recognized when the total of estimated future cash flows expected to result from the use of the asset and its eventual disposition is less than its carrying amount.
Bonus Accruals	'
	Bonus Accruals
	We have short-term bonus programs for eligible employees. Bonuses are determined based on various criteria, including the achievement of corporate, departmental and individual goals. Bonus accruals are estimated based on various factors, including target bonus percentages per level of employee and probability of achieving the goals upon which bonuses are based.
	In 2011, we granted special long-term retention and incentive cash bonus awards to certain employees. The awards have dual triggers of vesting based upon the achievement of certain performance conditions over a six-year timeframe from 2011 through December 31, 2016 and continued employment. As of December 31, 2013, we determined that the achievement of the requisite performance conditions was not probable and, as a result, no compensation expense has been recognized.
Deferred Rent	'
	Deferred Rent
	Deferred rent consists of the difference between cash payments and the recognition of rent expense on a straight-line basis for the buildings we occupy. Rent expense is being recognized ratably over the life of the leases. Because our facility operating leases provide for rent increases over the terms of the leases, average annual rent expense during the first 1.5 years of the leases exceeded our actual cash rent payments. Also included in deferred rent are lease incentives of $2.6 million as of December 31, 2013, which is being recognized ratably over the life of the leases.
Revenue Recognition	'
	Revenue Recognition
	Revenue is recognized when the four basic criteria of revenue recognition are met: (1) persuasive evidence of an arrangement exists; (2) delivery has occurred or services have been rendered; (3) the fee is fixed or determinable; and (4) collectability is reasonably assured. Determination of criteria (3) and (4) are based on management's judgments regarding the nature of the fee charged for products or services delivered and the collectability of those fees. Where the revenue recognition criteria are not met, we defer the recognition of revenue by recording deferred revenue until such time that all criteria are met.
Collaborative Arrangements and Multiple-Element Arrangements	'
	Collaborative Arrangements and Multiple-Element Arrangements
	Revenue from nonrefundable, up-front license or technology access payments under license and collaborative arrangements that are not dependent on any future performance by us is recognized when such amounts are earned. If we have continuing obligations to perform under the arrangement, such fees are recognized over the estimated period of continuing performance obligation.
	We account for multiple element arrangements, such as license and development agreements in which a customer may purchase several deliverables, in accordance with FASB ASC Subtopic 605-25, "Multiple Element Arrangements." For new or materially amended multiple element arrangements, we identify the deliverables at the inception of the arrangement and each deliverable within a multiple deliverable revenue arrangement is accounted for as a separate unit of accounting if both of the following criteria are met: (1) the delivered item or items have value to the customer on a standalone basis and (2) for an arrangement that includes a general right of return relative to the delivered item(s), delivery or performance of the undelivered item(s) is considered probable and substantially in our control. We allocate revenue to each non-contingent element based on the relative selling price of each element. When applying the relative selling price method, we determine the selling price for each deliverable using vendor-specific objective evidence ("VSOE") of selling price, if it exists, or third-party evidence ("TPE") of selling price, if it exists. If neither VSOE nor TPE of selling price exist for a deliverable, we use the best estimated selling price for that deliverable. Revenue allocated to each element is then recognized based on when the basic four revenue recognition criteria are met for each element.
	For multiple-element arrangements entered into prior to January 1, 2011, we determined the deliverables under our collaborative arrangements did not meet the criteria to be considered separate accounting units for the purposes of revenue recognition. As a result, we recognized revenue from non-refundable, upfront fees and development contingent payments ratably over the term of its performance under the agreements. These upfront or contingent payments received, pending recognition as revenue, are recorded as deferred revenue and are classified as a short-term or long-term liability on the consolidated balance sheets and amortized over the estimated period of performance. We periodically review the estimated performance periods of our contracts based on the progress of our programs.
	Where a portion of non-refundable upfront fees or other payments received are allocated to continuing performance obligations under the terms of a collaborative arrangement, they are recorded as deferred revenue and recognized as revenue or as an accrued liability and recognized as a reduction of research and development expenses ratably over the term of our estimated performance period under the agreement. We determine the estimated performance periods, and they are periodically reviewed based on the progress of the related program. The effect of any change made to an estimated performance period and, therefore revenue recognized, would occur on a prospective basis in the period that the change was made.
	Under certain collaborative arrangements, we have been reimbursed for a portion of our research and development expenses. These reimbursements have been reflected as a reduction of research and development expense in our consolidated statements of operations, as we do not consider performing research and development services to be a part of our ongoing and central operations. Therefore, the reimbursement of research and developmental services and any amounts allocated to our research and development services are recorded as a reduction of research and development expense.
	Amounts deferred under a collaborative arrangement in which the performance obligations are terminated will result in an immediate recognition of any remaining deferred revenue and accrued liability in the period that termination occurred, provided that all performance obligations have been satisfied.
	We account for contingent payments in accordance with FASB Subtopic ASC 605-28 "Revenue Recognition—Milestone Method." We recognize revenue from milestone payments when (i) the milestone event is substantive and its achievability was not reasonably assured at the inception of the agreement and (ii) we do not have ongoing performance obligations related to the achievement of the milestone. Milestone payments are considered substantive if all of the following conditions are met: the milestone payment (a) is commensurate with either our performance to achieve the milestone or the enhancement of the value of the delivered item or items as a result of a specific outcome resulting from our performance to achieve the milestone, (b) relates solely to past performance, and (c) is reasonable relative to all of the deliverables and payment terms (including other potential milestone consideration) within the arrangement. See Note 3, "Collaborative Arrangements," for analysis of each milestone event deemed to be substantive or non-substantive.
	In accordance with FASB Subtopic ASC 808-10, "Collaborative Arrangements," and pursuant to our agreement with Astellas, we recognized as revenue the net impact of transactions with Astellas related to VIBATIV® inventories including revenue specifically attributable to any sales, and cost of inventories either transferred or expensed as unrealizable.
Product Revenues	'
	Product Revenues
	We sell VIBATIV® in the U.S. through a limited number of distributors, and title and risk of loss transfer upon receipt by these distributors. Healthcare providers order VIBATIV® through these distributors. For all product shipped in 2013, we are deferring the recognition of revenue until the product is sold through to healthcare providers, the end customers, due to the inherent uncertainties in estimating normal channel inventory at the distributors, and during which period we also provided extended payment terms and expanded return rights that allow distributors to return the product. As of December 31, 2013, we had deferred revenue of $0.9 million related to VIBATIV® shipments included in current liabilities in the consolidated balance sheet.
	Product sales are recorded net of estimated government-mandated rebates and chargebacks, distribution fees, estimated product returns and other deductions. We reflect such reductions in revenue as either an allowance to the related account receivable from the distributor, or as an accrued liability, depending on the nature of the sales deduction. Sales deductions are based on management's estimates that consider payer mix in target markets, industry benchmarks and experience to date. We monitor inventory levels in the distribution channel, as well as sales of VIBATIV® by distributors to healthcare providers, using product-specific data provided by the distributors. Product return allowances are based on amounts owed or to be claimed on related sales. These estimates take into consideration the terms of our agreements with customers, historical product returns of VIBATIV® experienced by Astellas, rebates or discounts taken, estimated levels of inventory in the distribution channel, the shelf life of the product, and specific known market events, such as competitive pricing and new product introductions. We update our estimates and assumptions each quarter and if actual future results vary from our estimates, we may adjust these estimates, which could have an effect on product sales and earnings in the period of adjustment.
	Sales Discounts:    We offer cash discounts to our customers, generally 2% of the sales price, as an incentive for prompt payment. We expect our customers to comply with the prompt payment terms to earn the cash discount. We account for cash discounts by reducing accounts receivable by the full amount and recognizing the discount as a reduction of revenue in the same period the related revenue is recognized.
	Chargebacks and Government Rebates:    For VIBATIV® sales in the U.S., we estimate reductions to product sales for qualifying federal and state government programs including discounted pricing offered to Public Health Service (PHS) as well as government-managed Medicaid programs. Our reduction for PHS is based on actual chargebacks that distributors have claimed for reduced pricing offered to such health care providers. Our accrual for Medicaid is based upon statutorily-defined discounts, estimated payer mix, expected sales to qualified healthcare providers, and our expectation about future utilization. The Medicaid accrual and government rebates that are invoiced directly to us are recorded in other accrued liabilities on the consolidated balance sheet. For qualified programs that can purchase our products through distributors at a lower contractual government price, the distributors charge back to us the difference between their acquisition cost and the lower contractual government price, which we record as an allowance against accounts receivable.
	Distribution Fees and Product Returns:    We have written contracts with our distributors that include terms for distribution-related fees. We record distribution-related fees based on a percentage of the product sales price. We offer our distributors a right to return product purchased directly from us, which is principally based upon the product's expiration date. Additionally, we have granted more expansive return rights to our distributors following our product launch of VIBATIV®. We will generally accept returns for expired product during the six months prior to and twelve months after the product expiration date on product that had been sold to our distributors. Product returned is generally not resalable given the nature of our products and method of administration. We have developed estimates for VIBATIV® product returns based upon historical VIBATIV® sales from our former collaborative partner, Astellas. We record distribution fees and product returns as an allowance against accounts receivable.
	Allowance for Doubtful Accounts:    We maintain a policy to record allowances for potentially doubtful accounts for estimated losses resulting from the inability of our customers to make required payments. As of December 31, 2013, there was no allowance for doubtful accounts.
	Royalties:    We recognize royalty revenue on licensee net sales of our products in the period in which the royalties are earned and reported to us and collectability is reasonably assured.
Intangible assets	'
	Intangible Assets
	We capitalize fees paid to licensors related to agreements for approved products or commercialized products. We capitalize these fees as finite-lived intangible assets and amortize these intangible assets on a straight-line basis over their estimated useful lives once we begin recognizing the related royalty revenue. Consistent with our policy for classification of costs under the research and development collaborative arrangements, the amortization of these intangible assets will be recognized as a reduction of royalty revenue. We review our intangible assets for impairment when events or changes in circumstances indicate that the carrying amount of such assets may not be recoverable. The recoverability of finite-lived intangible assets is measured by comparing the asset's carrying amount to the expected undiscounted future cash flows that the asset is expected to generate. The determination of recoverability typically requires various estimates and assumptions, including estimating the useful life over which cash flows will occur, their amount, and the asset's residual value, if any. We derive the required cash flow estimates from near-term forecasted product sales and long-term projected sales in the corresponding market.
Research and Development Costs	'
	Research and Development Costs
	Research and development costs are expensed in the period that services are rendered or goods are received. Research and development costs consist of salaries and benefits, laboratory supplies and facility costs, as well as fees paid to third parties that conduct certain research and development activities on behalf of us, net of certain external research and development costs reimbursed under our collaborative arrangements.
Preclinical Study and Clinical Study Expenses	'
	Preclinical Study and Clinical Study Expenses
	A substantial portion of our preclinical studies and all of our clinical studies have been performed by third-party contract research organizations (CROs). Some CROs bill monthly for services performed, while others bill based upon milestones achieved. We review the activities performed under the significant contracts each quarter. For preclinical studies, the significant factors used in estimating accruals include the percentage of work completed to date and contract milestones achieved. For clinical study expenses, the significant factors used in estimating accruals include the number of patients enrolled and percentage of work completed to date. Vendor confirmations are obtained for contracts with longer duration when necessary to validate our estimate of expenses. Our estimates are highly dependent upon the timeliness and accuracy of the data provided by our CROs regarding the status of each program and total program spending and adjustments are made when deemed necessary.
Advertising Expenses	'
	Advertising Expenses
	We expense the costs of advertising, including promotional expenses, as incurred. Advertising expenses were not significant in 2013 and were $0 in 2012 and 2011.
Fair Value of Stock-Based Compensation Awards	'
	Fair Value of Stock-Based Compensation Awards
	We use the Black-Scholes-Merton option pricing model to estimate the fair value of options granted under our equity incentive plans and rights to acquire stock granted under our employee stock purchase plan (ESPP). The Black-Scholes-Merton option valuation model requires the use of assumptions, including the expected term of the award and the expected stock price volatility. We use the "simplified" method as described in Staff Accounting Bulletin No. 107, "Share-Based Payment," for the expected option term because the usage of its historical option exercise data is limited due to post-IPO exercise restrictions. Beginning April 1, 2011, we used our historical volatility to estimate expected stock price volatility. Prior to April 1, 2011, we used peer company price volatility to estimate expected stock price volatility due to our limited historical common stock price volatility since our initial public offering in 2004.
	Restricted Stock Units (RSUs) and Restricted Stock Awards (RSAs) are measured based on the fair market values of the underlying stock on the dates of grant.
	Stock-based compensation expense was calculated based on awards ultimately expected to vest and was reduced for estimated forfeitures at the time of grant and revised, if necessary, in subsequent periods if actual forfeitures differed from those estimates. Our estimated annual forfeiture rates for stock options, RSUs and RSAs are based on our historical forfeiture experience.
	The estimated fair value of stock options, RSUs and RSAs is expensed on a straight-line basis over the expected term of the grant and the estimated fair value of performance-contingent RSUs and RSAs is expensed using an accelerated method over the term of the award once we have determined that it is probable that performance milestones will be achieved. Compensation expense for RSUs and RSAs that contain performance conditions is based on the grant date fair value of the award. Compensation expense is recorded over the requisite service period based on management's best estimate as to whether it is probable that the shares awarded are expected to vest. We assess the probability of the performance milestones being met on a continuous basis.
	Compensation expense for purchases under the ESPP is recognized based on the fair value of the common stock on the date of offering, less the purchase discount percentage provided for in the plan.
	We have not recognized, and do not expect to recognize in the near future, any income tax benefit related to employee stock-based compensation expense as a result of the full valuation allowance on our deferred tax assets including deferred tax assets related to our net operating loss carryforwards.
Other Income (Expense), net	'
	Other Income (Expense), net
	In May 2013, we entered into a royalty participation agreement with Elan Corporation, plc ("Elan"). The closing of the transaction was subject to closing conditions, including the approval of the transaction by Elan's shareholders. Elan's shareholders did not approve the transaction at an Extraordinary General Meeting. Subsequently, we terminated the agreement and, as a result, Elan paid us a $10.0 million termination fee in June 2013, which is reflected in other income on the consolidated statements of operations. Other expense is comprised of third party expenses related to the aforementioned royalty participation agreement and the change in the estimated fair value of the capped-call instruments related to our convertible subordinated notes issued in January 2013, which is reflected in other expense.
Income Taxes	'
	Income Taxes
	We utilize the asset and liability method of accounting for income taxes. Under this method, deferred tax assets and liabilities are determined based on differences between financial reporting and tax basis of assets and liabilities and are measured using enacted tax rates and laws that will be in effect when the differences are expected to reverse. A valuation allowance is provided when it is more likely than not that some portion or all of a deferred tax asset will not be realized.
	None of our currently unrecognized tax benefits would affect our effective income tax rate if recognized, due to the valuation allowance that currently offsets our deferred tax assets. We do not anticipate the total amount of unrecognized income tax benefits relating to uncertain tax positions existing at December 31, 2013 will significantly increase or decrease in the next 12 months.
	We assess all material positions taken in any income tax return, including all significant uncertain positions, in all tax years that are still subject to assessment or challenge by relevant taxing authorities. Assessing an uncertain tax position begins with the initial determination of the position's sustainability and is measured at the largest amount of benefit that is greater than 50% likely to be realized upon ultimate settlement. As of each balance sheet date, unresolved uncertain tax positions must be reassessed, and we will determine whether: the factors underlying the sustainability assertion have changed and whether the amount of the recognized tax benefit is still appropriate.
	The recognition and measurement of tax benefits requires significant judgment. Judgments concerning the recognition and measurement of a tax benefit might change as new information becomes available.
Comprehensive Loss	'
	Comprehensive Loss
	Comprehensive loss is comprised of net loss and other comprehensive income (loss). Other comprehensive income (loss) consists of changes in unrealized gains and losses on our available-for-sale securities, net of tax.
Related Parties	'
	Related Parties
	Transactions with GSK are described in Note 3, "Collaborative Arrangements".
	Robert V. Gunderson, Jr. is a director of the Company. We have engaged Gunderson Dettmer Stough Villeneuve Franklin & Hachigian, LLP, of which Mr. Gunderson is a partner, as our primary legal counsel. Fees incurred in the ordinary course of business were $3.2 million in 2013, $1.2 million in 2012, and $0.3 million in 2011.

Description_of_Operations_and_2

Description of Operations and Summary of Significant Accounting Policies (Tables)	12 Months Ended
	Dec. 31, 2013
Description of Operations and Summary of Significant Accounting Policies	'
Net Accounts Receivable Concentration Risk by Distributor	'
	The following table summarizes accounts receivable, net balances at December 31, 2013 by distributor:
	Distributor	Accounts Receivable		Percentage of Total
		(In thousands)		Accounts Receivable
				Balance
	McKesson Corporation	$	132		66	%
	AmerisourceBergen Drug Corporation		66		33
	Other		1		1
	Total	$	199		100	%
Property and Equipment	'
	Leasehold improvements	Shorter of remaining lease terms or useful life
	Equipment, furniture and fixtures	5 - 7 years
	Software and computer equipment	3 years

Net_Loss_per_Share_Tables

Net Loss per Share (Tables)	12 Months Ended
	Dec. 31, 2013
Net Loss per Share	'
Computations for basic and diluted net income loss per share	'
		Year Ended December 31,
	(In thousands, except for per share data)	2013			2012			2011
	Numerator:
	Net loss	$	(170,701	)	$	(18,542	)	$	(115,344	)
	Denominator:
	Weighted-average shares of stock outstanding		104,789			93,410			84,493
	Less: unvested RSAs		(2,364	)		(2,501	)		(2,442	)
	Weighted-average shares used to compute basic and diluted net loss per share		102,425			90,909			82,051
	Net loss per share:
	Basic and diluted net loss per share	$	(1.67	)	$	(0.20	)	$	(1.41	)
Schedule of anti-dilutive securities	'
		Year Ended December 31,
	(In thousands)	2013			2012			2011
	Shares issuable under Equity Incentive Plans and ESPP		4,095			5,367			5,464
	Shares issuable upon the conversion of convertible subordinated notes		2,780			6,668			6,668
	Total anti-dilutive securities		6,875			12,035			12,132

Collaborative_Arrangements_Tab

Collaborative Arrangements (Tables)	12 Months Ended
	Dec. 31, 2013
Collaborative Arrangements	'
Schedule of total net revenue recognized	'
		Year Ended December 31,
	(In thousands)	2013			2012			2011
	GSK	$	4,532		$	5,613		$	9,658
	Astellas		—			125,788			14,854
	Other		226			4,357			—
	Total net revenue	$	4,758		$	135,758		$	24,512
Schedule of revenue recognized from GSK under the LABA collaboration and strategic alliance agreements	'
		Year Ended December 31,
	(In thousands)	2013			2012			2011
	Royalty revenue	$	1,945		$	—		$	—
	Amortization of intangible assets		(743	)		—			—
	Net royalty revenue		1,202			—			—
	LABA collaboration(1)		1,815			3,629			4,718
	Strategic alliance agreement		—			—			1,858
	Strategic alliance—MABA program license(2)		1,515			1,984			3,082
	Total net revenue from GSK	$	4,532		$	5,613		$	9,658
	-1
	We revised the estimated performance period for the LABA program based on its progress in the fourth quarter of 2011, resulting in an increase to net loss of $0.4 million for the year ended December 31, 2011. Deferred revenue under this agreement was fully recognized in 2013.
	-2
	We revised the estimated performance period for the MABA program based on its progress as follows: (i) in the fourth quarter of 2011, resulting in an increase to net loss of $0.2 million for the year ended December 31, 2011, (ii) in the fourth quarter of 2012, resulting in an increase to net loss of $0.1 million for the year ended December 31, 2012 and (iii) in the fourth quarter of 2013, resulting in an increase to net loss of $0.1 million for the year ended December 31, 2013. We do not expect that these revisions will have a material impact on future revenue recognized under this program.
Schedule of revenue recognized under the Astellas collaboration agreement	'
		Year Ended December 31,
	(In thousands)	2013			2012			2011
	Recognition of deferred revenue	$	—		$	125,819		$	—
	Amortization of deferred revenue		—			—			12,975
	Royalties from net sales of VIBATIV®		—			—			2,422
	Proceeds from VIBATIV® delivered to Astellas		—			—			1,171
	Cost of VIBATIV® delivered to Astellas		—			—			(1,177	)
	Cost of unrealizable VIBATIV® inventories		—			—			(537	)
	Astellas-labeled product sales allowance		—			(31	)		—
	Total net revenue from Astellas	$	—		$	125,788		$	14,854
Summary of reductions to R&D expenses related to the reimbursement payments	'
		Year Ended December 31,
	(In thousands)	2013			2012			2011
	GSK	$	473		$	168		$	449
	Merck		4,937			756			—
	Alfa Wasserman		1,500			185			—
	R-Pharm		86			—			—
	Astellas		—			—			390
	Total reduction to R&D expense	$	6,996		$	1,109		$	839

AvailableforSale_Securities_Ta

Available-for-Sale Securities (Tables)	12 Months Ended
	Dec. 31, 2013
Available-for-Sale Securities	'
Schedule of available-for-sale securities	'
	(In thousands)	December 31,		December 31,
		2013		2012
	Cash and cash equivalents	$	125,009	$	86,298
	Short-term investments		321,615		153,640
	Marketable securities		55,374		95,194
	Restricted cash		833		833
	Total	$	502,831	$	335,965
Schedule of amortized cost and estimated fair values for available-for-sale securities	'
		December 31, 2013
	(In thousands)	Amortized		Gross		Gross			Estimated
		Cost		Unrealized		Unrealized			Fair Value
				Gains		Losses
	U.S. government securities	$	42,104	$	55	$	(1	)	$	42,158
	U.S. government agencies		141,278		61		(8	)		141,331
	U.S. corporate notes		94,923		54		—			94,977
	U.S. commercial paper		102,021		2		(1	)		102,022
	Money market funds		122,343		—		—			122,343
	Total	$	502,669	$	172	$	(10	)	$	502,831
		December 31, 2012
	(In thousands)	Amortized		Gross		Gross			Estimated
		Cost		Unrealized		Unrealized			Fair Value
				Gains		Losses
	U.S. government securities	$	27,197	$	10	$	(2	)	$	27,205
	U.S. government agencies		115,397		85		(16	)		115,466
	U.S. corporate notes		91,544		32		(10	)		91,566
	U.S. commercial paper		23,082		—		—			23,082
	Money market funds		78,646		—		—			78,646
	Total	$	335,866	$	127	$	(28	)	$	335,965

Fair_Value_Measurements_Tables

Fair Value Measurements (Tables)	12 Months Ended
	Dec. 31, 2013
Fair Value Measurements	'
Schedule of estimated fair values	'
		Estimated Fair Value Measurements at
		Reporting Date Using:
		Quoted Prices		Significant		Significant
		in Active		Other		Unobservable
		Markets for		Observable		Inputs
		Identical		Inputs
		Assets
	Types of Instruments	Level 1		Level 2		Level 3		Total
	(In thousands)
	Assets at December 31, 2013:
	U.S. government securities	$	42,158	$	—	$	—	$	42,158
	U.S. government agency securities		98,236		43,095		—		141,331
	U.S. corporate notes		61,591		33,386		—		94,977
	U.S. commercial paper		3,499		98,523		—		102,022
	Money market funds		122,343		—		—		122,343
	Total assets measured at estimated fair value	$	327,827	$	175,004	$	—	$	502,831
	Liabilities at December 31, 2013:
	Convertible subordinated notes due 2023	$	—	$	408,250	$	—	$	408,250
		Estimated Fair Value Measurements at
		Reporting Date Using:
		Quoted Prices		Significant		Significant
		in Active		Other		Unobservable
		Markets for		Observable		Inputs
		Identical		Inputs
		Assets
	Types of Instruments	Level 1		Level 2		Level 3		Total
	(In thousands)
	Assets at December 31, 2012:
	U.S. government securities	$	27,205	$	—	$	—	$	27,205
	U.S. government agency securities		56,969		58,497		—		115,466
	U.S. corporate notes		40,472		51,094		—		91,566
	U.S. commercial paper		—		23,082		—		23,082
	Money market funds		78,646		—		—		78,646
	Total assets measured at estimated fair value	$	203,292	$	132,673	$	—	$	335,965
	Liabilities at December 31, 2012:
	Convertible subordinated notes due 2015	$	—	$	194,050	$	—	$	194,050

Inventories_Tables

Inventories (Tables)	12 Months Ended
	Dec. 31, 2013
Inventories	'
Schedule of inventory	'
		December 31,
	(In thousands)	2013		2012
	Raw materials	$	5,138	$	5,668
	Work-in-process		360		1,846
	Finished goods		4,908		—
	Total inventories	$	10,406	$	7,514

Property_and_Equipment_Tables

Property and Equipment (Tables)	12 Months Ended
	Dec. 31, 2013
Property and Equipment	'
Schedule of property and equipment	'
		December 31,
	(In thousands)	2013			2012
	Computer equipment	$	3,084		$	3,027
	Software		5,391			5,073
	Furniture and fixtures		3,890			3,829
	Laboratory equipment		31,910			29,229
	Leasehold improvements		17,769			17,416
			62,044			58,574
	Less accumulated depreciation and amortization		(51,806	)		(49,420	)
	Property and equipment, net	$	10,238		$	9,154

Intangible_Assets_Tables

Intangible Assets (Tables)	12 Months Ended
	Dec. 31, 2013
Intangible Assets	'
Schedule of intangible assets	'
		December 31, 2013
	(In thousands)	Weighted		Gross		Accumulated			Net Carrying
		Average		Carrying		Amortization			Value
		Remaining		Value
		Amortization
		Period
		(Years)
	FDA approval and launch of BREO® ELLIPTA® in the U.S.		15.7	$	60,000	$	(632	)	$	59,368
	MHLW approval and launch of RELVAR® ELLIPTA® in Japan		14.9		20,000		(111	)		19,889
	European Commission approval of RELVAR® ELLIPTA®		15		15,000		—			15,000
	FDA approval of ANOROTM ELLIPTATM in the U.S.		15.2		30,000		—			30,000
	Total intangible assets			$	125,000	$	(743	)	$	124,257

LongTerm_Debt_Tables

Long-Term Debt (Tables)	12 Months Ended
	Dec. 31, 2013
Long-Term Debt	'
Schedule of long-term debt	'
		December 31,
	(In thousands)	2013		2012
	Convertible Subordinated Notes Due 2015	$	—	$	172,500
	Convertible Subordinated Notes Due 2023		287,500		—
	Total long-term debt	$	287,500	$	172,500

StockBased_Compensation_Tables

Stock-Based Compensation (Tables)	12 Months Ended
	Dec. 31, 2013
Stock-Based Compensation	'
Schedule of stock-based compensation expense included in the consolidated statements of operations	'
		Year Ended December 31,
	(In thousands)	2013			2012		2011
	Research and development	$	16,017		$	13,667	$	13,422
	Selling, general and administrative		9,670			10,116		11,494
	Total stock-based compensation expense	$	25,687		$	23,783	$	24,916
Schedule of stock-based compensation expense by award type included in the consolidated statements of operations	'
		Year Ended December 31,
	(In thousands)	2013			2012		2011
	Employee stock options	$	4,132		$	3,417	$	4,528
	Employee RSUs		10,174			10,803		10,876
	Employee RSAs		9,723			7,602		5,498
	Employee performance RSUs		61			743		2,414
	Employee performance RSAs		1,061			366		—
	Non-employee options and RSUs		—			—		307
	ESPP		536			852		1,293
	Total stock-based compensation expense	$	25,687		$	23,783	$	24,916
Schedule of unrecognized compensation cost, net of expected forfeitures, and the estimated weighted-average amortization period, using the straight-line attribution method	'
	As of December 31, 2013, the unrecognized stock-based compensation cost, net of expected forfeitures, and the estimated weighted-average amortization period, using the straight-line attribution method, was as follows:
	(In thousands, except amortization period)	Unrecognized			Weighted-average
		Compensation			amortization
		Cost			period (years)
	Stock options	$	16, 916			3.1
	RSUs		15,473			2.4
	RSAs		23,296			2.5
	Performance RSUs		4			0.1
	Performance RSAs		627			2.9
	Total unrecognized stock-based compensation expense	$	56,316
Summary of equity award activity under the 2012 plan and prior plans	'
	(In thousands, except per share data)	Number of			Weighted-		Number of			Weighted-		Number of			Weighted-
		Shares			average		Shares			average		Shares			average
		Subject to			Exercise Price		Subject to			Fair Value		Outstanding			Fair Value
		Outstanding			of		Outstanding			per		Subject to			per
		Options			Outstanding		RSUs			Share at		Vesting or			Share at
					Options					Grant		Performance			Grant
												Conditions
												with
												Vesting
	Balance at December 31, 2010		7,654		$	16.91		1,897		$	12.45		33		$	26.1
	Granted		629			21.98		471			24.96		2,483			24.61
	Exercised		(1,265	)		8.87		—			—		—			—
	Released RSUs/RSAs		—			—		(797	)		13.89		(74	)		24.96
	Forfeited		(127	)		29.15		(29	)		15.35		—			—
	Balance at December 31, 2011		6,891			18.62		1,542			15.47		2,442			24.62
	Granted		335			21.91		528			18.45		447			18.11
	Exercised		(947	)		7.98		—			—		—			—
	Released RSUs/RSAs		—			—		(752	)		14.19		(388	)		24.77
	Forfeited		(159	)		24.43		(78	)		18.48		—			—
	Balance at December 31, 2012		6,120			20.3		1,240			17.32		2,501			23.43
	Granted		820			35.54		572			23.47		510			23.25
	Exercised		(1,977	)		14.04		—			—		—			—
	Released RSUs/RSAs		—			—		(630	)		15.38		(452	)		21.64
	Forfeited		(139	)		25.69		(67	)		18.14		(194	)		24.37
	Balance at December 31, 2013		4,824			25.3		1,115			21.53		2,365			23.66
Schedule of weighted-average assumptions used to estimate the fair value of stock options granted and employee stock purchase plan issuances	'
		Year Ended December 31,
		2013		2012		2011
	Employee stock options
	Risk-free interest rate	0.76% - 2.02%		0.74% - 1.17%		1.10% - 2.57%
	Expected life (in years)	6-May		6-May		6-May
	Volatility	58% - 60%		55% - 60%		49% - 55%
	Dividend yield	—%		—%		—%
	Weighted-average estimated fair value of stock options granted	$19.96		$11.50		$11.11
	Employee stock purchase plan issuances
	Risk-free interest rate	0.09% - 0.26%		0.14% - 0.29%		0.05% - 0.54%
	Expected life (in years)	0.5 - 2		0.5 - 2		0.5 - 2
	Volatility	56% - 61%		51% - 64%		48% - 59%
	Dividend yield	—%		—%		—%
	Weighted-average estimated fair value of ESPP issuances	$16.44		$8.07		$9.46
Schedule of outstanding options to purchase common stock based on range of stock option exercise prices	'
	As of December 31, 2013, all outstanding options to purchase our common stock are summarized in the following table (in thousands, except years and per share data):
		Options Outstanding								Options Exercisable
	Range of Exercise Prices	Number			Weighted-		Weighted-			Options		Weighted-			Weighted-
		Outstanding			average		average			Exercisable		average			average
					Remaining		Exercise					Remaining			Exercise
					Contractual		Prices					Contractual			Price
					Life in Years							Life in Years
	$3.10 - $9.69		280			0.5	$	8.99			280		0.5		$	8.99
	$9.70 - $16.00		557			3.1		14.77			551		3.1			14.8
	$16.01 - $19.80		936			3.8		18.26			785		3.1			18.24
	$19.81 - $24.71		467			6.7		22.08			271		5.6			22
	$24.72 - $29.70		987			3.2		28.23			939		2.9			28.31
	$29.71 - $35.00		916			3.6		33.34			893		3.4			33.39
	$35.01 - $41.53		681			9.7		37.46			8		3.1			35.46
	Total		4,824			4.5		25.3			3,727		3.1			23.51

Income_Taxes_Tables

Income Taxes (Tables)	12 Months Ended
	Dec. 31, 2013
Income Taxes	'
Significant components of the Company's deferred tax assets	'
		December 31,
	(In thousands)	2013			2012
	Deferred tax assets:
	Net operating loss carryforwards	$	479,000		$	411,000
	Deferred revenues		6,000			4,000
	Capitalized research and development expenditures		30,000			35,000
	Research and development tax credit carryforwards		44,000			38,000
	Other		32,000			33,000
	Total deferred tax assets		591,000			521,000
	Valuation allowance		(591,000	)		(521,000	)
	Net deferred tax assets	$	—		$	—
Schedule of the differences between the U.S. federal statutory income tax rate to the Company's effective tax rate	'
		Year Ended December 31,
		2013			2012			2011
	U.S. federal statutory income tax rate		34	%		34	%		34	%
	Federal and state research credits		3.63			(4.21	)		1.67
	Non-deductible executive compensation		(0.07	)		(13.24	)		—
	Stock-based compensation		0.28			(1.36	)		(0.32	)
	Expiration of net operating loss		—			(1.81	)		(0.42	)
	Other		(2.51	)		(2.09	)		0.75
	Change in valuation allowance		(35.33	)		(11.29	)		(35.68	)
	Effective tax rate		(0.00	)%		(0.00	)%		(0.00	)%
Reconciliation of gross unrecognized tax benefits	'
	A reconciliation of the beginning and ending balances of the total amounts of unrecognized tax benefits are as follows (in thousands):
	Unrecognized tax benefits as of December 31, 2010	$	42,600
	Gross decrease for tax positions for prior years		—
	Gross increase in tax positions for current year		4,300
	Unrecognized tax benefits as of December 31, 2011		46,900
	Gross decrease for tax positions for prior years		—
	Gross increase in tax positions for current year		5,600
	Unrecognized tax benefits as of December 31, 2012		52,500
	Gross decrease for tax positions for prior years		(565	)
	Gross increase in tax positions for current year		5,485
	Unrecognized tax benefits as of December 31, 2013	$	57,420

Commitments_and_Contingencies_

Commitments and Contingencies (Tables)	12 Months Ended
	Dec. 31, 2013
Commitments and Contingencies	'
Schedule of future minimum lease payments under non-cancelable operating lease	'
	Future minimum lease payments under this lease, exclusive of executory costs, at December 31, 2013, were as follows:
	(In thousands)
	Years ending December 31:
	2014	$	4,859
	2015		5,770
	2016		5,943
	2017		6,121
	2018		6,305
	Thereafter		9,253
	Total	$	38,251
Schedule of expenses and income associated with operating leases	'
		Year Ended December 31,
	(In thousands)	2013		2012			2011
	Rent expense	$	5,972	$	5,720		$	6,702
	Sublease income	$	—	$	(160	)	$	(637	)

Description_of_Operations_and_3

Description of Operations and Summary of Significant Accounting Policies (Details) (USD $)	Dec. 31, 2013	Apr. 30, 2013	Dec. 31, 2012	Dec. 31, 2013
In Thousands, unless otherwise specified		Item		GSK
				LABA collaboration and Strategic Alliance agreements
Business Separation	'	'	'	'
Number of independent publicly traded companies created as a result of the separation of businesses as approved by the Board of Directors	'	2	'	'
Potential royalty revenues (as a percent)	'	'	'	15.00%
Cash, Cash Equivalents and Restricted Cash	'	'	'	'
Restricted cash	$833	'	$833	'

Description_of_Operations_and_4

Description of Operations and Summary of Significant Accounting Policies (Details 2) (USD $)	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2013	Dec. 31, 2013	Dec. 31, 2013	Dec. 31, 2013	Dec. 31, 2013
In Thousands, unless otherwise specified			VIBATIV	Accounts receivable	Accounts receivable	Accounts receivable	Accounts receivable
			Item	Distributor	Distributor	Distributor	Distributor
					McKesson Corporation	AmerisourceBergen Drug Corporation	Other
Concentration of Credit and Other Risks	'	'	'	'	'	'	'
Accounts receivable	$199	$0	'	$199	$132	$66	$1
Percentage of Total Accounts Receivable Balance	'	'	'	100.00%	66.00%	33.00%	1.00%
Number of suppliers providing fill-finish services related to the manufacturing of the product	'	'	1	'	'	'	'

Description_of_Operations_and_5

Description of Operations and Summary of Significant Accounting Policies (Details 3) (USD $)	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Information related to long-term retention and incentive cash bonus awards to certain employees	'	'	'
Stock-based compensation expense	$25,687,000	$23,783,000	$24,916,000
Deferred rent	'	'	'
Period over which average annual rent expense exceeded actual cash rent payments	'1 year 6 months	'	'
Lease incentives	2,600,000	'	'
Performance-contingent awards	'	'	'
Information related to long-term retention and incentive cash bonus awards to certain employees	'	'	'
Timeframe for achievement of performance conditions	'	'	'6 years
Stock-based compensation expense	$0	'	'
Equipment, furniture and fixtures | Minimum	'	'	'
Information related to useful life of property and equipment	'	'	'
Estimated useful life	'5 years	'	'
Equipment, furniture and fixtures | Maximum	'	'	'
Information related to useful life of property and equipment	'	'	'
Estimated useful life	'7 years	'	'
Software and computer equipment	'	'	'
Information related to useful life of property and equipment	'	'	'
Estimated useful life	'3 years	'	'
Capitalized software	'	'	'
Information related to useful life of property and equipment	'	'	'
Estimated useful life	'3 years	'	'

Description_of_Operations_and_6

Description of Operations and Summary of Significant Accounting Policies (Details 4) (USD $)	1 Months Ended	12 Months Ended
	Jun. 30, 2013	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Product Revenues	'	'	'	'
Deferred revenue, current	'	$9,289,000	$4,593,000	'
Allowance for doubtful accounts	'	'	'	'
Allowance for doubtful accounts	'	0	'	'
Advertising Expenses	'	'	'	'
Advertising expenses	'	'	0	0
Other Income (Expense), net	'	'	'	'
Non-operating income	10,000,000	'	'	'
VIBATIV	'	'	'	'
Product Revenues	'	'	'	'
Deferred revenue, current	'	$900,000	'	'
Cash discounts (as a percent)	'	2.00%	'	'
Expired product return acceptance period prior to product expiration date	'	'6 months	'	'
Expired product return acceptance period after product expiration date	'	'12 months	'	'

Description_of_Operations_and_7

Description of Operations and Summary of Significant Accounting Policies (Details 5) (Gunderson law firm, USD $)	12 Months Ended
In Millions, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Gunderson law firm	'	'	'
Related parties	'	'	'
Fees incurred related to related party	$3.20	$1.20	$0.30

Net_Loss_per_Share_Details

Net Loss per Share (Details) (USD $)	12 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Numerator:	'	'	'
Net loss	($170,701)	($18,542)	($115,344)
Denominator:	'	'	'
Weighted-average shares of stock outstanding	104,789	93,410	84,493
Less: unvested RSAs (in shares)	-2,364	-2,501	-2,442
Weighted average shares used to compute basic and diluted net loss per share	102,425	90,909	82,051
Net loss per share:	'	'	'
Basic and diluted net loss per share (in dollars per share)	($1.67)	($0.20)	($1.41)
Securities that could potentially dilute basic EPS in the future	'	'	'
Anti-dilutive securities (in shares)	6,875	12,035	12,132
Equity Incentive Plans and ESPP	'	'	'
Securities that could potentially dilute basic EPS in the future	'	'	'
Anti-dilutive securities (in shares)	4,095	5,367	5,464
Convertible subordinated notes	'	'	'
Securities that could potentially dilute basic EPS in the future	'	'	'
Anti-dilutive securities (in shares)	2,780	6,668	6,668

Collaborative_Arrangements_Det

Collaborative Arrangements (Details) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Information related to collaborative arrangements	'	'	'
Total net revenue	$4,758	$135,758	$24,512
GSK	'	'	'
Information related to collaborative arrangements	'	'	'
Total net revenue	4,532	5,613	9,658
Astellas	'	'	'
Information related to collaborative arrangements	'	'	'
Total net revenue	0	125,788	14,854
Other	'	'	'
Information related to collaborative arrangements	'	'	'
Total net revenue	$226	$4,357	$0

Collaborative_Arrangements_Det1

Collaborative Arrangements (Details 2) (USD $)

12 Months Ended

12 Months Ended

1 Months Ended

12 Months Ended

12 Months Ended

12 Months Ended

24 Months Ended

12 Months Ended

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Jan. 31, 2014

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

GSK

GSK

GSK

GSK

Long-acting beta agonist (LABA) collaboration

Long-acting beta agonist (LABA) collaboration

Long-acting beta agonist (LABA) collaboration

Long-acting beta agonist (LABA) collaboration

Long-acting beta agonist (LABA) collaboration

Long-acting beta agonist (LABA) collaboration

2004 Strategic alliance

2004 Strategic alliance

2004 Strategic alliance

2004 Strategic alliance

2004 Strategic alliance

2004 Strategic alliance

2004 Strategic alliance

2004 Strategic alliance

2004 Strategic alliance

2004 Strategic alliance

2004 Strategic alliance

2004 Strategic alliance

2004 Strategic alliance

2004 Strategic alliance

2004 Strategic alliance

Common stock purchase agreement

Governance agreement

MABA

GSK

GSK

GSK

GSK

GSK

GSK

GSK

GSK

GSK

GSK

GSK

GSK

GSK

GSK

GSK

GSK

GSK

GSK

GSK

GSK

GSK

GSK

GSK

Item

Subsequent events

Minimum

Maximum

MABA

MABA

MABA

MABA containing '081

MABA containing '081 - single-agent

MABA containing '081 - single-agent

MABA containing '081 - single-agent

MABA containing '081 - combination product

MABA containing additional MABA

MABA containing additional MABA - single-agent

MABA containing additional MABA - single-agent

MABA containing additional MABA - single-agent

Common Stock

Common Stock

Item

Maximum

Minimum

Maximum

Maximum

Minimum

Maximum

Information related to collaborative arrangements

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Obligation for milestone payments

'

'

'

'

'

'

'

$220,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Number of combination products

'

'

'

'

'

'

'

2

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Registrational and launch-related milestone fees paid

'

'

'

'

'

'

'

85,000,000

'

'

15,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Amount of liability accrued for registrational and launch-related milestone fees

'

'

'

'

'

'

'

40,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Portion of potential milestone payments that could be payable by the end of 2014

'

'

'

'

'

'

'

80,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Royalty rate for first level of annual global net sales (as a percent)

'

'

'

'

'

'

'

15.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

10.00%

20.00%

'

'

'

10.00%

15.00%

'

'

Annual global sales level used to determine royalty rate

'

'

'

'

'

'

'

3,000,000,000

'

'

'

'

'

'

'

'

'

'

'

'

3,500,000,000

'

'

'

'

3,500,000,000

'

'

'

'

Number of products which Company is obligated to use diligent efforts to discover after license of a program

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

1

'

'

'

'

'

'

'

'

'

'

'

'

'

Number of preclinical MABA compounds discovered

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

6

'

'

'

'

'

'

'

'

'

'

'

'

'

Royalty rate for sales above first level of annual global net sales (as a percent)

'

'

'

'

'

'

'

5.00%

'

'

'

'

'

'

'

'

'

'

'

'

7.50%

'

'

'

'

10.00%

'

'

'

'

Royalty rate for combination products

'

'

'

'

'

'

'

'

'

'

'

6.50%

10.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Royalty rate for combination products as a percentage of the rate applied to single products

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

70.00%

'

50.00%

'

'

'

'

Potential contingent payments that the Company could receive

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

125,000,000

'

'

'

'

'

'

'

Potential contingent payments that the Company could receive in respect to single-agent and combination medicines

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

250,000,000

'

'

'

'

'

'

'

'

'

'

Potential future contingent payments receivable

'

'

'

'

'

'

363,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

129,000,000

'

'

'

'

'

Company's stock purchased by related party (in shares)

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

26,411,103

3,504,970

Company's stock purchased by related party

126,030,000

229,296,000

13,618,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

126,000,000

Royalty revenue

'

'

'

1,945,000

0

0

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Amortization of intangible asset

-743,000

0

0

-743,000

0

0

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Net royalty revenue

1,202,000

0

0

1,202,000

0

0

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Revenues

3,556,000

135,758,000

24,512,000

'

'

'

'

1,815,000

3,629,000

4,718,000

'

'

'

0

0

1,858,000

1,515,000

1,984,000

3,082,000

'

'

'

'

'

'

'

'

'

'

'

Increase in net loss due to revised estimated performance period

'

'

'

'

'

'

'

'

'

$400,000

'

'

'

'

'

'

$100,000

$100,000

$200,000

'

'

'

'

'

'

'

'

'

'

'

Collaborative_Arrangements_Det2

Collaborative Arrangements (Details 3) (USD $)	12 Months Ended			1 Months Ended	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011	Nov. 30, 2012	Dec. 31, 2013	Dec. 31, 2012	Oct. 31, 2012
				Research Collaboration and License Agreement	Research Collaboration and License Agreement	Research Collaboration and License Agreement	Research Collaboration and License Agreement
				Merck	Merck	Merck	Merck
				Item			Maximum
Information related to collaborative arrangements	'	'	'	'	'	'	'
Upfront payment	'	'	'	$5,000,000	'	'	'
Potential future contingent payments receivable	'	'	'	'	'	'	148,000,000
Initial research term	'	'	'	'12 months	'	'	'
Number of units of accounting based on the relative selling price method	'	'	'	3	'	'	'
Upfront payment received allocated to license	'	'	'	4,400,000	'	'	'
Upfront payment received allocated to research services	'	'	'	400,000	'	'	'
Upfront payment received allocated to committee participation	'	'	'	200,000	'	'	'
Increase in revenue due to revised estimated performance period	'	'	'	'	206,000	'	'
Revenues	$3,556,000	$135,758,000	$24,512,000	'	$226,000	$4,400,000	'

Collaborative_Arrangements_Det3

Collaborative Arrangements (Details 4) (Commercialization Agreement, Clinigen, USD $)	1 Months Ended	12 Months Ended
	Mar. 31, 2013	Dec. 31, 2013
	Item
Information related to collaborative arrangements	'	'
Upfront payment	$5,000,000	'
Agreement term	'	'15 years
Period of advance notice to terminate the agreement	'12 months	'
Number of units of accounting based on the relative selling price method	2	'
Upfront payment received allocated to license	4,900,000	'
Upfront payment received allocated to committee participation	$100,000	'
Minimum	'	'
Information related to collaborative arrangements	'	'
Royalty rate, as a percentage of net sales	'	20.00%
Maximum	'	'
Information related to collaborative arrangements	'	'
Royalty rate, as a percentage of net sales	'	30.00%

Collaborative_Arrangements_Det4

Collaborative Arrangements (Details 5) (Development and Commercialization Agreement, R-Pharm CJSC, USD $)	0 Months Ended	1 Months Ended
	Oct. 31, 2012	Oct. 31, 2012
		Item
Information related to collaborative arrangements	'	'
Number of development and commercialization agreements	2	2
Maximum	'	'
Information related to collaborative arrangements	'	'
Potential future contingent payments receivable	10,000,000	$10,000,000
VIBATIV	'	'
Information related to collaborative arrangements	'	'
Upfront payment	'	1,100,000
Royalty rate, as a percentage of net sales	25.00%	'
Upfront payment received allocated to license	'	1,000,000
Upfront payment received allocated to committee participation	'	33,000
Number of units of accounting based on the relative selling price method	'	2
TD-1792	'	'
Information related to collaborative arrangements	'	'
Upfront payment	'	1,100,000
Royalty rate, as a percentage of net sales	15.00%	'
Upfront payment received allocated to license	'	900,000
Upfront payment received allocated to committee participation	'	$100,000
Number of units of accounting based on the relative selling price method	'	2

Collaborative_Arrangements_Det5

Collaborative Arrangements (Details 6) (Development and Collaboration Arrangement, Alfa Wassermann, Velusetrag, USD $)	0 Months Ended
In Millions, unless otherwise specified	Oct. 31, 2012
Information related to collaborative arrangements	'
Option fee funding amount	$10
Maximum	'
Information related to collaborative arrangements	'
Potential future contingent payments receivable	$53.50
Royalty rate, as a percentage of net sales	20.00%

Collaborative_Arrangements_Det6

Collaborative Arrangements (Details 7) (USD $)	1 Months Ended	12 Months Ended
	Nov. 30, 2005	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Net revenue recognized under the collaboration	'	'	'	'
Total net revenue	'	$3,556,000	$135,758,000	$24,512,000
License, Development and Commercialization Agreement With Astellas | Astellas	'	'	'	'
Information related to collaborative arrangements	'	'	'	'
Non-refundable, cash payments	191,000,000	'	'	'
Term of royalty payment	'10 years	'	'	'
Percentage of royalties payable by the company on termination	2.00%	'	'	'
Net revenue recognized under the collaboration	'	'	'	'
Recognition of remaining deferred revenue	'	0	125,819,000	0
Amortization of deferred revenue	'	0	0	12,975,000
Royalties from net sales of VIBATIV	'	0	0	2,422,000
Proceeds from VIBATIV delivered to Astellas	'	0	0	1,171,000
Cost of VIBATIV delivered to Astellas	'	0	0	-1,177,000
Cost of unrealizable VIBATIV inventories	'	0	0	-537,000
Astellas-labeled product sales allowance	'	0	-31,000	0
Total net revenue	'	$0	$125,788,000	$14,854,000

Collaborative_Arrangements_Det7

Collaborative Arrangements (Details 8) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Information related to collaborative arrangements	'	'	'
Total reduction to R&D expense	$6,996	$1,109	$839
GSK	'	'	'
Information related to collaborative arrangements	'	'	'
Total reduction to R&D expense	473	168	449
Merck	'	'	'
Information related to collaborative arrangements	'	'	'
Total reduction to R&D expense	4,937	756	0
Alfa Wassermann	'	'	'
Information related to collaborative arrangements	'	'	'
Total reduction to R&D expense	1,500	185	0
R-Pharm	'	'	'
Information related to collaborative arrangements	'	'	'
Total reduction to R&D expense	86	0	0
Astellas	'	'	'
Information related to collaborative arrangements	'	'	'
Total reduction to R&D expense	$0	$0	$390

AvailableforSale_Securities_De

Available-for-Sale Securities (Details) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Available-for-sale securities	'	'	'
Amortized Cost	$502,669	$335,866	'
Gross Unrealized Gains	172	127	'
Gross Unrealized Losses	-10	-28	'
Estimated Fair Value	502,831	335,965	'
Maturity period for marketable securities	'	'	'
Maximum contractual maturity period	'2 years	'	'
Average contractual maturity period	'7 months	'	'
Amount of available-for-sale securities sold	22,600	49,729	17,321
Cash and cash equivalents	'	'	'
Available-for-sale securities	'	'	'
Estimated Fair Value	125,009	86,298	'
Short-term investments	'	'	'
Available-for-sale securities	'	'	'
Estimated Fair Value	321,615	153,640	'
Marketable securities	'	'	'
Available-for-sale securities	'	'	'
Estimated Fair Value	55,374	95,194	'
Restricted cash	'	'	'
Available-for-sale securities	'	'	'
Estimated Fair Value	833	833	'
U.S. government securities	'	'	'
Available-for-sale securities	'	'	'
Amortized Cost	42,104	27,197	'
Gross Unrealized Gains	55	10	'
Gross Unrealized Losses	-1	-2	'
Estimated Fair Value	42,158	27,205	'
U.S. government agencies	'	'	'
Available-for-sale securities	'	'	'
Amortized Cost	141,278	115,397	'
Gross Unrealized Gains	61	85	'
Gross Unrealized Losses	-8	-16	'
Estimated Fair Value	141,331	115,466	'
U.S. corporate notes	'	'	'
Available-for-sale securities	'	'	'
Amortized Cost	94,923	91,544	'
Gross Unrealized Gains	54	32	'
Gross Unrealized Losses	0	-10	'
Estimated Fair Value	94,977	91,566	'
U.S. commercial paper	'	'	'
Available-for-sale securities	'	'	'
Amortized Cost	102,021	23,082	'
Gross Unrealized Gains	2	0	'
Gross Unrealized Losses	-1	0	'
Estimated Fair Value	102,022	23,082	'
Money market funds	'	'	'
Available-for-sale securities	'	'	'
Amortized Cost	122,343	78,646	'
Gross Unrealized Gains	0	0	'
Gross Unrealized Losses	0	0	'
Estimated Fair Value	$122,343	$78,646	'

Fair_Value_Measurements_Detail

Fair Value Measurements (Details) (USD $)	Dec. 31, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified
Estimated fair values of entity's financial assets and liabilities	'	'
Total assets measured at fair value	$502,831	$335,965
Fair value measurements transfer to Level 1 From Level 2	'	0
Fair value measured transfer to Level 2 From Level 1	'	0
Fair value measurements, liabilities transfer from Level 1 to Level 2	'	0
Fair value measurements, liabilities transfer from Level 2 to Level 1	'	0
U.S. government securities	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total assets measured at fair value	42,158	27,205
U.S. government agency securities	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total assets measured at fair value	141,331	115,466
U.S. corporate notes	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total assets measured at fair value	94,977	91,566
U.S. commercial paper	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total assets measured at fair value	102,022	23,082
Money market funds	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total assets measured at fair value	122,343	78,646
Recurring basis | Quoted Prices in Active Markets for Identical Assets, Level 1	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total assets measured at fair value	327,827	203,292
Fair value measurements transfer to Level 1 From Level 2	6,800	7,000
Recurring basis | Quoted Prices in Active Markets for Identical Assets, Level 1 | U.S. government securities	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total assets measured at fair value	42,158	27,205
Recurring basis | Quoted Prices in Active Markets for Identical Assets, Level 1 | U.S. government agency securities	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total assets measured at fair value	98,236	56,969
Recurring basis | Quoted Prices in Active Markets for Identical Assets, Level 1 | U.S. corporate notes	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total assets measured at fair value	61,591	40,472
Recurring basis | Quoted Prices in Active Markets for Identical Assets, Level 1 | U.S. commercial paper	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total assets measured at fair value	3,499	0
Recurring basis | Quoted Prices in Active Markets for Identical Assets, Level 1 | Money market funds	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total assets measured at fair value	122,343	78,646
Recurring basis | Significant Other Observable Inputs, Level 2	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total assets measured at fair value	175,004	132,673
Fair value measured transfer to Level 2 From Level 1	2,900	2,900
Recurring basis | Significant Other Observable Inputs, Level 2 | U.S. government securities	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total assets measured at fair value	0	0
Recurring basis | Significant Other Observable Inputs, Level 2 | U.S. government agency securities	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total assets measured at fair value	43,095	58,497
Recurring basis | Significant Other Observable Inputs, Level 2 | U.S. corporate notes	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total assets measured at fair value	33,386	51,094
Recurring basis | Significant Other Observable Inputs, Level 2 | U.S. commercial paper	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total assets measured at fair value	98,523	23,082
Recurring basis | Significant Other Observable Inputs, Level 2 | Money market funds	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total assets measured at fair value	0	0
Recurring basis | Significant Unobservable Inputs, Level 3	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total assets measured at fair value	0	0
Recurring basis | Significant Unobservable Inputs, Level 3 | U.S. government securities	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total assets measured at fair value	0	0
Recurring basis | Significant Unobservable Inputs, Level 3 | U.S. government agency securities	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total assets measured at fair value	0	0
Recurring basis | Significant Unobservable Inputs, Level 3 | U.S. corporate notes	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total assets measured at fair value	0	0
Recurring basis | Significant Unobservable Inputs, Level 3 | U.S. commercial paper	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total assets measured at fair value	0	0
Recurring basis | Significant Unobservable Inputs, Level 3 | Money market funds	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total assets measured at fair value	0	0
Recurring basis | Total	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total assets measured at fair value	502,831	335,965
Recurring basis | Total | U.S. government securities	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total assets measured at fair value	42,158	27,205
Recurring basis | Total | U.S. government agency securities	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total assets measured at fair value	141,331	115,466
Recurring basis | Total | U.S. corporate notes	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total assets measured at fair value	94,977	91,566
Recurring basis | Total | U.S. commercial paper	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total assets measured at fair value	102,022	23,082
Recurring basis | Total | Money market funds	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total assets measured at fair value	122,343	78,646
Nonrecurring basis | Quoted Prices in Active Markets for Identical Assets, Level 1 | Convertible Subordinated Notes Due 2015	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total convertible subordinated notes	'	0
Nonrecurring basis | Quoted Prices in Active Markets for Identical Assets, Level 1 | Convertible Subordinated Notes Due 2023	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total convertible subordinated notes	0	'
Nonrecurring basis | Significant Other Observable Inputs, Level 2 | Convertible Subordinated Notes Due 2015	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total convertible subordinated notes	'	194,050
Nonrecurring basis | Significant Other Observable Inputs, Level 2 | Convertible Subordinated Notes Due 2023	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total convertible subordinated notes	408,250	'
Nonrecurring basis | Significant Unobservable Inputs, Level 3 | Convertible Subordinated Notes Due 2015	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total convertible subordinated notes	'	0
Nonrecurring basis | Significant Unobservable Inputs, Level 3 | Convertible Subordinated Notes Due 2023	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total convertible subordinated notes	0	'
Nonrecurring basis | Total | Convertible Subordinated Notes Due 2015	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total convertible subordinated notes	'	194,050
Nonrecurring basis | Total | Convertible Subordinated Notes Due 2023	'	'
Estimated fair values of entity's financial assets and liabilities	'	'
Total convertible subordinated notes	$408,250	'

Inventories_Details

Inventories (Details) (USD $)	Dec. 31, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified
Inventories	'	'
Raw materials	$5,138	$5,668
Work-in-process	360	1,846
Finished goods	4,908	0
Total inventories	$10,406	$7,514

Property_and_Equipment_Details

Property and Equipment (Details) (USD $)	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Property and Equipment	'	'	'
Property and equipment, gross	$62,044,000	$58,574,000	'
Less accumulated depreciation and amortization	-51,806,000	-49,420,000	'
Property and equipment, net	10,238,000	9,154,000	'
Depreciation expense	2,700,000	3,300,000	3,800,000
Amount of write-off recognized related to assets that could no longer be used in operations	'	200,000	'
Computer equipment	'	'	'
Property and Equipment	'	'	'
Property and equipment, gross	3,084,000	3,027,000	'
Software	'	'	'
Property and Equipment	'	'	'
Property and equipment, gross	5,391,000	5,073,000	'
Furniture and fixtures	'	'	'
Property and Equipment	'	'	'
Property and equipment, gross	3,890,000	3,829,000	'
Laboratory equipment	'	'	'
Property and Equipment	'	'	'
Property and equipment, gross	31,910,000	29,229,000	'
Leasehold improvements	'	'	'
Property and Equipment	'	'	'
Property and equipment, gross	$17,769,000	$17,416,000	'

Intangible_Assets_Details

Intangible Assets (Details) (USD $)	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2013	Dec. 31, 2013	Dec. 31, 2013	Dec. 31, 2013	Dec. 31, 2013
			GSK	GSK	GSK	GSK	GSK
				BREO ELLIPTA	RELVAR ELLIPTA Japan	RELVAR ELLIPTA Europe	ANORO ELLIPTA
Intangible assets	'	'	'	'	'	'	'
Weighted Average Remaining Amortization Period	'	'	'	'15 years 8 months 12 days	'14 years 10 months 24 days	'15 years	'15 years 2 months 12 days
Gross Carrying Value	'	'	$125,000,000	$60,000,000	$20,000,000	$15,000,000	$30,000,000
Accumulated Amortization	'	'	-743,000	-632,000	-111,000	0	0
Net Carrying Value	124,257,000	0	124,257,000	59,368,000	19,889,000	15,000,000	30,000,000
Estimated amortization expense for the year 2014	7,100,000	'	'	'	'	'	'
Estimated amortization expense for the year 2015	8,100,000	'	'	'	'	'	'
Estimated amortization expense for the year 2016	8,100,000	'	'	'	'	'	'
Estimated amortization expense for the year 2017	8,100,000	'	'	'	'	'	'
Estimated amortization expense for the year 2018	8,100,000	'	'	'	'	'	'
Estimated amortization expense after the year 2018	$84,700,000	'	'	'	'	'	'

LongTerm_Debt_Details

Long-Term Debt (Details) (USD $)

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

Jul. 03, 2013

Jan. 31, 2008

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Sep. 30, 2013

Jan. 31, 2013

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2013

Privately-negotiated capped call option

Convertible Subordinated Notes Due 2015

Convertible Subordinated Notes Due 2015

Convertible Subordinated Notes Due 2015

Convertible Subordinated Notes Due 2015

Convertible Subordinated Notes Due 2015

Convertible Subordinated Notes Due 2015

Convertible Subordinated Notes Due 2023

Convertible Subordinated Notes Due 2023

Convertible Subordinated Notes Due 2023

Convertible Subordinated Notes Due 2023

Convertible Subordinated Notes Due 2023

Convertible Subordinated Notes Due 2023

Convertible Subordinated Notes Due 2023

Item

Privately-negotiated capped call option

Stock prices below $27.79 per share

Stock prices above $38.00 per share

Stock prices above $38.00 per share

Minimum

Maximum

Debt disclosures

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Convertible subordinated notes

$287,500,000

$172,500,000

'

'

'

$0

$172,500,000

'

'

'

$287,500,000

$0

'

'

'

'

Loan amount

'

'

'

'

172,500,000

'

'

'

'

287,500,000

'

'

'

'

'

'

Interest rate (as a percent)

'

'

'

'

3.00%

'

'

'

'

2.13%

2.13%

'

'

'

'

'

Proceeds from issuance of debt, net of issuance costs

'

'

'

'

166,700,000

'

'

'

'

281,200,000

'

'

'

'

'

'

Payments on capped call option transactions

'

'

'

'

'

'

'

'

'

'

'

'

36,800,000

'

'

'

Number of derivative instruments purchased

'

'

2

'

'

'

'

'

'

'

'

'

'

'

'

'

Unamortized issuance costs

'

'

'

'

'

'

'

'

1,300,000

'

5,800,000

'

'

'

'

'

Amortization expense

'

'

'

'

'

400,000

800,000

800,000

'

'

500,000

'

'

'

'

'

Initial conversion rate of shares

'

'

'

'

'

0.0386548

'

'

'

'

0.0359903

'

'

'

'

'

Initial conversion price of convertible notes into common stock (in dollars per share)

'

'

'

'

'

$25.87

'

'

'

'

$27.79

'

'

'

'

'

Percentage of principal amount at which the entity may be forced to redeem some or all notes as a result of a fundamental change (as defined)

'

'

'

'

'

100.00%

'

'

'

'

100.00%

'

'

'

'

'

Principal amount of debt converted

'

'

'

172,500,000

'

'

'

'

'

'

'

'

'

'

'

'

Number of common shares issued upon debt conversion

'

'

'

6,667,932

'

'

'

'

'

'

'

'

'

'

'

'

Debt redeemed for cash

'

'

'

'

'

0

'

'

'

'

'

'

'

'

'

'

Strike price for the underlying number of shares (in dollars per share)

'

'

'

'

'

'

'

'

'

'

'

'

$27.79

'

$38

'

Cap price for the underlying number of shares (in dollars per share)

'

'

'

'

'

'

'

'

'

'

'

'

$38

'

'

'

Net shares settlement payable to the entity

'

'

'

'

'

'

'

'

'

'

'

'

'

0

'

2,779,659

Incremental anti-dilutive benefit

'

'

'

'

'

'

'

'

'

'

'

'

'

'

0

'

Change in fair value between the trade dates and the date at which the capped call derivative assets were reclassified to stockholders' equity

'

'

'

'

'

'

'

'

'

'

'

'

$1,400,000

'

'

'

StockBased_Compensation_Detail

Stock-Based Compensation (Details) (USD $)

Dec. 31, 2013

Apr. 30, 2013

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2011

Dec. 31, 2011

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2013

31-May-12

Dec. 31, 2013

31-May-12

Item

Non-employee director

Employee Stock Purchase Plan

Employee Stock Purchase Plan

RSAs

RSAs

RSAs

RSAs

RSAs

Stock options

Stock options

RSUs

RSUs

RSUs

2012 Equity Incentive Plan

2012 Equity Incentive Plan

Prior Plans

Item

Performance-contingent

Performance-contingent

Performance-contingent

Performance-contingent

Non-employee director

Non-employee director

Performance-contingent

2011 Restricted Stock Awards

2011 Restricted Stock Awards

2011 Restricted Stock Awards

Maximum

Stock-based compensation

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Shares remaining available for issuance

'

'

'

284,139

284,139

'

'

'

'

'

'

'

'

'

'

'

3,152,390

'

Purchase price as a percentage of fair market value of stock

'

'

'

'

85.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

Consecutive and overlapping offering periods

'

'

'

'

'24 months

'

'

'

'

'

'

'

'

'

'

'

'

'

Number of offering periods

'

'

'

'

4

'

'

'

'

'

'

'

'

'

'

'

'

'

Duration of purchase period

'

'

'

'

'6 months

'

'

'

'

'

'

'

'

'

'

'

'

'

Maximum contributions as a percentage of employee's eligible compensation

'

'

'

'

15.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

Shares of common stock approved and authorized for issuance

'

'

'

2,025,000

2,025,000

'

'

'

1,290,000

'

'

'

'

'

'

6,500,000

'

'

Additional number of shares of common stock approved and authorized for issuance

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

12,667,411

Reduction in the number of shares under the 2012 plan reserve for each stock option and SAR granted

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

1

'

'

Reduction in the number of shares 2012 plan reserve for each stock award other than option and SAR granted

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

1.45

'

'

Maximum term for stock options

'

'

'

'

'

'

'

'

'

'

'10 years

'

'

'

'

'

'

'

Vesting period

'

'

'

'

'

'

'

'

'

'

'4 years

'

'

'

'

'

'

'

Percentage of stock options to be vested at end of year one

'

'

'

'

'

'

'

'

'

'

25.00%

'

'

'

'

'

'

'

Percentage of stock options to be vested monthly over remaining three years

'

'

'

'

'

'

'

'

'

'

75.00%

'

'

'

'

'

'

'

Number of independent publicly traded companies created as a result of the separation of businesses as approved by the Board of Directors

'

2

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Stock issued during period (in shares)

'

'

'

'

1,740,861

'

'

'

'

'

'

'

'

'

'

'

'

'

Cumulative average sale price per share as of the period end (in dollars per share)

'

'

'

'

$11.29

'

'

'

'

'

'

'

'

'

'

'

'

'

Reversal of compensation expense

'

'

'

$800,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Period for which compensation committee has approved grants

'

'

'

'

'

'

'3 years

'

'

'

'

'

'

'

'

'

'

'

Timeframe for achievement of performance conditions

'

'

'

'

'

'

'

'

'6 years

'

'

'

'

'

'

'

'

'

Maximum potential expense

56,316,000

'

'

'

'

23,296,000

627,000

'

'

28,200,000

16,916,000

'

15,473,000

'

4,000

'

'

'

Stock-based compensation expenses that will be recognized subject to sufficient performance conditions

'

'

'

'

'

'

'

$6,700,000

'

'

'

'

'

'

'

'

'

'

Additional disclosures

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

One-time grant of shares

'

'

'

'

'

'

'

'

'

'

'

6,000

'

6,000

'

'

'

'

Annual grant of shares upon re-election to the Board

'

'

'

'

'

'

'

'

'

'

'

6,000

'

6,000

'

'

'

'

Vesting period of initial grant to newly appointed director

'

'

'2 years

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Vesting period of annual grant upon re-election as director

'

'

'12 months

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Proration vesting period of annual grant upon re-election as director

'

'

'12 months

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

StockBased_Compensation_Detail1

Stock-Based Compensation (Details 2) (USD $)	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Stock-based compensation	'	'	'
Stock-based compensation expense	$25,687,000	$23,783,000	$24,916,000
Total stock-based compensation expense capitalized to inventory	200,000	400,000	0
Total unrecognized compensation cost related to unvested stock-based compensation	56,316,000	'	'
Stock options	'	'	'
Stock-based compensation	'	'	'
Stock-based compensation expense	4,132,000	3,417,000	4,528,000
Total unrecognized compensation cost related to unvested stock-based compensation	16,916,000	'	'
Weighted-average remaining service period of recognition of unrecognized compensation cost	'3 years 1 month 6 days	'	'
RSUs	'	'	'
Stock-based compensation	'	'	'
Stock-based compensation expense	10,174,000	10,803,000	10,876,000
Total unrecognized compensation cost related to unvested stock-based compensation	15,473,000	'	'
Weighted-average remaining service period of recognition of unrecognized compensation cost	'2 years 4 months 24 days	'	'
RSUs | Performance	'	'	'
Stock-based compensation	'	'	'
Stock-based compensation expense	61,000	743,000	2,414,000
Total unrecognized compensation cost related to unvested stock-based compensation	4,000	'	'
Weighted-average remaining service period of recognition of unrecognized compensation cost	'1 month 6 days	'	'
RSAs	'	'	'
Stock-based compensation	'	'	'
Stock-based compensation expense	9,723,000	7,602,000	5,498,000
Total unrecognized compensation cost related to unvested stock-based compensation	23,296,000	'	'
Weighted-average remaining service period of recognition of unrecognized compensation cost	'2 years 6 months	'	'
RSAs | Performance	'	'	'
Stock-based compensation	'	'	'
Stock-based compensation expense	1,061,000	366,000	0
Total unrecognized compensation cost related to unvested stock-based compensation	627,000	'	'
Weighted-average remaining service period of recognition of unrecognized compensation cost	'2 years 10 months 24 days	'	'
Non-employee options and RSUs	'	'	'
Stock-based compensation	'	'	'
Stock-based compensation expense	0	0	307,000
Employee Stock Purchase Plan	'	'	'
Stock-based compensation	'	'	'
Stock-based compensation expense	536,000	852,000	1,293,000
Research and development	'	'	'
Stock-based compensation	'	'	'
Stock-based compensation expense	16,017,000	13,667,000	13,422,000
Selling, general and administrative	'	'	'
Stock-based compensation	'	'	'
Stock-based compensation expense	$9,670,000	$10,116,000	$11,494,000

StockBased_Compensation_Detail2

Stock-Based Compensation (Details 3) (USD $)	12 Months Ended
In Millions, except Share data in Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Number of Shares Subject to Outstanding Options	'	'	'
Exercised (in shares)	-2,000	'	'
Weighted-average exercise price of outstanding options	'	'	'
Exercised (in dollars per share)	$14.04	'	'
Performance Contingent	'	'	'
Number of shares outstanding subject to RSUs and vesting or performance conditions with vesting	'	'	'
Balance at the beginning of the period (in shares)	2,501	2,442	33
Granted (in shares)	510	447	2,483
Released RSUs and RSAs (in shares)	-452	-388	-74
Forfeited (in shares)	-194	0	0
Balance at the end of the period (in shares)	2,365	2,501	2,442
Weighted-average fair value per share at grant	'	'	'
Balance at the beginning of the period (in dollars per share)	$23.43	$24.62	$26.10
Granted (in dollars per share)	$23.25	$18.11	$24.61
Released RSUs and RSAs (in dollars per share)	$21.64	$24.77	$24.96
Forfeited (in dollars per share)	$24.37	$0	$0
Balance at the end of the period (in dollars per share)	$23.66	$23.43	$24.62
Stock options	'	'	'
Number of Shares Subject to Outstanding Options	'	'	'
Balance at the beginning of the period (in shares)	6,120	6,891	7,654
Granted (in shares)	820	335	629
Exercised (in shares)	-1,977	-947	-1,265
Forfeited (in shares)	-139	-159	-127
Balance at the end of the period (in shares)	4,824	6,120	6,891
Weighted-average exercise price of outstanding options	'	'	'
Balance at the beginning of the period (in dollars per share)	$20.30	$18.62	$16.91
Granted (in dollars per share)	$35.54	$21.91	$21.98
Exercised (in dollars per share)	$14.04	$7.98	$8.87
Forfeited (in dollars per share)	$25.69	$24.43	$29.15
Balance at the end of the period (in dollars per share)	$25.30	$20.30	$18.62
Additional disclosures	'	'	'
Aggregate intrinsic value of options outstanding	$51.20	'	'
Aggregate intrinsic value of options exercisable	45.3	'	'
Total intrinsic value of options exercised	41.4	15.2	17.1
Total estimated fair value of options vested	$3.70	$4.10	$6.40
Weighted-average assumptions	'	'	'
Risk-free interest rate, minimum (as a percent)	0.76%	0.74%	1.10%
Risk-free interest rate, maximum (as a percent)	2.02%	1.17%	2.57%
Volatility, minimum (as a percent)	58.00%	55.00%	49.00%
Volatility, maximum (as a percent)	60.00%	60.00%	55.00%
Dividend yield (as a percent)	0.00%	0.00%	0.00%
Weighted-average estimated fair value of awards granted (in dollars per share)	$19.96	$11.50	$11.11
Stock options | Minimum	'	'	'
Weighted-average assumptions	'	'	'
Expected life	'5 years	'5 years	'5 years
Stock options | Maximum	'	'	'
Weighted-average assumptions	'	'	'
Expected life	'6 years	'6 years	'6 years
RSUs	'	'	'
Number of shares outstanding subject to RSUs and vesting or performance conditions with vesting	'	'	'
Balance at the beginning of the period (in shares)	1,240	1,542	1,897
Granted (in shares)	572	528	471
Released RSUs and RSAs (in shares)	-630	-752	-797
Forfeited (in shares)	-67	-78	-29
Balance at the end of the period (in shares)	1,115	1,240	1,542
Weighted-average fair value per share at grant	'	'	'
Balance at the beginning of the period (in dollars per share)	$17.32	$15.47	$12.45
Granted (in dollars per share)	$23.47	$18.45	$24.96
Released RSUs and RSAs (in dollars per share)	$15.38	$14.19	$13.89
Forfeited (in dollars per share)	$18.14	$18.48	$15.35
Balance at the end of the period (in dollars per share)	$21.53	$17.32	$15.47
Employee Stock Purchase Plan	'	'	'
Weighted-average assumptions	'	'	'
Risk-free interest rate, minimum (as a percent)	0.09%	0.14%	0.05%
Risk-free interest rate, maximum (as a percent)	0.26%	0.29%	0.54%
Volatility, minimum (as a percent)	56.00%	51.00%	48.00%
Volatility, maximum (as a percent)	61.00%	64.00%	59.00%
Dividend yield (as a percent)	0.00%	0.00%	0.00%
Weighted-average estimated fair value of awards granted (in dollars per share)	$16.44	$8.07	$9.46
Employee Stock Purchase Plan | Minimum	'	'	'
Weighted-average assumptions	'	'	'
Expected life	'6 months	'6 months	'6 months
Employee Stock Purchase Plan | Maximum	'	'	'
Weighted-average assumptions	'	'	'
Expected life	'2 years	'2 years	'2 years

StockBased_Compensation_Detail3

Stock-Based Compensation (Details 4) (USD $)	12 Months Ended
In Millions, except Share data in Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Stockholders' Equity	'	'	'
Awards exercised (in shares)	2,000	'	'
Weighted-average exercise price of awards exercised (in dollars per share)	$14.04	'	'
Total cash proceed	$27.70	'	'
Stock options	'	'	'
Options Outstanding	'	'	'
Number Outstanding (in shares)	4,824	'	'
Weighted-average Remaining Contractual Life	'4 years 6 months	'	'
Weighted-average Exercise Prices (in dollars per share)	$25.30	'	'
Options Exercisable	'	'	'
Options Exercisable (in shares)	3,727	'	'
Weighted-average Remaining Contractual Life	'3 years 1 month 6 days	'	'
Weighted-average Exercise Price, Options Exercisable (in dollars per share)	$23.51	'	'
Stockholders' Equity	'	'	'
Awards exercised (in shares)	1,977	947	1,265
Weighted-average exercise price of awards exercised (in dollars per share)	$14.04	$7.98	$8.87
Stock options | $3.10 - $9.69	'	'	'
Options outstanding and exercisable	'	'	'
Exercise price range, low end of range (in dollars per share)	$3.10	'	'
Exercise price range, high end of range (in dollars per share)	$9.69	'	'
Options Outstanding	'	'	'
Number Outstanding (in shares)	280	'	'
Weighted-average Remaining Contractual Life	'6 months	'	'
Weighted-average Exercise Prices (in dollars per share)	$8.99	'	'
Options Exercisable	'	'	'
Options Exercisable (in shares)	280	'	'
Weighted-average Remaining Contractual Life	'6 months	'	'
Weighted-average Exercise Price, Options Exercisable (in dollars per share)	$8.99	'	'
Stock options | $9.70 - $16.00	'	'	'
Options outstanding and exercisable	'	'	'
Exercise price range, low end of range (in dollars per share)	$9.70	'	'
Exercise price range, high end of range (in dollars per share)	$16	'	'
Options Outstanding	'	'	'
Number Outstanding (in shares)	557	'	'
Weighted-average Remaining Contractual Life	'3 years 1 month 6 days	'	'
Weighted-average Exercise Prices (in dollars per share)	$14.77	'	'
Options Exercisable	'	'	'
Options Exercisable (in shares)	551	'	'
Weighted-average Remaining Contractual Life	'3 years 1 month 6 days	'	'
Weighted-average Exercise Price, Options Exercisable (in dollars per share)	$14.80	'	'
Stock options | $16.01- $19.80	'	'	'
Options outstanding and exercisable	'	'	'
Exercise price range, low end of range (in dollars per share)	$16.01	'	'
Exercise price range, high end of range (in dollars per share)	$19.80	'	'
Options Outstanding	'	'	'
Number Outstanding (in shares)	936	'	'
Weighted-average Remaining Contractual Life	'3 years 9 months 18 days	'	'
Weighted-average Exercise Prices (in dollars per share)	$18.26	'	'
Options Exercisable	'	'	'
Options Exercisable (in shares)	785	'	'
Weighted-average Remaining Contractual Life	'3 years 1 month 6 days	'	'
Weighted-average Exercise Price, Options Exercisable (in dollars per share)	$18.24	'	'
Stock options | $19.81- $24.71	'	'	'
Options outstanding and exercisable	'	'	'
Exercise price range, low end of range (in dollars per share)	$19.81	'	'
Exercise price range, high end of range (in dollars per share)	$24.71	'	'
Options Outstanding	'	'	'
Number Outstanding (in shares)	467	'	'
Weighted-average Remaining Contractual Life	'6 years 8 months 12 days	'	'
Weighted-average Exercise Prices (in dollars per share)	$22.08	'	'
Options Exercisable	'	'	'
Options Exercisable (in shares)	271	'	'
Weighted-average Remaining Contractual Life	'5 years 7 months 6 days	'	'
Weighted-average Exercise Price, Options Exercisable (in dollars per share)	$22	'	'
Stock options | $24.72 - $29.70	'	'	'
Options outstanding and exercisable	'	'	'
Exercise price range, low end of range (in dollars per share)	$24.72	'	'
Exercise price range, high end of range (in dollars per share)	$29.70	'	'
Options Outstanding	'	'	'
Number Outstanding (in shares)	987	'	'
Weighted-average Remaining Contractual Life	'3 years 2 months 12 days	'	'
Weighted-average Exercise Prices (in dollars per share)	$28.23	'	'
Options Exercisable	'	'	'
Options Exercisable (in shares)	939	'	'
Weighted-average Remaining Contractual Life	'2 years 10 months 24 days	'	'
Weighted-average Exercise Price, Options Exercisable (in dollars per share)	$28.31	'	'
Stock options | $29.71 $35.00	'	'	'
Options outstanding and exercisable	'	'	'
Exercise price range, low end of range (in dollars per share)	$29.71	'	'
Exercise price range, high end of range (in dollars per share)	$35	'	'
Options Outstanding	'	'	'
Number Outstanding (in shares)	916	'	'
Weighted-average Remaining Contractual Life	'3 years 7 months 6 days	'	'
Weighted-average Exercise Prices (in dollars per share)	$33.34	'	'
Options Exercisable	'	'	'
Options Exercisable (in shares)	893	'	'
Weighted-average Remaining Contractual Life	'3 years 4 months 24 days	'	'
Weighted-average Exercise Price, Options Exercisable (in dollars per share)	$33.39	'	'
Stock options | $35.01 - $41.53	'	'	'
Options outstanding and exercisable	'	'	'
Exercise price range, low end of range (in dollars per share)	$35.01	'	'
Exercise price range, high end of range (in dollars per share)	$41.53	'	'
Options Outstanding	'	'	'
Number Outstanding (in shares)	681	'	'
Weighted-average Remaining Contractual Life	'9 years 8 months 12 days	'	'
Weighted-average Exercise Prices (in dollars per share)	$37.46	'	'
Options Exercisable	'	'	'
Options Exercisable (in shares)	8	'	'
Weighted-average Remaining Contractual Life	'3 years 1 month 6 days	'	'
Weighted-average Exercise Price, Options Exercisable (in dollars per share)	$35.46	'	'

Income_Taxes_Details

Income Taxes (Details) (USD $)	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Income Taxes	'	'	'
Provision for income taxes	$0	$0	$0
Deferred tax assets:	'	'	'
Net operating loss carryforwards	479,000,000	411,000,000	'
Deferred revenues	6,000,000	4,000,000	'
Capitalized research and development expenditures	30,000,000	35,000,000	'
Research and development tax credit carryforwards	44,000,000	38,000,000	'
Other	32,000,000	33,000,000	'
Total deferred tax assets	591,000,000	521,000,000	'
Valuation allowance	-591,000,000	-521,000,000	'
Net deferred tax assets	0	0	'
Information related to valuation allowance	'	'	'
Increase in valuation allowance	70,100,000	3,000,000	50,000,000
The differences between the U.S. federal statutory income tax rate to the Company's effective tax rate	'	'	'
U.S. federal statutory income tax rate (as a percent)	34.00%	34.00%	34.00%
Federal and state research credits (as a percent)	3.63%	-4.21%	1.67%
Non-deductible executive compensation (as a percent)	-0.07%	-13.24%	0.00%
Stock-based compensation (as a percent)	0.28%	-1.36%	-0.32%
Expiration of net operating loss (as a percent)	0.00%	-1.81%	-0.42%
Other (as a percent)	-2.51%	-2.09%	0.75%
Change in valuation allowance (as a percent)	-35.33%	-11.29%	-35.68%
Effective tax rate (as a percent)	0.00%	0.00%	0.00%
Accrued interest or penalties due to our net operating losses	0	0	'
Gross unrecognized tax benefits	'	'	'
Gross unrecognized tax benefits at the beginning of the period	52,500,000	46,900,000	42,600,000
Gross decrease for tax positions for prior years	-565,000	0	0
Gross increase in tax positions for current year	5,485,000	5,600,000	4,300,000
Gross unrecognized tax benefits at the end of the period	57,420,000	52,500,000	46,900,000
Federal	'	'	'
Operating Loss and Tax Credit Carryforward	'	'	'
Net operating loss carryfowards	1,412,000,000	'	'
Federal | Research and Development	'	'	'
Operating Loss and Tax Credit Carryforward	'	'	'
Tax credit carryforward amount	52,700,000	'	'
State	'	'	'
Operating Loss and Tax Credit Carryforward	'	'	'
Net operating loss carryfowards	890,900,000	'	'
State | Research	'	'	'
Operating Loss and Tax Credit Carryforward	'	'	'
Tax credit carryforward amount	$57,900,000	'	'

Commitments_and_Contingencies_1

Commitments and Contingencies (Details) (USD $)	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
	sqft
	Item
Purchase Obligations	'	'	'
Information related to commitment and contingencies	'	'	'
Total purchase obligations for services, development and supply agreements	$800,000	'	'
Operating Leases	'	'	'
Operating Leases	'	'	'
Number of lease terms	2	'	'
Additional lease period	'5 years	'	'
Area of buildings in South San Francisco, California (in square feet)	150,000	'	'
Number of buildings	2	'	'
Future minimum lease payments	'	'	'
2014	4,859,000	'	'
2015	5,770,000	'	'
2016	5,943,000	'	'
2017	6,121,000	'	'
2018	6,305,000	'	'
Thereafter	9,253,000	'	'
Total	38,251,000	'	'
Information related to commitment and contingencies	'	'	'
Rent expense	5,972,000	5,720,000	6,702,000
Sublease income	$0	($160,000)	($637,000)

Commitments_and_Contingencies_2

Commitments and Contingencies (Details 2) (Special Long-Term Retention and Incentive Equity Awards Program, USD $)	12 Months Ended
In Millions, unless otherwise specified	Dec. 31, 2011	Dec. 31, 2013
		Cash bonus expense
Special Long-Term Retention and Incentive Equity Awards Program	'	'
Timeframe for achievement of performance conditions	'6 years	'
Maximum compensation expense to be recognized if sufficient performance conditions are achieved	'	$38.20
Long-term retention program bonus expense recognized during the period	'	0
Compensation expenses related to cash bonus to be recognized in next fiscal year if sufficient performance conditions are achieved	'	$9.50

Subsequent_Events_Details

Subsequent Events (Details) (Subsequent events, Common stock, GSK, USD $)	0 Months Ended
In Millions, except Share data, unless otherwise specified	Feb. 14, 2014
Subsequent events | Common stock | GSK	'
Subsequent events	'
Agreement to issue stock, number of shares	342,229
Agreement to issue stock in private placement, price per shares (in dollars per share)	$37.55
Agreement to issue stock in private placement, aggregate purchase price	$12.90

SCHEDULE_II_VALUATION_AND_QUAL1

SCHEDULE II - VALUATION AND QUALIFYING ACCOUNTS (Details) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013
Movement in valuation and qualifying accounts	'
Balance at Beginning of Year	$0
Charged to Costs and Expenses	0
Charged to Other Accounts	89
Deductions From Allowance Accounts	0
Balance at End of Year	89
Accounts Receivable Allowances	'
Movement in valuation and qualifying accounts	'
Balance at Beginning of Year	0
Charged to Costs and Expenses	0
Charged to Other Accounts	89
Deductions From Allowance Accounts	0
Balance at End of Year	$89