Ligand Pharmaceuticals (LGND) 10-Q 31 Oct 14 2014 Q3 Quarterly report Financial data

Document_and_Entity_Informatio

Document and Entity Information	9 Months Ended
	Sep. 30, 2014	Oct. 31, 2014
Document and Entity Information [Abstract]	'	'
Entity Registrant Name	'LIGAND PHARMACEUTICALS INC	'
Entity Central Index Key	'0000886163	'
Document Type	'10-Q	'
Document Period End Date	30-Sep-14	'
Amendment Flag	'false	'
Document Fiscal Year Focus	'2014	'
Document Fiscal Period Focus	'Q3	'
Current Fiscal Year End Date	'--12-31	'
Entity Filer Category	'Accelerated Filer	'
Entity Common Stock, Shares Outstanding	'	20,023,148

Condensed_Consolidated_Balance

Condensed Consolidated Balance Sheets (USD $)	Sep. 30, 2014	Dec. 31, 2013
In Thousands, unless otherwise specified
Current assets:	'	'
Cash and cash equivalents	$180,663	$11,639
Short-term investments	5,925	4,340
Accounts receivable	5,812	2,222
Inventory	1,071	1,392
Capitalized expenses, VIE	2,131	0
Other current assets	1,602	959
Current debt issuance costs	793	0
Current co-promote termination payments receivable	523	4,329
Total current assets	198,520	24,881
Restricted cash and investments	1,261	1,341
Property and equipment, net	551	867
Intangible assets, net	51,317	53,099
Goodwill	12,238	12,238
Commercial license rights	4,568	4,571
Long-term co-promote termination payments receivable	0	7,417
Long-term debt issuance costs	3,598	0
Other assets	230	299
Total assets	272,283	104,713
Current liabilities:	'	'
Accounts payable (including $2.2 million related to a VIE)	4,864	3,951
Accrued liabilities	4,311	5,337
Current contingent liabilities	4,184	1,712
Current deferred income taxes	1,574	1,574
Current note payable	337	9,109
Current co-promote termination liability	523	4,329
Current lease exit obligations	2,526	2,811
Current deferred revenue	114	116
Total current liabilities	18,433	28,939
Long-term co-promote termination liability	0	7,417
Long-term deferred revenue, net	2,085	2,085
Long-term lease exit obligations	1,133	3,071
Deferred income taxes	1,214	1,098
Long-term contingent liabilities	12,267	11,795
Long-term debt, net	193,631	0
Other long-term liabilities	737	695
Total liabilities	229,500	55,100
Commitments and Contingencies	'	'
Stockholders' equity:	'	'
Common stock, $0.001 par value; 33,333,333 shares authorized; 20,117,080 and 20,468,521 shares issued and outstanding at September 30, 2014 and December 31, 2013, respectively	20	21
Additional paid-in capital	707,180	718,017
Accumulated other comprehensive income	3,543	2,914
Accumulated deficit	-666,371	-671,339
Total stockholders' equity attributable to parent	44,372	49,613
Noncontrolling interests	-1,589	0
Total liabilities and stockholders' equity	$272,283	$104,713

Condensed_Consolidated_Balance1

Condensed Consolidated Balance Sheets (Parenthetical) (USD $)	Sep. 30, 2014	Dec. 31, 2013
In Thousands, except Share data, unless otherwise specified
Accounts payable	$4,864	$3,951
Common stock, par value (USD per share)	$0.00	$0.00
Common stock, shares authorized	33,333,333	33,333,333
Common stock, shares issued	20,117,080	20,468,521
Common stock, shares outstanding	20,117,080	20,468,521
Viking	'	'
Accounts payable	$2,225	'

Condensed_Consolidated_Stateme

Condensed Consolidated Statements of Operations (USD $)	3 Months Ended		9 Months Ended
In Thousands, except Share data, unless otherwise specified	Sep. 30, 2014	Sep. 30, 2013	Sep. 30, 2014	Sep. 30, 2013
Revenues:	'	'	'	'
Royalties	$7,482	$5,724	$20,573	$16,466
Material sales	6,334	6,728	15,525	12,260
Collaborative research and development and other revenues	1,157	553	5,441	5,511
Total revenues	14,973	13,005	41,539	34,237
Operating costs and expenses:	'	'	'	'
Cost of sales	1,496	2,538	5,133	4,416
Research and development	3,021	2,414	8,842	6,900
General and administrative	6,742	4,756	17,053	13,564
Lease exit and termination costs	182	227	522	359
Write-off of in-process research and development	0	0	0	480
Total operating costs and expenses	11,441	9,935	31,550	25,719
Income from operations	3,532	3,070	9,989	8,518
Other (expense) income:	'	'	'	'
Interest expense, net	-1,516	-394	-1,946	-1,755
(Increase) decrease in contingent liabilities	-1,620	-532	-4,880	368
Other, net	505	-119	1,128	69
Total other expense, net	-2,631	-1,045	-5,698	-1,318
Income before income taxes	901	2,025	4,291	7,200
Income tax expense	-124	-60	-131	-237
Income from continuing operations	777	1,965	4,160	6,963
Discontinued operations:	'	'	'	'
Gain on sale of Avinza Product Line before income taxes	0	0	0	2,588
Income from discontinued operations	0	0	0	2,588
Net income including noncontrolling interests:	777	1,965	4,160	9,551
Less: Net loss attributable to noncontrolling interests	-503	0	-809	0
Net income	$1,280	$1,965	$4,969	$9,551
Basic per share amounts:	'	'	'	'
Income from continuing operations (in usd per share)	$0.06	$0.10	$0.24	$0.34
Income from discontinued operations (in usd per share)	$0	$0	$0	$0.13
Net income (in usd per share)	$0.06	$0.10	$0.24	$0.47
Diluted per share amounts:	'	'	'	'
Income from continuing operations (in usd per share)	$0.06	$0.09	$0.23	$0.33
Income from discontinued operations (in usd per share)	$0	$0	$0	$0.13
Net income (in usd per share)	$0.06	$0.09	$0.23	$0.46
Weighted average number of common shares-basic (in shares)	20,417,187	20,357,558	20,584,469	20,268,261
Weighted average number of common shares-diluted (in shares)	21,345,311	20,843,742	21,632,521	20,562,622

Condensed_Consolidated_Stateme1

Condensed Consolidated Statements of Comprehensive Income (USD $)	3 Months Ended		9 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2014	Sep. 30, 2013	Sep. 30, 2014	Sep. 30, 2013
Statement of Comprehensive Income [Abstract]	'	'	'	'
Net income	$1,280	$1,965	$4,969	$9,551
Unrealized net (loss) gain on available-for-sale securities, net of tax of $0	-1,224	806	1,870	2,201
Less: Reclassification of net realized (losses) gains included in net income	-274	0	1,241	0
Comprehensive (loss) income	($218)	$2,771	$8,080	$11,752

Condensed_Consolidated_Stateme2

Condensed Consolidated Statements of Comprehensive Income (Parenthetical) (USD $)	3 Months Ended		9 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2014	Sep. 30, 2013	Sep. 30, 2014	Sep. 30, 2013
Statement of Comprehensive Income [Abstract]	'	'	'	'
Tax on unrealized net gain on available-for-sale securities	$0	$0	$0	$0

Condensed_Consolidated_Stateme3

Condensed Consolidated Statements of Cash Flows (USD $)	9 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2014	Sep. 30, 2013
Operating activities	'	'
Net income including noncontrolling interests:	$4,160	$9,551
Less: gain from discontinued operations	0	2,588
Income from continuing operations	4,160	6,963
Adjustments to reconcile net income including noncontrolling interests to net cash provided by operating activities:	'	'
Non-cash change in estimated fair value of contingent liabilities	4,880	-368
Write-off of in-process research and development	0	480
Realized gain on sale of short-term investment	-1,241	0
Gain on write-off of assets	-16	0
Depreciation and amortization	1,998	2,007
Amortization of debt discount and issuance fees	1,223	0
Stock-based compensation	8,795	4,149
Non-cash upfront fee	-1,211	0
Deferred income taxes	116	237
Accretion of note payable	225	321
Other	0	-13
Changes in operating assets and liabilities:	'	'
Accounts receivable	-3,590	-918
Inventory	321	86
Other current assets	-615	-683
Other long-term assets	-1,245	173
Accounts payable and accrued liabilities	-3,478	-2,702
Deferred revenue	-2	-434
Net cash provided by operating activities of continuing operations	10,320	9,298
Net cash used in operating activities of discontinued operations	0	-642
Net cash provided by operating activities	10,320	8,656
Investing activities	'	'
Purchase of commercial license rights	0	-3,571
Payments to CVR holders and other contingency payments	-1,936	-100
Purchases of property and equipment	0	263
Proceeds from sale of property and equipment	125	3
Proceeds from sale of short-term investments	1,496	0
Other, net	-1	-40
Net cash used in investing activities	-316	-3,971
Financing activities	'	'
Repayment of debt	-9,364	-16,224
Gross proceeds from issuance of 2019 Convertible Senior Notes	245,000	0
Payment of debt issuance costs	-5,711	0
Proceeds from issuance of warrants	11,637	0
Purchase of convertible bond hedge	-48,143	0
Net proceeds from stock option exercises and ESPP	4,124	2,429
Share repurchase	-38,523	0
Net cash provided by (used in) financing activities	159,020	-13,795
Net increase (decrease) in cash and cash equivalents	169,024	-9,110
Cash and cash equivalents at beginning of period	11,639	12,381
Cash and cash equivalents at end of period	180,663	3,271
Supplemental disclosure of cash flow information	'	'
Interest paid	494	1,566
Taxes paid	3	5
Supplemental schedule of non-cash activity	'	'
Liability for commercial license rights	0	1,000
Accrued inventory purchases	0	227
Unrealized gain on AFS investments	$1,870	$2,201

Basis_of_Presentation

Basis of Presentation	9 Months Ended
	Sep. 30, 2014
Organization, Consolidation and Presentation of Financial Statements [Abstract]	'
Basis of Presentation	'
	Basis of Presentation
	Ligand Pharmaceuticals Incorporated, a Delaware corporation (the "Company" or "Ligand") is a biopharmaceutical company that develops and acquires royalty and other revenue generating assets and couples them with a lean corporate cost structure. The Company diversifies its portfolio of assets across numerous technology types, therapeutic areas, drug targets, and industry partners. The Company added Captisol® to its technology portfolio in January 2011. Captisol is a formulation technology that has enabled six FDA approved products, including Onyx's Kyprolis® and Baxter International's Nexterone®, and is currently being developed in a number of clinical-stage partner programs. The Company's therapies address the unmet medical needs of patients for a broad spectrum of diseases including hepatitis, multiple myeloma, muscle wasting, Alzheimer’s disease, dyslipidemia, diabetes, anemia, asthma, Focal Segmental Glomerulosclerosis ("FSGS") and osteoporosis. Ligand has established multiple alliances with the world’s leading pharmaceutical companies including GlaxoSmithKline, Onyx Pharmaceuticals (a subsidiary of Amgen, Inc.), Merck, Pfizer, Baxter International, Lundbeck Inc. and Spectrum Pharmaceuticals, Inc. The Company’s principal market is the United States. The Company sold its Oncology Product Line ("Oncology") and Avinza Product Line ("Avinza") on October 25, 2006 and February 26, 2007, respectively. The operating results for Oncology and Avinza have been presented in the accompanying condensed consolidated financial statements as "Discontinued Operations."
	The Company has incurred significant losses since its inception. As of September 30, 2014, the Company’s accumulated deficit was approximately $666.4 million and the Company had working capital of approximately $180.1 million. Management believes that cash flows from operations will increase due to Captisol® sales, an increase in royalty revenues driven primarily from continued increases in Promacta® and Kyprolis® sales, and also from anticipated new license and milestone revenues. The Company expects to build cash in future months as it continues to generate significant cash flows from operations. The Company’s future operating and capital requirements will depend on many factors, including, but not limited to: the pace of scientific progress in its research and development programs; the potential success of these programs; the scope and results of preclinical testing and clinical trials; the time and costs involved in obtaining regulatory approvals; the costs involved in preparing, filing, prosecuting, maintaining and enforcing patent claims; competing technological and market developments; the amount of royalties on sales of the commercial products of its partners; the efforts of its collaborative partners; obligations under its operating lease agreements; and the capital requirements of any companies the Company may acquire in the future. The ability of the Company to achieve its operational targets is dependent upon the Company’s ability to further implement its business goals and generate sufficient operating cash flow.
	Principles of Consolidation
	The accompanying unaudited condensed consolidated financial statements include Ligand and its wholly owned subsidiaries, Ligand JVR, Allergan Ligand Retinoid Therapeutics, Seragen, Inc., Pharmacopeia, Inc. ("Pharmacopeia"), Neurogen Corporation ("Neurogen"), CyDex Pharmaceuticals, Inc. ("CyDex"), Metabasis Therapeutics, Inc. ("Metabasis") and Nexus VI, Inc. Also included is Viking Therapeutics, Inc. ("Viking"), a variable interest entity ("VIE") for which the Company is deemed under applicable accounting guidance to be the primary beneficiary. All significant intercompany accounts and transactions have been eliminated in consolidation.
	Basis of Presentation
	The Company’s accompanying unaudited condensed consolidated financial statements as of September 30, 2014 and for the three and nine months ended September 30, 2014 and 2013 have been prepared in accordance with accounting principles generally accepted in the United States for interim financial information. Accordingly, they do not include all of the information and footnotes required by accounting principles generally accepted in the United States for annual financial statements. The Company’s unaudited condensed consolidated balance sheet at December 31, 2013 has been derived from the audited financial statements at that date, but does not include all of the information and footnotes required by accounting principles generally accepted in the United States for complete financial statements. In the opinion of management, all adjustments (consisting of normal recurring adjustments) considered necessary for a fair presentation of the financial position and results of operations of the Company and its subsidiaries, have been included. Operating results for the three and nine months ended September 30, 2014 are not necessarily indicative of the results that may be expected for the year ending December 31, 2014. These financial statements should be read in conjunction with the consolidated financial statements and notes therein included in the Company’s annual report on Form 10-K for the year ended December 31, 2013.
	Use of Estimates
	The preparation of condensed consolidated financial statements in conformity with accounting principles generally accepted in the United States requires the use of estimates and assumptions that affect the reported amounts of assets, liabilities, revenue, expenses, contingent assets and liabilities, definite and indefinite lived intangible assets, goodwill, co-promote termination payments receivable and co-promote termination liabilities, uncertain tax positions, deferred revenue, lease exit liability and income tax net operating loss carryforwards during the reporting period. The Company’s critical accounting policies are those that are both most important to the Company’s financial condition and results of operations and require the most difficult, subjective or complex judgments on the part of management in their application, often as a result of the need to make estimates about the effect of matters that are inherently uncertain. Because of the uncertainty of factors surrounding the estimates or judgments used in the preparation of the condensed consolidated financial statements, actual results may materially vary from these estimates.
	Income Per Share
	Basic income per share is calculated by dividing net income by the weighted-average number of common shares and vested restricted stock units outstanding. Diluted income per share is computed by dividing net income by the weighted-average number of common shares and vested restricted stock units outstanding and the weighted-average number of dilutive common stock equivalents, including stock options, non-vested restricted stock units, convertible notes and warrants. Common stock equivalents are only included in the diluted income per share calculation when their effect is dilutive. The total number of potential common shares excluded from the computation of diluted income per share because their inclusion would have been anti-dilutive was 5.0 million and 0.9 million, as of September 30, 2014 and 2013, respectively.
	The following table sets forth the computation of basic and diluted net income per share for the periods indicated (in thousands, except per share amounts):
		Three months ended						Nine months ended
		September 30,						September 30,
		2014			2013			2014		2013
	EPS attributable to common shareholders:
	Net income from continuing operations	$	1,280		$	1,965		4,969		$	6,963
	Net income from discontinued operations	—			—			—		2,588
	Net income	$	1,280		$	1,965		$	4,969	$	9,551
	Shares used to compute basic income per share	20,417,187			20,357,558			20,584,469		20,268,261
	Dilutive potential common shares:
	Restricted stock	22,531			77,609			37,387		62,051
	Stock options	905,593			408,575			1,010,665		232,310
	Shares used to compute diluted income per share	21,345,311			20,843,742			21,632,521		20,562,622
	Basic per share amounts:
	Income from continuing operations	$	0.06		$	0.1		$	0.24	$	0.34
	Income from discontinued operations	—			—			—		0.13
	Net income	$	0.06		$	0.1		$	0.24	$	0.47
	Diluted per share amounts:
	Income from continuing operations	$	0.06		$	0.09		$	0.23	$	0.33
	Income from discontinued operations	—			—			—		0.13
	Net income	$	0.06		$	0.09		$	0.23	$	0.46
	Cash, Cash Equivalents and Short-term Investments
	Cash and cash equivalents consist of cash and highly liquid securities with maturities at the date of acquisition of three months or less. Securities received by the Company as a result of a milestone payment from licensees are considered short-term investments and have been classified by management as available-for-sale. Such investments are carried at fair value, with unrealized gains and losses included in the statement of comprehensive income (loss). The Company determines the cost of investments based on the specific identification method.
	Restricted Cash and Investments
	Restricted cash and investments consist of certificates of deposit held with a financial institution as collateral under a facility lease and third-party service provider arrangements.
	The following table summarizes the various investment categories at September 30, 2014 and December 31, 2013 (in thousands):
		Cost			Gross unrealized			Gross unrealized		Estimated
					gains			losses		fair value
	30-Sep-14
	Short-term investments	$	1,426		$	4,499		$	—	$	5,925
	Certificates of deposit-restricted	1,261			—			—		1,261
		$	2,687		$	4,499		$	—	$	7,186
	31-Dec-13
	Short-term investments	$	1,426		$	2,914		$	—	$	4,340
	Certificates of deposit-restricted	1,341			—			—		1,341
		$	2,767		$	2,914		$	—	$	5,681
	Concentrations of Credit Risk
	Financial instruments that potentially subject the Company to significant concentrations of credit risk consist primarily of cash equivalents, investments and accounts receivable.
	The Company invests its excess cash principally in U.S. government debt securities, investment-grade corporate debt securities and certificates of deposit. The Company has established guidelines relative to diversification and maturities that maintain safety and liquidity. These guidelines are periodically reviewed and modified to take advantage of trends in yields and interest rates. The Company did not experience any significant losses on its cash equivalents, short-term investments or restricted investments for the periods ending September 30, 2014 and December 31, 2013.
	As of September 30, 2014 and December 31, 2013, cash deposits held at financial institutions in excess of FDIC insured amounts of $250,000 were approximately $92.8 million and $11.1 million, respectively.
	Accounts receivable from one customer was 57% of total accounts receivable at September 30, 2014. Accounts receivable from two customers was 75% of total accounts receivable at December 31, 2013.
	The Company currently obtains Captisol from a single supplier.  If this supplier were not able to supply the requested amounts of Captisol and the Company's existing inventory was depleted, the Company would be unable to continue to derive revenues from the sale of Captisol until it obtained an alternative source, which might take a considerable length of time. The Company maintains inventory of Captisol, which has a five year shelf life, at three geographically spread storage locations in the United States and Europe.  If a disaster were to strike any of these locations, it could lead to supply interruptions.
	Inventory
	Inventory is stated at the lower of cost or market value. The Company determines cost using the first-in, first-out method. The Company analyzes its inventory levels periodically and writes down inventory to its net realizable value if it has become obsolete, has a cost basis in excess of its expected net realizable value or is in excess of expected requirements. There were no write downs related to obsolete inventory recorded for the three and nine months ended September 30, 2014 and 2013.
	Property and Equipment
	Property and equipment is stated at cost and consists of the following (in thousands):
		September 30,			December 31,
		2014			2013
	Lab and office equipment	$	2,509		$	3,737
	Leasehold improvements	273			387
	Computer equipment and software	631			616
		3,413			4,740
Less accumulated depreciation and amortization	(2,862		)	(3,873		)
Total property and equipment, net	$	551		$	867
Depreciation of equipment is computed using the straight-line method over the estimated useful lives of the assets, which range from three to ten years. Leasehold improvements are amortized using the straight-line method over their estimated useful lives or their related lease term, whichever is shorter. Depreciation expense recognized for the three months ended September 30, 2014 and 2013 was $0.1 million. Depreciation expense for the nine months ended September 30, 2014 and 2013 was $0.2 million. Depreciation expense is included in operating expenses.
Other Current Assets
Other current assets consist of the following (in thousands):
	September 30,			December 31,
	2014			2013
Prepaid expenses	$	1,178		$	786
Other receivables	424			173
Total current assets	$	1,602		$	959
Goodwill and Other Identifiable Intangible Assets
Goodwill and other identifiable intangible assets consist of the following (in thousands):
	September 30,			December 31,
	2014			2013
Indefinite lived intangible assets
Acquired in-process research and development	$	12,556		$	12,556
Goodwill	12,238			12,238
Definite lived intangible assets
Complete technology	15,267			15,267
Less: Accumulated amortization	(2,807		)	(2,235		)
Trade name	2,642			2,642
Less: Accumulated amortization	(487		)	(387		)
Customer relationships	29,600			29,600
Less: Accumulated amortization	(5,454		)	(4,344		)
Total goodwill and other identifiable intangible assets, net	$	63,555		$	65,337
The Company accounts for goodwill and other intangible assets in accordance with Accounting Standards Codification ("ASC") Topic 350 - Intangibles - Goodwill and Other which, among other things, establishes standards for goodwill acquired in a business combination, eliminates the amortization of goodwill and requires the carrying value of goodwill and certain non-amortizing intangibles to be evaluated for impairment on an annual basis. The Company uses the income approach and the market approach, each weighted at 50%, when performing its goodwill impairment analysis. For the income approach, the Company considers the present value of future cash flows and the carrying value of its assets and liabilities, including goodwill. The market approach is based on an analysis of revenue multiples of peer public companies. If the carrying value of the assets and liabilities, including goodwill, were to exceed the Company’s estimation of the fair value, the Company would record an impairment charge in an amount equal to the excess of the carrying value of goodwill over the implied fair value of the goodwill. The Company performs an evaluation of goodwill and other intangibles as of December 31 of each year, absent any indicators of earlier impairment, to ensure that impairment charges, if applicable, are reflected in the Company's financial results before December 31 of each year. When it is determined that impairment has occurred, a charge to operations is recorded. Goodwill and other intangible asset balances are included in the identifiable assets of the business segment to which they have been assigned. Any goodwill impairment, as well as the amortization of other purchased intangible assets, is charged against the respective business segments' operating income.
Amortization of definite-lived intangible assets is computed using the straight-line method over the estimated useful life of the asset of 20 years. Amortization expense of $0.6 million and $1.8 million was recognized for each of the three and nine months ended September 30, 2014 and 2013, respectively. Estimated amortization expense for the years ending December 31, 2014 through 2018 is $2.4 million per year.
Acquired In-Process Research and Development
Intangible assets related to acquired in-process research and development ("IPR&D") are considered to be indefinite-lived until the completion or abandonment of the associated research and development efforts. During the period the assets are considered to be indefinite-lived, they will not be amortized but will be tested for impairment on an annual basis and between annual tests if the Company becomes aware of any events occurring or changes in circumstances that would indicate a reduction in the fair value of the IPR&D projects below their respective carrying amounts. If and when development is complete, which generally occurs if and when regulatory approval to market a product is obtained, the associated assets would be deemed definite-lived and would then be amortized based on their respective estimated useful lives at that point in time. For the three and nine months ended September 30, 2014 and the three months ended September 30, 2013 there was no impairment of IPR&D. For the nine months ended September 30, 2013, the Company recorded a non-cash impairment charge of $0.5 million for the write-off of IPR&D for Captisol-enabled Clopidogrel (MDCO-157). The asset was impaired upon notification from the Medicines Company that they intended to terminate the license agreement and return the rights of the compound to the Company. MDCO-157 is an intravenous option of the anti-platelet medication designed for situations where the administration of oral platelet inhibitors is not feasible or desirable.
Impairment of Long-Lived Assets
Management reviews long-lived assets for impairment annually or whenever events or changes in circumstances indicate the carrying amount of an asset may not be recoverable. Recoverability of assets to be held and used is measured by a comparison of the carrying amount of an asset to future undiscounted net cash flows expected to be generated by the asset. If such assets are considered to be impaired, the impairment to be recognized is measured as the amount by which the carrying amount of the assets exceeds the fair value of the assets. Fair value for the Company’s long-lived assets is determined using the expected cash flows discounted at a rate commensurate with the risk involved. As of September 30, 2014, management does not believe there have been any events or circumstances indicating that the carrying amount of its long-lived assets may not be recoverable.
Commercial license rights
Commercial license rights represent a portfolio of future milestone and royalty payment rights acquired in accordance with the Royalty Stream and Milestone Payments Purchase Agreement entered into with Selexis SA ("Selexis") in April 2013.  The portfolio consists of over 15 Selexis commercial license agreement programs with various pharmaceutical-company counterparties.  The purchase price was $4.6 million, inclusive of acquisition costs. The Company paid $3.6 million upon closing and paid an additional $1.0 million in April 2014. Individual commercial license rights acquired under the agreement are carried at allocated cost and approximate fair value. The carrying value of the license rights will be reduced on a pro-rata basis as revenue is realized over the term of the agreement. Declines in the fair value of individual license rights below their carrying value that are deemed to be other than temporary are reflected in earnings in the period such determination is made. As of September 30, 2014, management does not believe there have been any events or circumstances indicating that the carrying amount of its commercial license rights may not be recoverable.
Accrued Liabilities
Accrued liabilities consist of the following (in thousands):
	September 30,			December 31,
	2014			2013
Compensation	$	1,388		$	1,929
Professional fees	805			697
Accrued interest payable	230			—
Other	1,888			2,711
Total accrued liabilities	$	4,311		$	5,337
Other Long-Term Liabilities
Other long-term liabilities consist of the following (in thousands):
	September 30,			December 31,
	2014			2013
Deposits	$	402		$	345
Deferred rent	335			350
Total other long-term liabilities	$	737		$	695
Contingent Liabilities
In connection with the Company’s acquisition of CyDex in January 2011, the Company recorded a $17.6 million contingent liability, inclusive of the $4.3 million payment made in January 2012, for amounts potentially due to holders of the CyDex contingent value rights ("CVRs") and former license holders. The liability is periodically assessed based on events and circumstances related to the underlying milestones, royalties and material sales. Any change in fair value is recorded in the Company’s consolidated statements of operations. The carrying amount of the liability may fluctuate significantly and actual amounts paid under the CVR agreements may be materially different than the carrying amount of the liability. The fair value of the liability at September 30, 2014 and December 31, 2013 was $12.9 million and $9.3 million, respectively. The Company recorded a fair-value adjustment to increase the liability for CyDex-related contingent liabilities by $2.8 million and $5.6 million for the three and nine months ended September 30, 2014, respectively, and an adjustment to increase the liability by $1.2 million and to decrease the liability by $2.1 million for the three and nine months ended September 30, 2013, respectively. There was a revenue-sharing payment of $1.6 million made during the nine months ended September 30, 2014, and no revenue sharing payments were made during the three months ended September 30, 2014 and three and nine months ended September 30, 2013. Other contingency payments related to the CyDex acquisition of $0.3 million were made during the three and nine months ended September 30, 2014 and other contingency payments of $0.1 million were made during the three and nine months ended September 30, 2013.
In connection with the Company’s acquisition of Metabasis in January 2010, the Company issued to Metabasis stockholders four tradable CVRs, one CVR from each of four respective series of CVR, for each Metabasis share. The CVRs will entitle Metabasis stockholders to cash payments as frequently as every six months as cash is received by the Company from proceeds from the sale or partnering of any of the Metabasis drug development programs, among other triggering events. The fair values of the CVRs are remeasured at each reporting date through the term of the related agreement. Changes in the fair values are reported in the statement of operations as income (decreases) or expense (increases). The carrying amount of the liability may fluctuate significantly based upon quoted market prices and actual amounts paid under the agreements may be materially different than the carrying amount of the liability. The fair value of the liability was estimated to be $3.5 million and $4.2 million as of September 30, 2014 and December 31, 2013, respectively. The Company recorded a decrease in the liability for Metabasis-related CVRs of $1.2 million and an increase in the liability of $0.7 million for the three and nine months ended September 30, 2014, respectively. The Company recorded a decrease in the liability of $0.7 million for the three months ended September 30, 2013 and an increase in the liability of $1.7 million for the nine months ended September 30, 2013.
Fair Value of Financial Instruments
Fair value is defined as the exit price that would be received to sell an asset or paid to transfer a liability. Fair value is a market-based measurement that should be determined using assumptions that market participants would use in pricing an asset or liability. The Company establishes a three-level hierarchy to prioritize the inputs used in measuring fair value. The levels are described in the below with level 1 having the highest priority and level 3 having the lowest:
Level 1 - Quoted prices in active markets;
Level 2 - Inputs other than the quoted prices in active markets that are observable either directly or indirectly; and
Level 3 - Unobservable inputs in which there is little or no market data, which require the Company to develop its own assumptions.
The Company’s short-term investments include investments in equity securities which the Company received as a result of event-based and upfront payments from licensees. Additionally, there is a liability related to the investment in equity securities for amounts owed to former license holders. The Metabasis CVR liability is marked-to-market at each reporting period based upon the quoted market prices of the underlying CVR. The fair value of the CyDex contingent liabilities are determined at each reporting period based upon an income valuation model. The co-promote termination payments receivable represents a non-interest-bearing receivable for future payments to be made by Pfizer related to Avinza product sales and is recorded at its fair value. The receivable and liability will remain equal, and are adjusted each quarter for changes in the fair value of the obligation including any changes in the estimate of future net Avinza product sales.
The Company evaluates its financial instruments at each reporting period to determine if any transfers between the various three-level hierarchy have occurred and appropriately reclassifies its financial instruments to the appropriate level within the hierarchy.
Revenue Recognition
Royalties on sales of products commercialized by the Company’s partners are recognized in the quarter reported by the respective partner. Generally, the Company receives royalty reports from its licensees approximately one quarter in arrears due to the fact that its agreements require partners to report product sales between 30 and 60 days after the end of the quarter. The Company recognizes royalty revenues when it can reliably estimate such amounts and collectability is reasonably assured. Under this accounting policy, the royalty revenues reported are not based upon estimates and such royalty revenues are typically reported to the Company by its partners in the same period in which payment is received.
Revenue from material sales of Captisol is recognized upon transfer of title, which normally passes upon shipment to the customer. The Company’s credit and exchange policy includes provisions for the return of product between 30 to 90 days, depending on the specific terms of the individual agreement, when that product (1) does not meet specifications, (2) is damaged in shipment (in limited circumstances where title does not transfer until delivery), or (3) is exchanged for an alternative grade of Captisol.
Revenue from research funding under our collaboration agreements is earned and recognized on a percentage-of completion basis as research hours are incurred in accordance with the provisions of each agreement.
Nonrefundable, upfront license fees are recognized as revenue upon delivery of the license, if the license is determined to have standalone value that is not dependent on any future performance by the Company under the applicable collaboration agreement. Nonrefundable contingent event-based payments are recognized as revenue when the contingent event is met, which is usually the earlier of when payments are received or collections are assured, provided that it does not require future performance by the Company. The Company occasionally has sub-license obligations related to arrangements for which it receives license fees, milestones and royalties. The Company evaluates the determination of gross versus net reporting based on each individual agreement.
Sales-based contingent payments from partners are accounted for similarly to royalties, with revenue recognized upon achievement of the sales targets assuming all other revenue recognition criteria for milestones are met. Revenue from development and regulatory milestones is recognized when earned, as evidenced by written acknowledgement from the collaborator, provided that (1) the milestone event is substantive, its achievability was not reasonably assured at the inception of the agreement, and the Company has no further performance obligations relating to that event, and (2) collectability is reasonably assured. If these criteria are not met, the milestone payment is recognized over the remaining period of the Company’s performance obligations under the arrangement.
The Company analyzes its revenue arrangements and other agreements to determine whether there are multiple elements that should be separated and accounted for individually or as a single unit of accounting. For multiple element contracts, arrangement consideration is allocated at the inception of the arrangement to all deliverables on the basis of relative selling price, using a hierarchy to determine selling price. Management first considers vendor-specific objective evidence ("VSOE"), then third-party evidence ("TPE") and if neither VSOE nor TPE exist, the Company uses its best estimate of selling price.
Many of the Company's revenue arrangements involve the bundling of a license with the option to purchase manufactured product. Licenses are granted to pharmaceutical companies for the use of Captisol in the development of pharmaceutical compounds. The licenses may be granted for the use of the Captisol product for all phases of clinical trials and through commercial availability of the host drug or may be limited to certain phases of the clinical trial process. Management believes that the Company's licenses have stand-alone value at the outset of an arrangement because the customer obtains the right to use Captisol in its formulations without any additional input by the Company.
Allowance for Doubtful Accounts
The Company maintains an allowance for doubtful accounts based on the best estimate of the amount of probable losses in the Company’s existing accounts receivable. Accounts receivable that are outstanding longer than their contractual payment terms, ranging from 30 to 90 days, are considered past due. When determining the allowance for doubtful accounts, several factors are taken into consideration, including historical write-off experience and review of specific customer accounts for collectability. Account balances are charged off against the allowance after collection efforts have been exhausted and the potential for recovery is considered remote. There was no allowance for doubtful accounts included in the balance sheets at September 30, 2014 and December 31, 2013.
Accounting for Stock-Based Compensation
Stock-based compensation expense for awards to employees and non-employee directors is recognized on a straight-line basis over the vesting period until the last tranche vests. Compensation cost for consultant awards is recognized over each separate tranche’s vesting period. The following table summarizes stock-based compensation expense recorded as components of research and development expenses and general and administrative expenses for the periods indicated (in thousands):
	Three months ended						Nine months ended
	September 30,						September 30,
	2014			2013			2014		2013
Stock-based compensation expense as a component of:
Research and development expenses	$	1,169		$	438		$	2,814	$	1,272
General and administrative expenses	2,533			1,095			5,981		2,877
	$	3,702		$	1,533		$	8,795	$	4,149
The fair-value for options that were awarded to employees and directors was estimated at the date of grant using the Black-Scholes option valuation model with the following weighted-average assumptions:
	Three months ended			Nine months ended
	September 30,			September 30,
	2014		2013	2014		2013
Risk-free interest rate	1.90%		1.80%	1.90%		1.40%
Dividend yield	—		—	—		—
Expected volatility	67%		70%	68%		70%
Expected term	6.4		6.3	6.4		6.3
Forfeiture rate	8.60%		8.80%	8.6%-9.7%		8.4%-9.8%
The risk-free interest rate is based on the U.S. Treasury yield curve at the time of the grant. The expected term of the employee and non-employee director options is the estimated weighted-average period until exercise or cancellation of vested options (forfeited unvested options are not considered) based on historical experience. The expected term for consultant awards is the remaining period to contractual expiration. Volatility is a measure of the expected amount of variability in the stock price over the expected life of an option expressed as a standard deviation. In making this assumption, the Company used the historical volatility of the Company’s stock price over a period equal to the expected term. The forfeiture rate is based on historical data at the time of the grant.
Preclinical Study and Clinical Trial Accruals
Substantial portions of the Company’s preclinical studies and all of the Company's clinical trials have been performed by third-party laboratories, contract research organizations, or other vendors (collectively "CROs"). Some CROs bill monthly for services performed, while others bill based upon milestone achievement. The Company accrues for each of the agreements it has with CROs on a monthly basis. For preclinical studies, accruals are estimated based upon the percentage of work completed and the contract milestones achieved. For clinical studies, accruals are estimated based upon a percentage of work completed, the number of patients enrolled and the duration of the study. The Company monitors patient enrollment, the progress of clinical studies and related activities to the extent possible through internal reviews of data reported to it by the CROs, correspondence with the CROs and clinical site visits. The Company's estimates are dependent upon the timelines and accuracy of the data provided by its CROs regarding the status of each program and total program spending. The Company periodically evaluates its estimates to determine if adjustments are necessary or appropriate based on information it receives concerning changing circumstances, and conditions or events that may affect such estimates. No material adjustments to preclinical study and clinical trial accrued expenses have been recognized to date.
Sale of Royalty Rights
The Company previously sold to third parties the rights to future royalties of certain of its products. As part of the underlying royalty agreements, the partners have the right to offset a portion of any future royalty payments owed to the Company to the extent of previous milestone payments. Accordingly, the Company deferred a portion of the revenue associated with each tranche of royalty right sold, equal to the pro-rata share of the potential royalty offset. Such amounts associated with the offset rights against future royalty payments will be recognized as revenue upon receipt of future royalties from the respective partners. As of September 30, 2014 there was no deferred revenue remaining related to the sale of royalty rights. As of December 31, 2013, the Company had deferred $0.1 million of revenue related to the sale of royalty rights.
Product Returns
In connection with the sale of the Avinza and Oncology product lines, the Company retained the obligation for returns of product that were shipped to wholesalers prior to the close of the transactions. The accruals for product returns, which were recorded as part of the accounting for the sales transactions, are based on historical experience. Any subsequent changes to the Company’s estimate of product returns are accounted for as a component of discontinued operations.
Milestone Payments
In May 2014, the Company entered into a licensing agreement and research collaboration with Omthera Pharmaceuticals. The research collaboration will target the development of novel products that utilize the proprietary Ligand-developed LTP TECHNOLOGY™ to improve lipid-lowering activity of certain omega-3 fatty acids. The Company is eligible to receive development, regulatory and event-based payments. The completion of a proof of concept under the development program would trigger a $1.0 million payment which would represent a milestone under the milestone method of accounting as (1) it is an event that can only be achieved in part on the Company's past performance, (2) there was substantive uncertainty at the date the arrangement was entered into that the event would be achieved and (3) it results in additional payment being due to the Company. None of the other event-based payments represents a milestone under the milestone method of accounting. No event based payment or milestone was achieved during the periods presented.
Cost of Goods Sold
The Company determines cost using the first-in, first-out method. Cost of goods sold include all costs of purchase and other costs incurred in bringing the inventories to their present location and condition, including costs to store and distribute.
Research and Development
Collaborative research and development expense consists of labor, material, equipment and allocated facility costs of the Company’s scientific staff who are working pursuant to the Company’s collaborative agreements. From time to time, collaborative research and development expense includes costs related to research efforts in excess of those required under certain collaborative agreements. Management has the discretion to set the scope of such excess efforts and may increase or decrease the level of such efforts depending on the Company’s strategic priorities.
Proprietary research and development expense consists of intellectual property in-licensing costs, labor, materials, contracted services, and allocated facility costs that are incurred in connection with internally funded drug discovery and development programs.
Income Taxes
Income taxes are accounted for under the liability method.  This approach requires the recognition of deferred tax assets and liabilities for the expected future tax consequences of differences between the tax basis of assets or liabilities and their carrying amounts in the consolidated financial statements.  A valuation allowance is provided for deferred tax assets if it is more likely than not that these items will either expire before the Company is able to realize their benefit or if future deductibility is uncertain.  As of September 30, 2014, the Company had provided a full valuation allowance against its deferred tax assets as recoverability was uncertain.  Developing the provision for income taxes requires significant judgment and expertise in federal and state income tax laws, regulations and strategies, including the determination of deferred tax assets and liabilities and, if necessary, any valuation allowances that may be required for deferred tax assets.  The Company's judgments and tax strategies are subject to audit by various taxing authorities.  While management believes the Company has provided adequately for its income tax liabilities in its consolidated financial statements, adverse determinations by these taxing authorities could have a material adverse effect on the Company's consolidated financial condition and results of operations.
The Company's ending deferred tax liability represents a future tax obligation for current tax amortization claimed on acquired IPR&D.  As the Company cannot estimate when the IPR&D assets will be amortizable for financial reporting purposes, the deferred tax liability associated with the IPR&D assets cannot be used to support the realization of the Company's deferred tax assets.  As a result, the Company is required to increase its valuation allowance and record a charge to deferred taxes.
Discontinued Operations-Oncology Product Line
In September 2006, the Company and Eisai Inc. and Eisai Co., Ltd. (collectively "Eisai"), entered into a purchase agreement (the "Oncology Purchase Agreement"), pursuant to which Eisai agreed to acquire all of the Company's worldwide rights in and to its oncology products, including, among other things, all related inventory, equipment, records and intellectual property, and to assume certain liabilities as set forth in the Oncology Purchase Agreement. The Oncology product line included the Company's four marketed oncology drugs: Ontak, Targretin capsules, Targretin gel and Panretin gel.
Discontinued Operations-Avinza Product Line
In September 2006, the Company and King Pharmaceuticals, now a subsidiary of Pfizer, entered into a purchase agreement (the "Avinza Purchase Agreement"), pursuant to which Pfizer acquired all of the rights in and to Avinza in the United States, its territories and Canada, including, among other things, all Avinza inventory, records and related intellectual property, and to assume certain liabilities as set forth in the Avinza Purchase Agreement.
Pursuant to the terms of the Avinza Purchase Agreement, the Company retained the liability for returns of product from wholesalers that had been sold by the Company prior to the close of the transaction. Accordingly, as part of the accounting for the gain on the sale of Avinza, the Company recorded a reserve for Avinza product returns.
During the three and nine months ended September 30, 2014 and the three months ended September 30, 2013 the Company did not recognize any gain or loss on the sale of the Avinza product line. The Company recognized a pre-tax gain of$2.6 million for the nine months ended September 30, 2013, due to subsequent changes in certain estimates and liabilities recorded as of the sale date.
Segment Reporting
Under ASC 280, Segment Reporting ("ASC 280"), operating segments are defined as components of an enterprise about which separate financial information is available that is regularly evaluated by the entity’s chief operating decision maker, in deciding how to allocate resources and in assessing performance. The Company has evaluated this codification and has identified two reportable segments: the development and commercialization of drugs using Captisol technology by CyDex and the biopharmaceutical company with a business model that is based upon the concept of developing or acquiring royalty revenue generating assets and coupling them with a lean corporate cost structure.
Comprehensive Income
Comprehensive income represents net income adjusted for the change during the periods presented in unrealized gains and losses on available-for-sale securities less reclassification adjustments for realized gains or losses included in net income. The unrealized gains or losses are reported on the consolidated statements of comprehensive income.
Consolidation of Variable Interest Entities
The Company identifies an entity as a VIE if either: (1) the entity does not have sufficient equity investment at risk to permit the entity to finance its activities without additional subordinated financial support, or (2) the entity's equity investors lack the essential characteristics of a controlling financial interest. The Company performs ongoing qualitative assessments of its VIEs to determine whether the Company has a controlling financial interest in any VIE and therefore is the primary beneficiary. If the Company is the primary beneficiary of a VIE, it must consolidate the VIE under applicable accounting guidance. The Company determined it holds a variable interest in Viking based on management's assessment that it does not have sufficient resources to carry out its principal activities without the support of the Company. The Company's variable interests in Viking are a loan provided by the Company to Viking and a license agreement executed concurrently. As of September 30, 2014, the Company's total assets include $2.9 million related to Viking and the Company's total liabilities include $4.5 million related to Viking. Viking's consolidated assets are owned by Viking, and Viking's consolidated liabilities are without recourse against Ligand.
New Accounting Pronouncements
In February 2013, the Financial Accounting Standards Board ("FASB") issued Accounting Standards Update ("ASU") 2013-02, Reporting of Amounts Reclassified Out of Accumulated Other Comprehensive Income. Under ASU 2013-02, an entity is required to provide information about the amounts reclassified out of Accumulated Other Comprehensive Income ("AOCI") by component. In addition, an entity is required to present, either on the face of the financial statements or in the notes, significant amounts reclassified out of AOCI by the respective line items of net income, but only if the amount reclassified is required to be reclassified in its entirety in the same reporting period. For amounts that are not required to be reclassified in their entirety to net income, an entity is required to cross-reference to other disclosures that provide additional details about those amounts. Implementing ASU 2013-02 did not change the current requirements for reporting net income or other comprehensive income in the financial statements. The amendments in this ASU are effective for the Company for fiscal years, and interim periods within those years, beginning after January 1, 2014. The Company's adoption of this standard did not materially affect the consolidated financial statements.
In July 2013, FASB issued ASU 2013-11, Presentation of an Unrecognized Tax Benefit When a Net Operating Loss Carryforward, a Similar Tax Loss, or a Tax Credit Carryforward Exists. ASU 2013-11 requires the netting of unrecognized tax benefits ("UTBs") against a deferred tax asset for a loss or other carryforward that would apply in settlement of the uncertain tax positions. UTBs are required to be netted against all available same-jurisdiction loss or other tax carryforwards that would be utilized, rather than only against carryforwards that are created by the UTBs. ASU 2013-11 is effective for the Company for interim and annual periods beginning after December 15, 2013. The Company's adoption of this standard did not materially affect the consolidated financial statements.
In April 2014, FASB issued ASU 2014-08, Reporting Discontinued Operations and Disclosures of Disposals of Components of an Entity. ASU 2014-08 raises the threshold for a disposal to qualify as a discontinued operation and modifies the related disclosure requirements. Under the new guidance, only disposals resulting in a strategic shift that will have a major effect on an entity's operations and financial results will be reported as discontinued operations. ASU 2014-08 also removes the requirement that an entity not have any significant continuing involvement in the operations of the component after disposal to qualify for reporting of the disposal as a discontinued operation. The guidance is effective for annual and interim periods beginning after December 15, 2014, with early adoption permitted for any disposal transaction not previously reported. Management does not believe the adoption of this guidance will have a material impact on the Company's consolidated financial statements.
In May 2014, FASB issued ASU 2014-09, Revenue from Contracts with Customers. ASU 2014-09 is effective for annual periods beginning after December 15, 2016 and interim periods within those annual periods. The revenue standard’s core principle is built on the contract between a vendor and a customer for the provision of goods and services. It attempts to depict the exchange of rights and obligations between the parties in the pattern of revenue recognition based on the consideration to which the vendor is entitled. To accomplish this objective, the standard requires five basic steps: (1) identify the contract with the customer, (2) identify the performance obligations in the contract, (3) determine the transaction price, (4) allocate the transaction price to the performance obligations in the contract, (5) recognize revenue when (or as) the entity satisfies a performance obligation. Management is currently evaluating the effect the adoption of this standard will have on the Company's financial statements.
In June 2014, FASB issued ASU 2014-12, Accounting for Share-Based Payments When the Terms of an Award Provide That a Performance Target Could Be Achieved after the Requisite Service Period. The amendments in this update require that a performance target that affects vesting and that could be achieved after the requisite service period be treated as a performance condition. A reporting entity should apply existing guidance in ASC 718, Compensation - Stock Compensation, as it relates to awards with performance conditions that affect vesting to account for such awards. The amendments in this update will be effective for the Company as of January 1, 2016. Earlier adoption is permitted. Entities may apply the amendments in this update either: (1) prospectively to all awards granted or modified after the effective date; or (2) retrospectively to all awards with performance targets that are outstanding as of the beginning of the earliest annual period presented in the financial statements and to all new or modified awards thereafter. If a retrospective transition is adopted, the cumulative effect of applying this update as of the beginning of the earliest annual period presented in the financial statements should be recognized as an adjustment to the opening retained earnings balance at that date. In addition, if a retrospective transition is adopted, an entity may use hindsight in measuring and recognizing the compensation cost. Management is currently assessing the impact of this update, and believes that its adoption on January 1, 2016 will not have a material impact on the Company's consolidated financial statements.
In August 2014, FASB issued ASU 2014-15, Presentation of Financial Statements - Going Concern. The amendments in this update require management to assess an entity’s ability to continue as a going concern by incorporating and expanding upon certain principles that are currently in U.S. auditing standards. Specifically, the amendments (1) provide a definition of the term substantial doubt, (2) require an evaluation every reporting period, including interim periods, (3) provide principles for considering the mitigating effect of management’s plans, (4) require certain disclosures when substantial doubt is alleviated as a result of consideration of management’s plans, (5) require an express statement and other disclosures when substantial doubt is not alleviated, and (6) require an assessment for a period of one year after the date that the financial statements are issued (or available to be issued). The amendments in this update are effective for the Company as of January 1, 2017. Early application is permitted. Management is currently assessing the impact of this update on its future discussion of its liquidity position in the Management’s Discussion and Analysis.

Fair_Value_Measurements

Fair Value Measurements	9 Months Ended
	Sep. 30, 2014
Fair Value Disclosures [Abstract]	'
Fair Value Measurements	'
	Fair Value Measurements
	The Company measures certain financial assets and liabilities at fair value on a recurring basis, including equity securities, co-promote termination payments receivable and the related liability, contingent liabilities, and the Company's convertible senior notes.
	Level 1
	The fair value of the Company’s investments which are classified as short-term investments is determined using quoted market prices in active markets. These securities were received by the Company in December 2012 and June 2014 as a result of an event-based payment and an upfront license payment, respectively, under licensees. Additionally, the liability for CVRs for Metabasis are determined using quoted market prices in active markets.
	Level 2
	The fair value of the Company's convertible senior notes is estimated by using the quoted market rate in an inactive market, which is classified as a Level 2 input.
	Level 3
	The co-promote termination payments receivable represents a non-interest bearing receivable for future payments to be made by Pfizer and is recorded at its fair value. The fair value is subjective and is affected by changes in inputs to the valuation model including management’s assumptions regarding future Avinza product sales. The receivable and liability will remain equal, and are adjusted each reporting period for changes in the fair value of the obligation including any changes in the estimate of future net Avinza product sales. The fair value of the liabilities for CyDex contingent liabilities were determined based on the income approach using a Monte Carlo analysis. The fair value is subjective and is affected by changes in inputs to the valuation model including management’s assumptions regarding revenue volatility, probability of commercialization of products, estimates of timing and probability of achievement of certain revenue thresholds and developmental and regulatory milestones which may be achieved and affect amounts owed to former license holders and CVR holders. Changes in these assumptions can materially affect the fair value estimate.
	The following table provides a summary of the carrying value of assets and liabilities that are measured at fair value on a recurring basis as of September 30, 2014 (in thousands):
	Fair Value Measurements at Reporting Date Using
					Quoted Prices in		Significant		Significant
					Active Markets		Other		Unobservable
					for Identical		Observable		Inputs
					Assets		Inputs
		Total			(Level 1)		(Level 2)		(Level 3)
	Assets:
	Current co-promote termination payments receivable	$	523		$	—	$	—	$	523
	Available-for-sale securities	5,925			5,925		—		—
	Total assets	$	6,448		$	5,925	$	—	$	523
	Liabilities:
	Current contingent liabilities-CyDex	$	4,184		$	—	$	—	$	4,184
	Current co-promote termination liability	523			—		—		523
	Long-term contingent liabilities-Metabasis	3,511			3,511		—		—
	Long-term contingent liabilities-CyDex	8,755			—		—		8,755
	Liability for short-term investments owed to former licensees	917			917		—		—
	Total liabilities	$	17,890		$	4,428	$	—	$	13,462
	The following table provides a summary of the assets and liabilities that are measured at fair value on a recurring basis as of December 31, 2013 (in thousands):
	Fair Value Measurements at Reporting Date Using
					Quoted Prices in		Significant		Significant
					Active Markets		Other		Unobservable
					for Identical		Observable		Inputs
					Assets		Inputs
		Total			(Level 1)		(Level 2)		(Level 3)
	Assets:
	Current portion of co-promote termination payments receivable	$	4,329		$	—	$	—	$	4,329
	Available-for-sale securities	4,340			4,340		—		—
	Long-term portion of co-promote termination payments receivable	7,417			—		—		7,417
	Total assets	$	16,086		$	4,340	$	—	$	11,746
	Liabilities:
	Current portion of contingent liabilities-CyDex	$	1,712		$	—	$	—	$	1,712
	Current portion of co-promote termination liability	4,329			—		—		4,329
	Long-term portion of contingent liabilities-Metabasis	4,196			4,196		—		—
	Long-term portion of contingent liabilities-CyDex	7,599			—		—		7,599
	Liability for short-term investments owed to licensors	651			651		—		—
	Long-term portion of co-promote termination liability	7,417			—		—		7,417
	Total liabilities	$	25,904		$	4,847	$	—	$	21,057
	Other Fair Value Measurements-2019 Convertible Senior Notes
	In August 2014, the Company issued $245.0 million aggregate principal amount of convertible senior unsecured notes due 2019 (the "2019 Convertible Senior Notes"). The Company uses a quoted market rate in an inactive market, which is classified as a Level 2 input, to estimate the current fair value of its 2019 Convertible Senior Notes. The estimated fair value of the 2019 Senior Convertible Notes was $229.8 million as of September 30, 2014. The carrying value of the notes does not reflect the market rate. See Note 7 Financing Arrangements for additional information.
	The following table represents significant unobservable inputs used in determining the fair value of contingent liabilities assumed in the acquisition of CyDex:
		30-Sep-14		31-Dec-13
	Range of annual revenue subject to revenue sharing (1)	$17.9 million-$20.5 million		$4.2 million-$19.8 million
	Revenue volatility	25%		25%
	Average of probability of commercialization	83.80%		67.60%
	Sales beta	0.6		0.6
	Credit rating	B		BBB
	Equity risk premium	6%		6%
	-1	Revenue subject to revenue sharing represent management’s estimate of the range of total annual revenue subject to revenue sharing (i.e. annual revenues in excess of $15 million) through December 31, 2016, which is the term of the CVR agreement.
	A reconciliation of the level 3 financial instruments as of September 30, 2014 is as follows (in thousands):
	Assets:
	Fair value of level 3 financial instrument assets as of December 31, 2013	$	11,746
	Assumed payments made by Pfizer or assignee	(1,002		)
	Fair value adjustments to co-promote termination liability	(10,221		)
	Fair value of level 3 financial instrument assets as of September 30, 2014	$	523
Liabilities:
Fair value of level 3 financial instrument liabilities as of December 31, 2013	$	21,057
Assumed payments made by Pfizer or assignee	(1,002		)
Payments to CVR and other former license holders	(1,936		)
Fair value adjustments to contingent liabilities	5,564
Fair value adjustments to co-promote termination liability	(10,221		)
Fair value of level 3 financial instrument liabilities as of September 30, 2014	$	13,462

Variable_Interest_Entities_Not

Variable Interest Entities (Notes)	9 Months Ended
	Sep. 30, 2014
Organization, Consolidation and Presentation of Financial Statements [Abstract]	'
Variable Interest Entities	'
	Variable Interest Entities
	The Company determined it holds a variable interest in Viking based on management's assessment that Viking does not have sufficient resources to carry out its principal activities without the support of the Company. The Company's variable interests in Viking are a loan provided by the Company to Viking and a license agreement executed concurrently. Additionally, the Company has a shared services and sublease agreement with Viking. The Company examines specific criteria and uses judgment when determining if the Company is the primary beneficiary of a VIE and therefore required to consolidate the investment. Factors considered in determining whether the Company is the primary beneficiary include risk and reward sharing, experience and financial condition of its partner, voting rights, involvement in day-to-day operating decisions, representation on Viking's executive committee, and level of economics between the Company and Viking.
	In May 2014, the Company entered into a Master License Agreement to license rights to five programs to Viking, an unrelated clinical-stage biopharmaceutical company focused on the development of novel therapies for metabolic and endocrine disorders. As part of this transaction, the Company extended a $2.5 million convertible loan facility to Viking that can be used to pay Viking’s operating and financing-related expenses. Under the terms of the convertible loan facility, the principal amount outstanding accrues interest at a fixed rate equal to the lesser of 5% and the maximum interest rate permitted by law. The loan is due and payable in May 2016, unless the loans are converted into equity prior to such time. Upon the earlier to occur of an Initial Public Offering ("IPO") or a qualified financing event, the Company may elect to be repaid in cash or equity equal to 200% of the accrued principal and interest. The Company funded $2.0 million towards the convertible loan facility as of September 30, 2014.
	The debt conversion feature embedded in the loan is accounted for under ASC Topic 815 Derivatives and Hedging. The valuation of the bifurcated debt conversion feature was performed using Level 3 inputs, requiring Viking to make assumptions about the probability of the occurrence of an IPO or qualified financing and the loan being converted based on the applicable conversion terms.
	As partial consideration for the grant of the rights and licenses under the license agreement, in the event Viking consummates an IPO or other qualified financing event, Viking will issue to the Company a certain amount of equity. At the closing of an IPO a number of shares of common stock having an aggregate value of $29.0 million will be issued to the Company, subject to adjustment in certain circumstances. In the event Viking consummates a private financing prior to an IPO, the Company has the option to receive a number of shares of the same class and type of securities issued in the private financing having an aggregate value of $29.0 million, subject to adjustment in certain circumstances. The Company has the right to terminate the license agreement on or after April 30, 2015 if Viking has neither completed an IPO nor received aggregate net proceeds of at least $20.0 million in one or more private financings. The Company also has the right to terminate the license agreement in the event of insolvency or bankruptcy of Viking. On July 1, 2014, Viking filed an initial Form S-1 with the Securities and Exchange Commission for an IPO. As of the date of this report, the filed Form S-1 has not been declared effective. As of September 30, 2014, no amounts have been recorded for the potential receipt of equity related to a financing transaction in accordance with authoritative guidance.
	The following table represents the consolidated assets and liabilities, which are owned by and are obligations of Viking and are with no recourse to the Company, as of September 30, 2014 (in thousands):
		30-Sep-14
	Cash and cash equivalents	$	794
	Other current assets	17
	Capitalized IPO expenses	2,131
	Total current assets	$	2,942
	Other assets	1
	Total assets	$	2,943
	Accounts payable	$	2,225
	Accrued liabilities	77
	Current portion of notes payable	337
	Total current liabilities	$	2,639
	Long-term portion of notes payable	1,893
	Total liabilities	$	4,532
	The Company has recorded 100% of the losses incurred since May 21, 2014, the effective date of the transaction, as net loss attributable to noncontrolling interest due to the fact that it is considered a primary beneficiary with no equity interest in the VIE. The advances under the loan agreement are included as notes payable by Viking and are eliminated in consolidation.

Avinza_CoPromotion

Avinza Co-Promotion	9 Months Ended
	Sep. 30, 2014
Co Promotion [Abstract]	'
AVINZA Co-Promotion	'
	Avinza Co-Promotion
	In 2003, the Company and Organon Pharmaceuticals USA Inc. ("Organon") entered into an agreement for the co-promotion of Avinza. Subsequently in 2006, the Company signed an agreement with Organon that terminated the Avinza co-promotion agreement between the two companies and returned Avinza co-promotion rights to the Company. In consideration of the early termination, the Company agreed to make quarterly royalty payments to Organon equal to 6.5% of Avinza net sales through December 31, 2012 and thereafter equal to 6.0% of Avinza net sales through patent expiration, currently anticipated to be November 2017.
	In January 2006, the Company and King Pharmaceuticals, now a subsidiary of Pfizer, entered into an agreement pursuant to which Pfizer acquired all of the Company’s rights in and to Avinza. Pfizer also assumed the Company’s co-promote termination obligation to make royalty payments to Organon based on net sales of Avinza. In connection with Pfizer's assumption of this obligation, Organon did not consent to the legal assignment of the co-promote termination obligation to Pfizer. Accordingly, the Company remains liable to Organon in the event of Pfizer's default of the obligation. Therefore, the Company recorded an asset as of February 26, 2007 to recognize Pfizer's assumption of the obligation, while continuing to carry the co-promote termination liability in the Company's consolidated financial statements to recognize the Company’s legal obligation as primary obligor to Organon. This asset represents a non-interest bearing receivable for future payments to be made by Pfizer and is recorded at its fair value. The receivable and liability will remain equal, and are adjusted each reporting period for changes in the fair value of the obligation including for any changes in the estimate of future net Avinza product sales. This receivable will be assessed on a quarterly basis or when a triggering event occurs for impairment (e.g. in the event Pfizer defaults on the assumed obligation to pay Organon).
	On a quarterly basis, management reviews the carrying value of the co-promote termination liability. In February 2014, Actavis launched a generic form of Avinza which resulted in a significant decrease in estimates of future net sales used to value the co-promote termination asset and liability. Due to assumptions and judgments inherent in determining the estimates of future net Avinza sales through November 2017, the actual amount of net Avinza sales used to determine the current fair value of the Company’s co-promote termination asset and liability may be materially different from current estimates.
	A summary of the co-promote termination liability as of September 30, 2014 is as follows (in thousands):
	Net present value of payments based on estimated future net Avinza product sales as of December 31, 2013	$	11,746
	Assumed payments made by Pfizer or assignee	(1,002		)
	Fair value adjustments	(10,221		)
	Total co-promote termination liability as of September 30, 2014	$	523

Lease_Obligations

Lease Obligations	9 Months Ended
	Sep. 30, 2014
Leases [Abstract]	'
Lease Obligations	'
	Lease Obligations
	The Company leases office and laboratory facilities in California, Kansas and New Jersey. These leases expire between 2014 and 2019, some of which are subject to annual rent increases which range from 3.0% to 3.5%. The Company currently subleases office and laboratory space in California and New Jersey. The following table provides a summary of operating lease obligations and payments expected to be received from sublease agreements as of September 30, 2014 (in thousands):
	Operating lease obligations:	Lease	Less than 1		1-3 years		3-5 years		More than		Total
		Termination	year						5 years
		Date
	Corporate headquarters-	Jul-19	$	677	$	1,409	$	1,293	$	—	$	3,379
	San Diego, CA
	Bioscience and Technology Business Center-	Dec-17	55		108		13		—		176
	Lawrence, KS
	Vacated office and research facility-San Diego, CA	Jul-15	1,912		—		—		—		1,912
	Vacated office and research facility-	Aug-16	2,576		2,397		—		—		4,973
	Cranbury, NJ
	Total operating lease obligations		$	5,220	$	3,914	$	1,306	$	—	$	10,440
	Sublease payments expected to be received:		Less than 1		1-3 years		3-5 years		More than		Total
			year						5 years
	Office and research facility-	Jul-15	$	771	$	—	$	—	$	—	$	771
	San Diego, CA
	Office and research facility-	August 2014 and 2016	492		464		—		—		956
	Cranbury, NJ
	Net operating lease obligations		$	3,957	$	3,450	$	1,306	$	—	$	8,713
	In 2010, the Company ceased use of its facility located in New Jersey. As a result, the Company recorded lease exit costs of $9.7 million for costs related to the difference between the remaining lease obligations of the abandoned operating leases, which run through August 2016, and management's estimate of potential future sublease income, discounted to present value. In addition, the Company wrote-off property and equipment with a net book value of approximately $5.4 million related to the facility closure.
	As of September 30, 2014 and December 31, 2013, the Company had lease exit obligations of $3.7 million and $5.9 million, respectively. For the three and nine months ended September 30, 2014, the Company made cash payments, net of sublease payments received of $0.8 million and $2.6 million, respectively. The Company recognized adjustments for accretion and changes in leasing assumptions of $0.2 million and $0.5 million for the three and nine months ended September 30, 2014, respectively. For the three and nine months ended September 30, 2013, the Company made cash payments, net of sublease payments received of $0.9 million and $2.8 million, respectively. The Company recognized adjustments for accretion and changes in leasing assumptions of $0.2 million and $0.4 million for the three and nine months ended September 30, 2013, respectively.
	Total rent expense under all office leases for each of the three and nine months ended September 30, 2014 and 2013 was $0.2 million and $0.5 million, respectively. The Company recognizes rent expense on a straight-line basis. Deferred rent at September 30, 2014 and December 31, 2013 was $0.3 million and $0.4 million, respectively, and is included in other long-term liabilities.

Segment_Reporting

Segment Reporting	9 Months Ended
	Sep. 30, 2014
Segment Reporting [Abstract]	'
Segment Reporting	'
	Segment Reporting
	The Company evaluates performance based on the operating income (loss) of the respective business segments. The segment results may not represent actual results that would be expected if they were independent, stand-alone businesses. Segment information is as follows (in thousands):
	Balance Sheet Data:	As of September 30, 2014
		Ligand			CyDex			Total
	Total assets	$	203,296		$	68,987		$	272,283
		As of December 31, 2013
		Ligand			CyDex			Total
	Total assets	$	38,408		$	66,305		$	104,713
	Operating Data:	For the three months ended September 30, 2014
		Ligand			CyDex			Total
	Net revenues from external customers	$	6,424		$	8,549		$	14,973
	Depreciation and amortization expense	(61		)	(601		)	(662		)
	Operating (loss) income	(1,683		)	5,215			3,532
	Interest expense, net	(1,516		)	—			(1,516		)
	Income tax expense from continuing operations	(115		)	(9		)	(124		)
		For the three months ended September 30, 2013
		Ligand			CyDex			Total
	Net revenues from external customers	4,731			8,274			$	13,005
	Depreciation and amortization expense	(62		)	(606		)	$	(668	)
	Operating (loss) income	(1,142		)	4,212			$	3,070
	Interest expense, net	(394		)	—			$	(394	)
	Income tax (expense) benefit from continuing operations	(70		)	10			$	(60	)
	Gain on sale of Avinza Product Line before income taxes	—			—			$	—
		For the nine months ended September 30, 2014
		Ligand			CyDex			Total
	Net revenues from external customers	18,907			22,632			$	41,539
	Depreciation and amortization expense	(194		)	(1,804		)	(1,998		)
	Operating (loss) income	(2,622		)	12,611			9,989
	Interest expense, net	(1,946		)	—			(1,946		)
	Income tax expense from continuing operations	(123		)	(8		)	(131		)
		For the nine months ended September 30, 2013
		Ligand			CyDex			Total
	Net revenues from external customers	$	14,789		$	19,448		$	34,237
	Depreciation and amortization expense	(179		)	(1,828		)	(2,007		)
	Write-off of in-process research and development	—			480			480
	Operating income	(944		)	9,462			8,518
	Interest expense, net	(1,755		)	—			(1,755		)
	Income tax (expense) benefit from continuing operations	(301		)	64			(237		)
	Gain on sale of Avinza Product Line before income taxes	2,588			—			2,588

Financing_Arrangements

Financing Arrangements	9 Months Ended
	Sep. 30, 2014
Debt Disclosure [Abstract]	'
Financing Arrangements	'
	Financing Arrangements
	Term loan facility
	The Company fully repaid its secured term loan credit facility on July 31, 2014. Under the terms of the secured debt, the Company made interest-only payments through February 2013. Subsequent to the interest-only payments, the note amortized with principal and interest payments through the remaining term of the loan. Additionally, the Company made an additional final payment equal to 6% of the total amount borrowed which was due at maturity and was accreted over the life of the loan.
	0.75% Convertible Senior Notes Due 2019
	In August 2014, the Company issued $245.0 million aggregate principal amount of its 2019 Convertible Senior Notes, resulting in net proceeds of $239.3 million. The 2019 Convertible Senior Notes are convertible into common stock at an initial conversion rate of 13.3251 shares per $1,000 principal amount of convertible notes, subject to adjustment upon certain events, which is equivalent to an initial conversion price of approximately $75.05 per share of common stock. The initial conversion price of the notes represents a premium of approximately 35% to the $55.59 per share close price of the Company's common stock on August 12, 2014. The notes bear interest at a rate of 0.75% per year, payable semi-annually. Holders of the 2019 Convertible Senior Notes may convert the notes at any time prior to the close of business on the business day immediately preceding May 15, 2019, under any of the following circumstances: (1) during any fiscal quarter (and only during such fiscal quarter) commencing after December 31, 2014, if, for at least 20 trading days (whether or not consecutive) during the 30 consecutive trading day period ending on the last trading day of the immediately preceding fiscal quarter, the last reported sale price of the Company's common stock on such trading day is greater than 130% of the conversion price on such trading day; (2) during the five business day period immediately following any ten consecutive trading day period, in which the trading price per $1,000 principal amount of notes was less than 98% of the product of the last reported sale price of the Company's common stock on such trading day and the conversion rate on each such trading day; or (3) upon the occurrence of certain specified corporate events as specified in the indenture governing the notes. On or after May 15, 2019 until the close of business on the second scheduled trading day immediately preceding August 15, 2019, holders of the notes may convert all or a portion of their notes at any time, regardless of the foregoing circumstances. Upon conversion, Ligand must deliver cash to settle the principal and may deliver cash or shares of common stock, at the option of the Company, to settle any premium due upon conversion.
	In accordance with accounting guidance for debt related to conversion and other options, the Company separately accounted for the debt and equity components of the 2019 Convertible Senior Notes by allocating the $245.0 million total proceeds between the debt component and the embedded conversion option, or equity component, due to Ligand's ability to settle the 2019 Convertible Senior Notes in cash for the principal portion and to settle any premium in cash or common stock, at the Company's election. The debt allocation was performed in a manner that reflected the Company's non-convertible borrowing rate for similar debt of 5.83% derived from independent valuation analysis. The initial debt value of $192.5 million accretes at 5.83% to reach $245.0 million at the maturity date. The equity component of the 2019 Convertible Senior Notes was recognized as a debt discount and represents the difference between the $245.0 million proceeds at issuance of the 2019 Convertible Senior Notes and the fair value of the debt allocation on their respective issuance dates. The debt discount is amortized to interest expense using the effective interest method over the expected life of a similar liability without an equity component. The notes will have a dilutive effect to the extent the average market price per share of common stock for a given reporting period exceeds the conversion price of $75.05. As of September 30, 2014, the “if-converted value” did not exceed the principal amount of the 2019 Convertible Senior Notes.
	In connection with the issuance of the 2019 Convertible Senior Notes, the Company incurred $5.7 million of issuance costs, which primarily consisted of underwriting, legal and other professional fees. The portions of these costs allocated to the equity components totaling $1.2 million were recorded as a reduction to additional paid-in capital. The portions of these costs allocated to the liability components totaling $4.5 million were recorded as assets on the balance sheet.  The portions allocated to the liability components are amortized to interest expense using the effective interest method over the expected life of the 2019 Convertible Senior Notes.
	The Company determined the expected life of the debt discount for the 2019 Convertible Senior Notes to be equal to the original five-year term of the notes. The carrying value of the equity component related to the 2019 Convertible Senior Notes as of September 30, 2014, net of issuance costs, was $51.3 million.
	Convertible Bond Hedge and Warrant Transactions
	In August 2014, in connection with the issuance of the 2019 Convertible Senior Notes, to minimize the impact of potential dilution to the Company's common stock upon conversion of such notes, the Company entered into convertible bond hedges and sold warrants covering approximately 3,264,643 shares of its common stock. The convertible bond hedges have an exercise price of $75.05 per share and are exercisable when and if the 2019 Convertible Senior Notes are converted. If upon conversion of the 2019 Convertible Senior Notes, the price of the Company's common stock is above the exercise price of the convertible bond hedges, the counterparties will deliver shares of common stock and/or cash with an aggregate value approximately equal to the difference between the price of common stock at the conversion date and the exercise price, multiplied by the number of shares of common stock related to the convertible bond hedge transaction being exercised. The convertible bond hedges and warrants described below are separate transactions entered into by the Company and are not part of the terms of the 2019 Convertible Senior Notes. Holders of the 2019 Convertible Senior Notes and warrants will not have any rights with respect to the convertible bond hedges. The Company paid $48.1 million for these convertible bond hedges and recorded the amount as a reduction to additional paid-in capital.
	Concurrently with the convertible bond hedge transactions, the Company entered into warrant transactions whereby it sold warrants to acquire, approximately 3,264,643 shares of common stock with an exercise price of approximately $125.08 per share, subject to certain adjustments. The warrants have various expiration dates ranging from November 13, 2019 to April 22, 2020. The warrants will have a dilutive effect to the extent the market price per share of common stock exceeds the applicable exercise price of the warrants, as measured under the terms of the warrant transactions. The Company received $11.6 million for these warrants and recorded this amount to additional paid-in capital. The common stock issuable upon exercise of the warrants will be in unregistered shares, and the Company does not have the obligation and does not intend to file any registration statement with the Securities and Exchange Commission registering the issuance of the shares under the warrants.
	The carrying values and the fixed contractual coupon rates of the Company's financing arrangements as of September 30, 2014 and December 31, 2013 were as follows (in thousands):
		30-Sep-14			31-Dec-13
	2019 Convertible Senior Notes
	Principal amount outstanding	$	245,000		$	—
	Unamortized discount	(51,369		)	—
	Net carrying amount	193,631			—
	Convertible notes payable, Viking Therapeutics, Inc.	337			—
	Current portion notes payable, 8.64%, due August 1, 2014	—			6,642
	Current portion notes payable, 8.9012%, due August 1, 2014	—			2,467
	Total notes payable	$	193,968		$	9,109

Stockholders_Equity

Stockholders' Equity	9 Months Ended
	Sep. 30, 2014
Equity [Abstract]	'
Stockholders' Equity	'
	Stockholders’ Equity
	The Company grants options and awards to employees, non-employee consultants, and non-employee directors. Only new shares of common stock are issued upon the exercise of stock options. Non-employee directors are accounted for as employees. Options and restricted stock granted to certain directors vest in equal monthly installments over the one-year period following the date of grant. Options granted to employees vest 1/8 on the six month anniversary of the date of grant, and 1/48 each month thereafter for 42 months. Option awards generally expire ten years from the date of grant.
	Stock Option Activity
	The following is a summary of the Company’s stock option plan activity and related information:
		Shares		Weighted-		Weighted-Average	Aggregate
				Average		Remaining	Intrinsic Value
				Exercise		Contractual Term in	(In thousands)
				Price		Years
	Balance as of December 31, 2013	1,746,709		$	16.79	7.6	$	62,705
	Granted	366,184		73.81
	Exercised	(262,820	)	15.43
	Forfeited	(49,967	)	16.69
	Cancelled	(4,414	)	80.81
	Balance as of September 30, 2014	1,795,692		28.46		7.5	$	43,200
	Exercisable as of September 30, 2014	1,052,706		20		7.5	$	30,339
	Options vested and expected to vest as of September 30, 2014	1,795,692		28.46		6.8	$	43,200
	The weighted-average grant date fair value of all stock options granted during the nine months ended September 30, 2014 was $47.44 per share. The total intrinsic value of all options exercised during the nine months ended September 30, 2014 and 2013 was approximately $14.7 million and $3.6 million, respectively. As of September 30, 2014, there was $14.6 million of total unrecognized compensation cost related to nonvested stock options. That cost is expected to be recognized over a weighted-average period of 2.3 years.
	Net cash received from options exercised during the nine months ended September 30, 2014 and 2013 was approximately $4.1 million and $2.3 million, respectively. There is no current tax benefit related to options exercised because of net operating losses for which a full valuation allowance has been established.
	As of September 30, 2014, 1.1 million shares were available for future option grants or direct issuance under the Company's 2002 Stock Incentive Plan, as amended.
	Restricted Stock Activity
	Restricted stock activity for the nine months ended September 30, 2014 was as follows:
		Shares		Weighted-
				Average Grant
				Date Fair Value
	Nonvested at December 31, 2013	115,386		$	21.93
	Granted	41,671		72.5
	Vested	(74,312	)	25.21
	Cancelled	(3,972	)	18.42
	Nonvested at September 30, 2014	78,773		$	45.77
	Restricted stock awards generally vest over three years. As of September 30, 2014, there was $2.3 million of total unrecognized compensation cost related to nonvested restricted stock. That cost is expected to be recognized over a weighted-average period of 1.5 years.
	Employee Stock Purchase Plan
	The Company's Employee Stock Purchase Plan, as amended and restated (the "Amended ESPP") allows participants to purchase up to 1,250 shares of Ligand common stock during each offering period, but in no event may a participant purchase more than 1,250 shares of common stock during any calendar year. The length of each offering period is six months, and employees are eligible to participate in the first offering period beginning after their hire date.
	The Amended ESPP allows employees to purchase Ligand common stock at the end of each six month period at a price equal to 85% of the lesser of fair market value on either the start date of the period or the last trading day of the period (the "Lookback Provision"). The 15% discount and the Lookback Provision make the Amended ESPP compensatory.  There were 2,230 and 5,016 shares of common stock issued under the amended ESPP during the nine months ended September 30, 2014 and 2013, respectively. The Company recorded compensation expense related to the ESPP of $43,515 and $37,000 for the nine months ended September 30, 2014 and 2013, respectively. As of September 30, 2014, 77,285 shares were available for future purchases under the Amended ESPP.
	Public Offerings
	During the three and nine months ended September 30, 2014 and 2013, the Company did not issue any common shares pursuant to its at-the-market equity issuance plan.
	Corporate Share Repurchases
	In August 2014, the Company's Board of Directors authorized the Company to repurchase up to $200.0 million of its common stock for a period of up to one year. During the three and nine months ended September 30, 2014 the Company repurchased 692,800 common shares pursuant to the repurchase program for an aggregate purchase price of approximately $38.5 million. Subsequent to the end of the quarter through October 30, 2014, the Company repurchased an additional 110,000 common shares for an aggregate purchase price of approximately $5.0 million.

Litigation

Litigation	9 Months Ended
	Sep. 30, 2014
Commitments and Contingencies Disclosure [Abstract]	'
Litigation	'
	Litigation
	The Company records an estimate of a loss when the loss is considered probable and estimable. Where a liability is probable and there is a range of estimated loss and no amount in the range is more likely than any other number in the range, the Company records the minimum estimated liability related to the claim in accordance with ASC Topic 450-Contingencies. As additional information becomes available, the Company assesses the potential liability related to its pending litigation and revises its estimates. Revisions in the Company's estimates of potential liability could materially impact its results of operations.
	Securities Litigation
	On June 8, 2012, a federal securities class action and shareholder derivative lawsuit was filed in the Eastern District of Pennsylvania against Genaera Corporation and its officers, directors, major shareholders and trustee ("Genaera Defendants") for allegedly breaching their fiduciary duties to Genaera shareholders.  The lawsuit also names the Company and its CEO as additional defendants for allegedly aiding and abetting the Genaera Defendants' various breaches of fiduciary duties based on the Company's purchase of a licensing interest in a development-stage pharmaceutical drug program from the Genaera Liquidating Trust in May 2010 and the Company's subsequent sale of half of its interest in the transaction to Biotechnology Value Fund, Inc.
	Following an amendment to the complaint and a round of motions to dismiss, the court dismissed the amended complaint with prejudice on August 12, 2013.  Plaintiff appealed that dismissal on September 10, 2013, and the Third Circuit reversed on October 17, 2014.  The Company intends to continue to vigorously defend against the claims against the Company and its CEO.  Due to the complex nature of the legal and factual issues involved, however, the outcome of this matter is not presently determinable.
	Other Litigation
	On June 19, 2014, a complaint was filed in California Superior Court seeking attorneys’ fees in connection with claims related to executive compensation matters described in the Company’s June 6, 2013 supplemental proxy materials.  On August 1, 2014 the Company filed an answer denying all allegations in the complaint and asserting several affirmative defenses.  Management believes the fees demanded by plaintiffs’ counsel are excessive and the Company intends to defend itself vigorously in the litigation.  Due to the complex nature of the legal and factual issues involved, however, the outcome of this matter is not presently determinable.

Basis_of_Presentation_Policies

Basis of Presentation (Policies)	9 Months Ended
	Sep. 30, 2014
Organization, Consolidation and Presentation of Financial Statements [Abstract]	'
Principles of Consolidation	'
	Principles of Consolidation
	The accompanying unaudited condensed consolidated financial statements include Ligand and its wholly owned subsidiaries, Ligand JVR, Allergan Ligand Retinoid Therapeutics, Seragen, Inc., Pharmacopeia, Inc. ("Pharmacopeia"), Neurogen Corporation ("Neurogen"), CyDex Pharmaceuticals, Inc. ("CyDex"), Metabasis Therapeutics, Inc. ("Metabasis") and Nexus VI, Inc. Also included is Viking Therapeutics, Inc. ("Viking"), a variable interest entity ("VIE") for which the Company is deemed under applicable accounting guidance to be the primary beneficiary. All significant intercompany accounts and transactions have been eliminated in consolidation.
Basis of Presentation	'
	Basis of Presentation
	The Company’s accompanying unaudited condensed consolidated financial statements as of September 30, 2014 and for the three and nine months ended September 30, 2014 and 2013 have been prepared in accordance with accounting principles generally accepted in the United States for interim financial information. Accordingly, they do not include all of the information and footnotes required by accounting principles generally accepted in the United States for annual financial statements. The Company’s unaudited condensed consolidated balance sheet at December 31, 2013 has been derived from the audited financial statements at that date, but does not include all of the information and footnotes required by accounting principles generally accepted in the United States for complete financial statements. In the opinion of management, all adjustments (consisting of normal recurring adjustments) considered necessary for a fair presentation of the financial position and results of operations of the Company and its subsidiaries, have been included. Operating results for the three and nine months ended September 30, 2014 are not necessarily indicative of the results that may be expected for the year ending December 31, 2014. These financial statements should be read in conjunction with the consolidated financial statements and notes therein included in the Company’s annual report on Form 10-K for the year ended December 31, 2013
Use of Estimates	'
	Use of Estimates
	The preparation of condensed consolidated financial statements in conformity with accounting principles generally accepted in the United States requires the use of estimates and assumptions that affect the reported amounts of assets, liabilities, revenue, expenses, contingent assets and liabilities, definite and indefinite lived intangible assets, goodwill, co-promote termination payments receivable and co-promote termination liabilities, uncertain tax positions, deferred revenue, lease exit liability and income tax net operating loss carryforwards during the reporting period. The Company’s critical accounting policies are those that are both most important to the Company’s financial condition and results of operations and require the most difficult, subjective or complex judgments on the part of management in their application, often as a result of the need to make estimates about the effect of matters that are inherently uncertain. Because of the uncertainty of factors surrounding the estimates or judgments used in the preparation of the condensed consolidated financial statements, actual results may materially vary from these estimates.
Income Per Share	'
	Income Per Share
	Basic income per share is calculated by dividing net income by the weighted-average number of common shares and vested restricted stock units outstanding. Diluted income per share is computed by dividing net income by the weighted-average number of common shares and vested restricted stock units outstanding and the weighted-average number of dilutive common stock equivalents, including stock options, non-vested restricted stock units, convertible notes and warrants. Common stock equivalents are only included in the diluted income per share calculation when their effect is dilutive.
Cash, Cash Equivalents and Short-term Investments	'
	Cash, Cash Equivalents and Short-term Investments
	Cash and cash equivalents consist of cash and highly liquid securities with maturities at the date of acquisition of three months or less. Securities received by the Company as a result of a milestone payment from licensees are considered short-term investments and have been classified by management as available-for-sale. Such investments are carried at fair value, with unrealized gains and losses included in the statement of comprehensive income (loss). The Company determines the cost of investments based on the specific identification method.
Restricted Cash and Investments	'
	Restricted Cash and Investments
	Restricted cash and investments consist of certificates of deposit held with a financial institution as collateral under a facility lease and third-party service provider arrangements.
Concentrations of Credit Risk	'
	Concentrations of Credit Risk
	Financial instruments that potentially subject the Company to significant concentrations of credit risk consist primarily of cash equivalents, investments and accounts receivable.
	The Company invests its excess cash principally in U.S. government debt securities, investment-grade corporate debt securities and certificates of deposit. The Company has established guidelines relative to diversification and maturities that maintain safety and liquidity. These guidelines are periodically reviewed and modified to take advantage of trends in yields and interest rates. The Company did not experience any significant losses on its cash equivalents, short-term investments or restricted investments for the periods ending September 30, 2014 and December 31, 2013.
	As of September 30, 2014 and December 31, 2013, cash deposits held at financial institutions in excess of FDIC insured amounts of $250,000 were approximately $92.8 million and $11.1 million, respectively.
	Accounts receivable from one customer was 57% of total accounts receivable at September 30, 2014. Accounts receivable from two customers was 75% of total accounts receivable at December 31, 2013.
	The Company currently obtains Captisol from a single supplier.  If this supplier were not able to supply the requested amounts of Captisol and the Company's existing inventory was depleted, the Company would be unable to continue to derive revenues from the sale of Captisol until it obtained an alternative source, which might take a considerable length of time. The Company maintains inventory of Captisol, which has a five year shelf life, at three geographically spread storage locations in the United States and Europe.  If a disaster were to strike any of these locations, it could lead to supply interruptions.
Inventory	'
	Inventory
	Inventory is stated at the lower of cost or market value. The Company determines cost using the first-in, first-out method. The Company analyzes its inventory levels periodically and writes down inventory to its net realizable value if it has become obsolete, has a cost basis in excess of its expected net realizable value or is in excess of expected requirements.
Property and Equipment	'
	Depreciation of equipment is computed using the straight-line method over the estimated useful lives of the assets, which range from three to ten years. Leasehold improvements are amortized using the straight-line method over their estimated useful lives or their related lease term, whichever is shorter. Depreciation expense recognized for the three months ended September 30, 2014 and 2013 was $0.1 million. Depreciation expense for the nine months ended September 30, 2014 and 2013 was $0.2 million. Depreciation expense is included in operating expenses.
Goodwill and Other Identifiable Intangible Assets	'
	The Company accounts for goodwill and other intangible assets in accordance with Accounting Standards Codification ("ASC") Topic 350 - Intangibles - Goodwill and Other which, among other things, establishes standards for goodwill acquired in a business combination, eliminates the amortization of goodwill and requires the carrying value of goodwill and certain non-amortizing intangibles to be evaluated for impairment on an annual basis. The Company uses the income approach and the market approach, each weighted at 50%, when performing its goodwill impairment analysis. For the income approach, the Company considers the present value of future cash flows and the carrying value of its assets and liabilities, including goodwill. The market approach is based on an analysis of revenue multiples of peer public companies. If the carrying value of the assets and liabilities, including goodwill, were to exceed the Company’s estimation of the fair value, the Company would record an impairment charge in an amount equal to the excess of the carrying value of goodwill over the implied fair value of the goodwill. The Company performs an evaluation of goodwill and other intangibles as of December 31 of each year, absent any indicators of earlier impairment, to ensure that impairment charges, if applicable, are reflected in the Company's financial results before December 31 of each year. When it is determined that impairment has occurred, a charge to operations is recorded. Goodwill and other intangible asset balances are included in the identifiable assets of the business segment to which they have been assigned. Any goodwill impairment, as well as the amortization of other purchased intangible assets, is charged against the respective business segments' operating income.
	Amortization of definite-lived intangible assets is computed using the straight-line method over the estimated useful life of the asset of 20 years. Amortization expense of $0.6 million and $1.8 million was recognized for each of the three and nine months ended September 30, 2014 and 2013, respectively. Estimated amortization expense for the years ending December 31, 2014 through 2018 is $2.4 million per year.
Acquired In-Process Research and Development	'
	Acquired In-Process Research and Development
	Intangible assets related to acquired in-process research and development ("IPR&D") are considered to be indefinite-lived until the completion or abandonment of the associated research and development efforts. During the period the assets are considered to be indefinite-lived, they will not be amortized but will be tested for impairment on an annual basis and between annual tests if the Company becomes aware of any events occurring or changes in circumstances that would indicate a reduction in the fair value of the IPR&D projects below their respective carrying amounts. If and when development is complete, which generally occurs if and when regulatory approval to market a product is obtained, the associated assets would be deemed definite-lived and would then be amortized based on their respective estimated useful lives at that point in time. For the three and nine months ended September 30, 2014 and the three months ended September 30, 2013 there was no impairment of IPR&D. For the nine months ended September 30, 2013, the Company recorded a non-cash impairment charge of $0.5 million for the write-off of IPR&D for Captisol-enabled Clopidogrel (MDCO-157). The asset was impaired upon notification from the Medicines Company that they intended to terminate the license agreement and return the rights of the compound to the Company. MDCO-157 is an intravenous option of the anti-platelet medication designed for situations where the administration of oral platelet inhibitors is not feasible or desirable.
Impairment of Long-Lived Assets	'
	Impairment of Long-Lived Assets
	Management reviews long-lived assets for impairment annually or whenever events or changes in circumstances indicate the carrying amount of an asset may not be recoverable. Recoverability of assets to be held and used is measured by a comparison of the carrying amount of an asset to future undiscounted net cash flows expected to be generated by the asset. If such assets are considered to be impaired, the impairment to be recognized is measured as the amount by which the carrying amount of the assets exceeds the fair value of the assets. Fair value for the Company’s long-lived assets is determined using the expected cash flows discounted at a rate commensurate with the risk involved. As of September 30, 2014, management does not believe there have been any events or circumstances indicating that the carrying amount of its long-lived assets may not be recoverable.
Commercial license rights	'
	Commercial license rights
	Commercial license rights represent a portfolio of future milestone and royalty payment rights acquired in accordance with the Royalty Stream and Milestone Payments Purchase Agreement entered into with Selexis SA ("Selexis") in April 2013.  The portfolio consists of over 15 Selexis commercial license agreement programs with various pharmaceutical-company counterparties.  The purchase price was $4.6 million, inclusive of acquisition costs. The Company paid $3.6 million upon closing and paid an additional $1.0 million in April 2014. Individual commercial license rights acquired under the agreement are carried at allocated cost and approximate fair value. The carrying value of the license rights will be reduced on a pro-rata basis as revenue is realized over the term of the agreement. Declines in the fair value of individual license rights below their carrying value that are deemed to be other than temporary are reflected in earnings in the period such determination is made. As of September 30, 2014, management does not believe there have been any events or circumstances indicating that the carrying amount of its commercial license rights may not be recoverable.
Contingent Liabilities	'
	Contingent Liabilities
	In connection with the Company’s acquisition of CyDex in January 2011, the Company recorded a $17.6 million contingent liability, inclusive of the $4.3 million payment made in January 2012, for amounts potentially due to holders of the CyDex contingent value rights ("CVRs") and former license holders. The liability is periodically assessed based on events and circumstances related to the underlying milestones, royalties and material sales. Any change in fair value is recorded in the Company’s consolidated statements of operations. The carrying amount of the liability may fluctuate significantly and actual amounts paid under the CVR agreements may be materially different than the carrying amount of the liability. The fair value of the liability at September 30, 2014 and December 31, 2013 was $12.9 million and $9.3 million, respectively. The Company recorded a fair-value adjustment to increase the liability for CyDex-related contingent liabilities by $2.8 million and $5.6 million for the three and nine months ended September 30, 2014, respectively, and an adjustment to increase the liability by $1.2 million and to decrease the liability by $2.1 million for the three and nine months ended September 30, 2013, respectively. There was a revenue-sharing payment of $1.6 million made during the nine months ended September 30, 2014, and no revenue sharing payments were made during the three months ended September 30, 2014 and three and nine months ended September 30, 2013. Other contingency payments related to the CyDex acquisition of $0.3 million were made during the three and nine months ended September 30, 2014 and other contingency payments of $0.1 million were made during the three and nine months ended September 30, 2013.
	In connection with the Company’s acquisition of Metabasis in January 2010, the Company issued to Metabasis stockholders four tradable CVRs, one CVR from each of four respective series of CVR, for each Metabasis share. The CVRs will entitle Metabasis stockholders to cash payments as frequently as every six months as cash is received by the Company from proceeds from the sale or partnering of any of the Metabasis drug development programs, among other triggering events. The fair values of the CVRs are remeasured at each reporting date through the term of the related agreement. Changes in the fair values are reported in the statement of operations as income (decreases) or expense (increases). The carrying amount of the liability may fluctuate significantly based upon quoted market prices and actual amounts paid under the agreements may be materially different than the carrying amount of the liability.
Fair Value of Financial Instruments	'
	Fair Value of Financial Instruments
	Fair value is defined as the exit price that would be received to sell an asset or paid to transfer a liability. Fair value is a market-based measurement that should be determined using assumptions that market participants would use in pricing an asset or liability. The Company establishes a three-level hierarchy to prioritize the inputs used in measuring fair value. The levels are described in the below with level 1 having the highest priority and level 3 having the lowest:
	Level 1 - Quoted prices in active markets;
	Level 2 - Inputs other than the quoted prices in active markets that are observable either directly or indirectly; and
	Level 3 - Unobservable inputs in which there is little or no market data, which require the Company to develop its own assumptions.
	The Company’s short-term investments include investments in equity securities which the Company received as a result of event-based and upfront payments from licensees. Additionally, there is a liability related to the investment in equity securities for amounts owed to former license holders. The Metabasis CVR liability is marked-to-market at each reporting period based upon the quoted market prices of the underlying CVR. The fair value of the CyDex contingent liabilities are determined at each reporting period based upon an income valuation model. The co-promote termination payments receivable represents a non-interest-bearing receivable for future payments to be made by Pfizer related to Avinza product sales and is recorded at its fair value. The receivable and liability will remain equal, and are adjusted each quarter for changes in the fair value of the obligation including any changes in the estimate of future net Avinza product sales.
	The Company evaluates its financial instruments at each reporting period to determine if any transfers between the various three-level hierarchy have occurred and appropriately reclassifies its financial instruments to the appropriate level within the hierarchy.
Revenue Recognition	'
	Revenue Recognition
	Royalties on sales of products commercialized by the Company’s partners are recognized in the quarter reported by the respective partner. Generally, the Company receives royalty reports from its licensees approximately one quarter in arrears due to the fact that its agreements require partners to report product sales between 30 and 60 days after the end of the quarter. The Company recognizes royalty revenues when it can reliably estimate such amounts and collectability is reasonably assured. Under this accounting policy, the royalty revenues reported are not based upon estimates and such royalty revenues are typically reported to the Company by its partners in the same period in which payment is received.
	Revenue from material sales of Captisol is recognized upon transfer of title, which normally passes upon shipment to the customer. The Company’s credit and exchange policy includes provisions for the return of product between 30 to 90 days, depending on the specific terms of the individual agreement, when that product (1) does not meet specifications, (2) is damaged in shipment (in limited circumstances where title does not transfer until delivery), or (3) is exchanged for an alternative grade of Captisol.
	Revenue from research funding under our collaboration agreements is earned and recognized on a percentage-of completion basis as research hours are incurred in accordance with the provisions of each agreement.
	Nonrefundable, upfront license fees are recognized as revenue upon delivery of the license, if the license is determined to have standalone value that is not dependent on any future performance by the Company under the applicable collaboration agreement. Nonrefundable contingent event-based payments are recognized as revenue when the contingent event is met, which is usually the earlier of when payments are received or collections are assured, provided that it does not require future performance by the Company. The Company occasionally has sub-license obligations related to arrangements for which it receives license fees, milestones and royalties. The Company evaluates the determination of gross versus net reporting based on each individual agreement.
	Sales-based contingent payments from partners are accounted for similarly to royalties, with revenue recognized upon achievement of the sales targets assuming all other revenue recognition criteria for milestones are met. Revenue from development and regulatory milestones is recognized when earned, as evidenced by written acknowledgement from the collaborator, provided that (1) the milestone event is substantive, its achievability was not reasonably assured at the inception of the agreement, and the Company has no further performance obligations relating to that event, and (2) collectability is reasonably assured. If these criteria are not met, the milestone payment is recognized over the remaining period of the Company’s performance obligations under the arrangement.
	The Company analyzes its revenue arrangements and other agreements to determine whether there are multiple elements that should be separated and accounted for individually or as a single unit of accounting. For multiple element contracts, arrangement consideration is allocated at the inception of the arrangement to all deliverables on the basis of relative selling price, using a hierarchy to determine selling price. Management first considers vendor-specific objective evidence ("VSOE"), then third-party evidence ("TPE") and if neither VSOE nor TPE exist, the Company uses its best estimate of selling price.
	Many of the Company's revenue arrangements involve the bundling of a license with the option to purchase manufactured product. Licenses are granted to pharmaceutical companies for the use of Captisol in the development of pharmaceutical compounds. The licenses may be granted for the use of the Captisol product for all phases of clinical trials and through commercial availability of the host drug or may be limited to certain phases of the clinical trial process. Management believes that the Company's licenses have stand-alone value at the outset of an arrangement because the customer obtains the right to use Captisol in its formulations without any additional input by the Company.
Allowance for Doubtful Accounts	'
	Allowance for Doubtful Accounts
	The Company maintains an allowance for doubtful accounts based on the best estimate of the amount of probable losses in the Company’s existing accounts receivable. Accounts receivable that are outstanding longer than their contractual payment terms, ranging from 30 to 90 days, are considered past due. When determining the allowance for doubtful accounts, several factors are taken into consideration, including historical write-off experience and review of specific customer accounts for collectability. Account balances are charged off against the allowance after collection efforts have been exhausted and the potential for recovery is considered remote.
Accounting for Stock-Based Compensation	'
	The risk-free interest rate is based on the U.S. Treasury yield curve at the time of the grant. The expected term of the employee and non-employee director options is the estimated weighted-average period until exercise or cancellation of vested options (forfeited unvested options are not considered) based on historical experience. The expected term for consultant awards is the remaining period to contractual expiration. Volatility is a measure of the expected amount of variability in the stock price over the expected life of an option expressed as a standard deviation. In making this assumption, the Company used the historical volatility of the Company’s stock price over a period equal to the expected term. The forfeiture rate is based on historical data at the time of the grant.
	Accounting for Stock-Based Compensation
	Stock-based compensation expense for awards to employees and non-employee directors is recognized on a straight-line basis over the vesting period until the last tranche vests. Compensation cost for consultant awards is recognized over each separate tranche’s vesting period.
Preclinical Study and Clinical Trial Accruals	'
	Preclinical Study and Clinical Trial Accruals
	Substantial portions of the Company’s preclinical studies and all of the Company's clinical trials have been performed by third-party laboratories, contract research organizations, or other vendors (collectively "CROs"). Some CROs bill monthly for services performed, while others bill based upon milestone achievement. The Company accrues for each of the agreements it has with CROs on a monthly basis. For preclinical studies, accruals are estimated based upon the percentage of work completed and the contract milestones achieved. For clinical studies, accruals are estimated based upon a percentage of work completed, the number of patients enrolled and the duration of the study. The Company monitors patient enrollment, the progress of clinical studies and related activities to the extent possible through internal reviews of data reported to it by the CROs, correspondence with the CROs and clinical site visits. The Company's estimates are dependent upon the timelines and accuracy of the data provided by its CROs regarding the status of each program and total program spending. The Company periodically evaluates its estimates to determine if adjustments are necessary or appropriate based on information it receives concerning changing circumstances, and conditions or events that may affect such estimates. No material adjustments to preclinical study and clinical trial accrued expenses have been recognized to date.
Sale of Royalty Rights	'
	Sale of Royalty Rights
	The Company previously sold to third parties the rights to future royalties of certain of its products. As part of the underlying royalty agreements, the partners have the right to offset a portion of any future royalty payments owed to the Company to the extent of previous milestone payments. Accordingly, the Company deferred a portion of the revenue associated with each tranche of royalty right sold, equal to the pro-rata share of the potential royalty offset. Such amounts associated with the offset rights against future royalty payments will be recognized as revenue upon receipt of future royalties from the respective partners.
Product Returns	'
	Product Returns
	In connection with the sale of the Avinza and Oncology product lines, the Company retained the obligation for returns of product that were shipped to wholesalers prior to the close of the transactions. The accruals for product returns, which were recorded as part of the accounting for the sales transactions, are based on historical experience. Any subsequent changes to the Company’s estimate of product returns are accounted for as a component of discontinued operations.
Milestone Payments	'
	Milestone Payments
	In May 2014, the Company entered into a licensing agreement and research collaboration with Omthera Pharmaceuticals. The research collaboration will target the development of novel products that utilize the proprietary Ligand-developed LTP TECHNOLOGY™ to improve lipid-lowering activity of certain omega-3 fatty acids. The Company is eligible to receive development, regulatory and event-based payments. The completion of a proof of concept under the development program would trigger a $1.0 million payment which would represent a milestone under the milestone method of accounting as (1) it is an event that can only be achieved in part on the Company's past performance, (2) there was substantive uncertainty at the date the arrangement was entered into that the event would be achieved and (3) it results in additional payment being due to the Company. None of the other event-based payments represents a milestone under the milestone method of accounting. No event based payment or milestone was achieved during the periods presented.
Cost of Goods Sold	'
	Cost of Goods Sold
	The Company determines cost using the first-in, first-out method. Cost of goods sold include all costs of purchase and other costs incurred in bringing the inventories to their present location and condition, including costs to store and distribute.
Research and Development	'
	Research and Development
	Collaborative research and development expense consists of labor, material, equipment and allocated facility costs of the Company’s scientific staff who are working pursuant to the Company’s collaborative agreements. From time to time, collaborative research and development expense includes costs related to research efforts in excess of those required under certain collaborative agreements. Management has the discretion to set the scope of such excess efforts and may increase or decrease the level of such efforts depending on the Company’s strategic priorities.
	Proprietary research and development expense consists of intellectual property in-licensing costs, labor, materials, contracted services, and allocated facility costs that are incurred in connection with internally funded drug discovery and development programs.
Income Taxes	'
	Income Taxes
	Income taxes are accounted for under the liability method.  This approach requires the recognition of deferred tax assets and liabilities for the expected future tax consequences of differences between the tax basis of assets or liabilities and their carrying amounts in the consolidated financial statements.  A valuation allowance is provided for deferred tax assets if it is more likely than not that these items will either expire before the Company is able to realize their benefit or if future deductibility is uncertain.  As of September 30, 2014, the Company had provided a full valuation allowance against its deferred tax assets as recoverability was uncertain.  Developing the provision for income taxes requires significant judgment and expertise in federal and state income tax laws, regulations and strategies, including the determination of deferred tax assets and liabilities and, if necessary, any valuation allowances that may be required for deferred tax assets.  The Company's judgments and tax strategies are subject to audit by various taxing authorities.  While management believes the Company has provided adequately for its income tax liabilities in its consolidated financial statements, adverse determinations by these taxing authorities could have a material adverse effect on the Company's consolidated financial condition and results of operations.
	The Company's ending deferred tax liability represents a future tax obligation for current tax amortization claimed on acquired IPR&D.  As the Company cannot estimate when the IPR&D assets will be amortizable for financial reporting purposes, the deferred tax liability associated with the IPR&D assets cannot be used to support the realization of the Company's deferred tax assets.  As a result, the Company is required to increase its valuation allowance and record a charge to deferred taxes.
Discontinued Operations	'
	Discontinued Operations-Oncology Product Line
	In September 2006, the Company and Eisai Inc. and Eisai Co., Ltd. (collectively "Eisai"), entered into a purchase agreement (the "Oncology Purchase Agreement"), pursuant to which Eisai agreed to acquire all of the Company's worldwide rights in and to its oncology products, including, among other things, all related inventory, equipment, records and intellectual property, and to assume certain liabilities as set forth in the Oncology Purchase Agreement. The Oncology product line included the Company's four marketed oncology drugs: Ontak, Targretin capsules, Targretin gel and Panretin gel.
	Discontinued Operations-Avinza Product Line
	In September 2006, the Company and King Pharmaceuticals, now a subsidiary of Pfizer, entered into a purchase agreement (the "Avinza Purchase Agreement"), pursuant to which Pfizer acquired all of the rights in and to Avinza in the United States, its territories and Canada, including, among other things, all Avinza inventory, records and related intellectual property, and to assume certain liabilities as set forth in the Avinza Purchase Agreement.
	Pursuant to the terms of the Avinza Purchase Agreement, the Company retained the liability for returns of product from wholesalers that had been sold by the Company prior to the close of the transaction. Accordingly, as part of the accounting for the gain on the sale of Avinza, the Company recorded a reserve for Avinza product returns.
Segment Reporting	'
	Segment Reporting
	Under ASC 280, Segment Reporting ("ASC 280"), operating segments are defined as components of an enterprise about which separate financial information is available that is regularly evaluated by the entity’s chief operating decision maker, in deciding how to allocate resources and in assessing performance. The Company has evaluated this codification and has identified two reportable segments: the development and commercialization of drugs using Captisol technology by CyDex and the biopharmaceutical company with a business model that is based upon the concept of developing or acquiring royalty revenue generating assets and coupling them with a lean corporate cost structure.
Comprehensive Income	'
	Comprehensive Income
	Comprehensive income represents net income adjusted for the change during the periods presented in unrealized gains and losses on available-for-sale securities less reclassification adjustments for realized gains or losses included in net income. The unrealized gains or losses are reported on the consolidated statements of comprehensive income.
Consolidation of Variable Interest Entities	'
	Consolidation of Variable Interest Entities
	The Company identifies an entity as a VIE if either: (1) the entity does not have sufficient equity investment at risk to permit the entity to finance its activities without additional subordinated financial support, or (2) the entity's equity investors lack the essential characteristics of a controlling financial interest. The Company performs ongoing qualitative assessments of its VIEs to determine whether the Company has a controlling financial interest in any VIE and therefore is the primary beneficiary. If the Company is the primary beneficiary of a VIE, it must consolidate the VIE under applicable accounting guidance. The Company determined it holds a variable interest in Viking based on management's assessment that it does not have sufficient resources to carry out its principal activities without the support of the Company. The Company's variable interests in Viking are a loan provided by the Company to Viking and a license agreement executed concurrently. As of September 30, 2014, the Company's total assets include $2.9 million related to Viking and the Company's total liabilities include $4.5 million related to Viking. Viking's consolidated assets are owned by Viking, and Viking's consolidated liabilities are without recourse against Ligand.
New Accounting Pronouncements	'
	New Accounting Pronouncements
	In February 2013, the Financial Accounting Standards Board ("FASB") issued Accounting Standards Update ("ASU") 2013-02, Reporting of Amounts Reclassified Out of Accumulated Other Comprehensive Income. Under ASU 2013-02, an entity is required to provide information about the amounts reclassified out of Accumulated Other Comprehensive Income ("AOCI") by component. In addition, an entity is required to present, either on the face of the financial statements or in the notes, significant amounts reclassified out of AOCI by the respective line items of net income, but only if the amount reclassified is required to be reclassified in its entirety in the same reporting period. For amounts that are not required to be reclassified in their entirety to net income, an entity is required to cross-reference to other disclosures that provide additional details about those amounts. Implementing ASU 2013-02 did not change the current requirements for reporting net income or other comprehensive income in the financial statements. The amendments in this ASU are effective for the Company for fiscal years, and interim periods within those years, beginning after January 1, 2014. The Company's adoption of this standard did not materially affect the consolidated financial statements.
	In July 2013, FASB issued ASU 2013-11, Presentation of an Unrecognized Tax Benefit When a Net Operating Loss Carryforward, a Similar Tax Loss, or a Tax Credit Carryforward Exists. ASU 2013-11 requires the netting of unrecognized tax benefits ("UTBs") against a deferred tax asset for a loss or other carryforward that would apply in settlement of the uncertain tax positions. UTBs are required to be netted against all available same-jurisdiction loss or other tax carryforwards that would be utilized, rather than only against carryforwards that are created by the UTBs. ASU 2013-11 is effective for the Company for interim and annual periods beginning after December 15, 2013. The Company's adoption of this standard did not materially affect the consolidated financial statements.
	In April 2014, FASB issued ASU 2014-08, Reporting Discontinued Operations and Disclosures of Disposals of Components of an Entity. ASU 2014-08 raises the threshold for a disposal to qualify as a discontinued operation and modifies the related disclosure requirements. Under the new guidance, only disposals resulting in a strategic shift that will have a major effect on an entity's operations and financial results will be reported as discontinued operations. ASU 2014-08 also removes the requirement that an entity not have any significant continuing involvement in the operations of the component after disposal to qualify for reporting of the disposal as a discontinued operation. The guidance is effective for annual and interim periods beginning after December 15, 2014, with early adoption permitted for any disposal transaction not previously reported. Management does not believe the adoption of this guidance will have a material impact on the Company's consolidated financial statements.
	In May 2014, FASB issued ASU 2014-09, Revenue from Contracts with Customers. ASU 2014-09 is effective for annual periods beginning after December 15, 2016 and interim periods within those annual periods. The revenue standard’s core principle is built on the contract between a vendor and a customer for the provision of goods and services. It attempts to depict the exchange of rights and obligations between the parties in the pattern of revenue recognition based on the consideration to which the vendor is entitled. To accomplish this objective, the standard requires five basic steps: (1) identify the contract with the customer, (2) identify the performance obligations in the contract, (3) determine the transaction price, (4) allocate the transaction price to the performance obligations in the contract, (5) recognize revenue when (or as) the entity satisfies a performance obligation. Management is currently evaluating the effect the adoption of this standard will have on the Company's financial statements.
	In June 2014, FASB issued ASU 2014-12, Accounting for Share-Based Payments When the Terms of an Award Provide That a Performance Target Could Be Achieved after the Requisite Service Period. The amendments in this update require that a performance target that affects vesting and that could be achieved after the requisite service period be treated as a performance condition. A reporting entity should apply existing guidance in ASC 718, Compensation - Stock Compensation, as it relates to awards with performance conditions that affect vesting to account for such awards. The amendments in this update will be effective for the Company as of January 1, 2016. Earlier adoption is permitted. Entities may apply the amendments in this update either: (1) prospectively to all awards granted or modified after the effective date; or (2) retrospectively to all awards with performance targets that are outstanding as of the beginning of the earliest annual period presented in the financial statements and to all new or modified awards thereafter. If a retrospective transition is adopted, the cumulative effect of applying this update as of the beginning of the earliest annual period presented in the financial statements should be recognized as an adjustment to the opening retained earnings balance at that date. In addition, if a retrospective transition is adopted, an entity may use hindsight in measuring and recognizing the compensation cost. Management is currently assessing the impact of this update, and believes that its adoption on January 1, 2016 will not have a material impact on the Company's consolidated financial statements.
	In August 2014, FASB issued ASU 2014-15, Presentation of Financial Statements - Going Concern. The amendments in this update require management to assess an entity’s ability to continue as a going concern by incorporating and expanding upon certain principles that are currently in U.S. auditing standards. Specifically, the amendments (1) provide a definition of the term substantial doubt, (2) require an evaluation every reporting period, including interim periods, (3) provide principles for considering the mitigating effect of management’s plans, (4) require certain disclosures when substantial doubt is alleviated as a result of consideration of management’s plans, (5) require an express statement and other disclosures when substantial doubt is not alleviated, and (6) require an assessment for a period of one year after the date that the financial statements are issued (or available to be issued). The amendments in this update are effective for the Company as of January 1, 2017. Early application is permitted. Management is currently assessing the impact of this update on its future discussion of its liquidity position in the Management’s Discussion and Analysis.

Basis_of_Presentation_Tables

Basis of Presentation (Tables)	9 Months Ended
	Sep. 30, 2014
Organization, Consolidation and Presentation of Financial Statements [Abstract]	'
Summary of computation of basic and diluted net income (loss) per share	'
	The following table sets forth the computation of basic and diluted net income per share for the periods indicated (in thousands, except per share amounts):
		Three months ended						Nine months ended
		September 30,						September 30,
		2014			2013			2014		2013
	EPS attributable to common shareholders:
	Net income from continuing operations	$	1,280		$	1,965		4,969		$	6,963
	Net income from discontinued operations	—			—			—		2,588
	Net income	$	1,280		$	1,965		$	4,969	$	9,551
	Shares used to compute basic income per share	20,417,187			20,357,558			20,584,469		20,268,261
	Dilutive potential common shares:
	Restricted stock	22,531			77,609			37,387		62,051
	Stock options	905,593			408,575			1,010,665		232,310
	Shares used to compute diluted income per share	21,345,311			20,843,742			21,632,521		20,562,622
	Basic per share amounts:
	Income from continuing operations	$	0.06		$	0.1		$	0.24	$	0.34
	Income from discontinued operations	—			—			—		0.13
	Net income	$	0.06		$	0.1		$	0.24	$	0.47
	Diluted per share amounts:
	Income from continuing operations	$	0.06		$	0.09		$	0.23	$	0.33
	Income from discontinued operations	—			—			—		0.13
	Net income	$	0.06		$	0.09		$	0.23	$	0.46
Summary of investment categories	'
	The following table summarizes the various investment categories at September 30, 2014 and December 31, 2013 (in thousands):
		Cost			Gross unrealized			Gross unrealized		Estimated
					gains			losses		fair value
	30-Sep-14
	Short-term investments	$	1,426		$	4,499		$	—	$	5,925
	Certificates of deposit-restricted	1,261			—			—		1,261
		$	2,687		$	4,499		$	—	$	7,186
	31-Dec-13
	Short-term investments	$	1,426		$	2,914		$	—	$	4,340
	Certificates of deposit-restricted	1,341			—			—		1,341
		$	2,767		$	2,914		$	—	$	5,681
Summary of property and equipment	'
	Property and equipment is stated at cost and consists of the following (in thousands):
		September 30,			December 31,
		2014			2013
	Lab and office equipment	$	2,509		$	3,737
	Leasehold improvements	273			387
	Computer equipment and software	631			616
		3,413			4,740
	Less accumulated depreciation and amortization	(2,862		)	(3,873		)
	Total property and equipment, net	$	551		$	867
Summary of other current assets	'
	Other current assets consist of the following (in thousands):
		September 30,			December 31,
		2014			2013
	Prepaid expenses	$	1,178		$	786
	Other receivables	424			173
	Total current assets	$	1,602		$	959
Summary of goodwill and other identifiable intangible assets	'
	Goodwill and other identifiable intangible assets consist of the following (in thousands):
		September 30,			December 31,
		2014			2013
	Indefinite lived intangible assets
	Acquired in-process research and development	$	12,556		$	12,556
	Goodwill	12,238			12,238
	Definite lived intangible assets
	Complete technology	15,267			15,267
	Less: Accumulated amortization	(2,807		)	(2,235		)
	Trade name	2,642			2,642
	Less: Accumulated amortization	(487		)	(387		)
	Customer relationships	29,600			29,600
	Less: Accumulated amortization	(5,454		)	(4,344		)
	Total goodwill and other identifiable intangible assets, net	$	63,555		$	65,337
Summary of accrued liabilities	'
	Accrued liabilities consist of the following (in thousands):
		September 30,			December 31,
		2014			2013
	Compensation	$	1,388		$	1,929
	Professional fees	805			697
	Accrued interest payable	230			—
	Other	1,888			2,711
	Total accrued liabilities	$	4,311		$	5,337
Summary of other long-term liabilities	'
	Other long-term liabilities consist of the following (in thousands):
		September 30,			December 31,
		2014			2013
	Deposits	$	402		$	345
	Deferred rent	335			350
	Total other long-term liabilities	$	737		$	695
Schedule for accounting for share-based compensation	'
	The following table summarizes stock-based compensation expense recorded as components of research and development expenses and general and administrative expenses for the periods indicated (in thousands):
		Three months ended						Nine months ended
		September 30,						September 30,
		2014			2013			2014		2013
	Stock-based compensation expense as a component of:
	Research and development expenses	$	1,169		$	438		$	2,814	$	1,272
	General and administrative expenses	2,533			1,095			5,981		2,877
		$	3,702		$	1,533		$	8,795	$	4,149
Summary of fair-value options awarded to employees and directors	'
	The fair-value for options that were awarded to employees and directors was estimated at the date of grant using the Black-Scholes option valuation model with the following weighted-average assumptions:
		Three months ended			Nine months ended
		September 30,			September 30,
		2014		2013	2014		2013
	Risk-free interest rate	1.90%		1.80%	1.90%		1.40%
	Dividend yield	—		—	—		—
	Expected volatility	67%		70%	68%		70%
	Expected term	6.4		6.3	6.4		6.3
	Forfeiture rate	8.60%		8.80%	8.6%-9.7%		8.4%-9.8%

Fair_Value_Measurements_Tables

Fair Value Measurements (Tables)	9 Months Ended
	Sep. 30, 2014
Fair Value Disclosures [Abstract]	'
Summary of the assets and liabilities measured at fair value on recurring basis	'
	The following table provides a summary of the carrying value of assets and liabilities that are measured at fair value on a recurring basis as of September 30, 2014 (in thousands):
	Fair Value Measurements at Reporting Date Using
					Quoted Prices in		Significant		Significant
					Active Markets		Other		Unobservable
					for Identical		Observable		Inputs
					Assets		Inputs
		Total			(Level 1)		(Level 2)		(Level 3)
	Assets:
	Current co-promote termination payments receivable	$	523		$	—	$	—	$	523
	Available-for-sale securities	5,925			5,925		—		—
	Total assets	$	6,448		$	5,925	$	—	$	523
	Liabilities:
	Current contingent liabilities-CyDex	$	4,184		$	—	$	—	$	4,184
	Current co-promote termination liability	523			—		—		523
	Long-term contingent liabilities-Metabasis	3,511			3,511		—		—
	Long-term contingent liabilities-CyDex	8,755			—		—		8,755
	Liability for short-term investments owed to former licensees	917			917		—		—
	Total liabilities	$	17,890		$	4,428	$	—	$	13,462
	The following table provides a summary of the assets and liabilities that are measured at fair value on a recurring basis as of December 31, 2013 (in thousands):
	Fair Value Measurements at Reporting Date Using
					Quoted Prices in		Significant		Significant
					Active Markets		Other		Unobservable
					for Identical		Observable		Inputs
					Assets		Inputs
		Total			(Level 1)		(Level 2)		(Level 3)
	Assets:
	Current portion of co-promote termination payments receivable	$	4,329		$	—	$	—	$	4,329
	Available-for-sale securities	4,340			4,340		—		—
	Long-term portion of co-promote termination payments receivable	7,417			—		—		7,417
	Total assets	$	16,086		$	4,340	$	—	$	11,746
	Liabilities:
	Current portion of contingent liabilities-CyDex	$	1,712		$	—	$	—	$	1,712
	Current portion of co-promote termination liability	4,329			—		—		4,329
	Long-term portion of contingent liabilities-Metabasis	4,196			4,196		—		—
	Long-term portion of contingent liabilities-CyDex	7,599			—		—		7,599
	Liability for short-term investments owed to licensors	651			651		—		—
	Long-term portion of co-promote termination liability	7,417			—		—		7,417
	Total liabilities	$	25,904		$	4,847	$	—	$	21,057
CyDex Acquisition	'
	The following table represents significant unobservable inputs used in determining the fair value of contingent liabilities assumed in the acquisition of CyDex:
		30-Sep-14		31-Dec-13
	Range of annual revenue subject to revenue sharing (1)	$17.9 million-$20.5 million		$4.2 million-$19.8 million
	Revenue volatility	25%		25%
	Average of probability of commercialization	83.80%		67.60%
	Sales beta	0.6		0.6
	Credit rating	B		BBB
	Equity risk premium	6%		6%
	-1	Revenue subject to revenue sharing represent management’s estimate of the range of total annual revenue subject to revenue sharing (i.e. annual revenues in excess of $15 million) through December 31, 2016, which is the term of the CVR agreement.
Reconciliation of level 3 financial instruments	'
	A reconciliation of the level 3 financial instruments as of September 30, 2014 is as follows (in thousands):
	Assets:
	Fair value of level 3 financial instrument assets as of December 31, 2013	$	11,746
	Assumed payments made by Pfizer or assignee	(1,002		)
	Fair value adjustments to co-promote termination liability	(10,221		)
	Fair value of level 3 financial instrument assets as of September 30, 2014	$	523
	Liabilities:
	Fair value of level 3 financial instrument liabilities as of December 31, 2013	$	21,057
	Assumed payments made by Pfizer or assignee	(1,002		)
	Payments to CVR and other former license holders	(1,936		)
	Fair value adjustments to contingent liabilities	5,564
	Fair value adjustments to co-promote termination liability	(10,221		)
	Fair value of level 3 financial instrument liabilities as of September 30, 2014	$	13,462

Variable_Interest_Entities_Tab

Variable Interest Entities (Tables)	9 Months Ended
	Sep. 30, 2014
Organization, Consolidation and Presentation of Financial Statements [Abstract]	'
Schedule of Variable Interest Entities	'
	The following table represents the consolidated assets and liabilities, which are owned by and are obligations of Viking and are with no recourse to the Company, as of September 30, 2014 (in thousands):
		30-Sep-14
	Cash and cash equivalents	$	794
	Other current assets	17
	Capitalized IPO expenses	2,131
	Total current assets	$	2,942
	Other assets	1
	Total assets	$	2,943
	Accounts payable	$	2,225
	Accrued liabilities	77
	Current portion of notes payable	337
	Total current liabilities	$	2,639
	Long-term portion of notes payable	1,893
	Total liabilities	$	4,532

Avinza_CoPromotion_Tables

Avinza Co-Promotion (Tables)	9 Months Ended
	Sep. 30, 2014
Co Promotion [Abstract]	'
Summary of co-promote termination liability	'
	A summary of the co-promote termination liability as of September 30, 2014 is as follows (in thousands):
	Net present value of payments based on estimated future net Avinza product sales as of December 31, 2013	$	11,746
	Assumed payments made by Pfizer or assignee	(1,002		)
	Fair value adjustments	(10,221		)
	Total co-promote termination liability as of September 30, 2014	$	523

Lease_Obligations_Tables

Lease Obligations (Tables)	9 Months Ended
	Sep. 30, 2014
Leases [Abstract]	'
Payments expected to received from sublease agreements	'
	The following table provides a summary of operating lease obligations and payments expected to be received from sublease agreements as of September 30, 2014 (in thousands):
	Operating lease obligations:	Lease	Less than 1		1-3 years		3-5 years		More than		Total
		Termination	year						5 years
		Date
	Corporate headquarters-	Jul-19	$	677	$	1,409	$	1,293	$	—	$	3,379
	San Diego, CA
	Bioscience and Technology Business Center-	Dec-17	55		108		13		—		176
	Lawrence, KS
	Vacated office and research facility-San Diego, CA	Jul-15	1,912		—		—		—		1,912
	Vacated office and research facility-	Aug-16	2,576		2,397		—		—		4,973
	Cranbury, NJ
	Total operating lease obligations		$	5,220	$	3,914	$	1,306	$	—	$	10,440
	Sublease payments expected to be received:		Less than 1		1-3 years		3-5 years		More than		Total
			year						5 years
	Office and research facility-	Jul-15	$	771	$	—	$	—	$	—	$	771
	San Diego, CA
	Office and research facility-	August 2014 and 2016	492		464		—		—		956
	Cranbury, NJ
	Net operating lease obligations		$	3,957	$	3,450	$	1,306	$	—	$	8,713

Segment_Reporting_Tables

Segment Reporting (Tables)	9 Months Ended
	Sep. 30, 2014
Segment Reporting [Abstract]	'
Summary of segment information	'
	Segment information is as follows (in thousands):
	Balance Sheet Data:	As of September 30, 2014
		Ligand			CyDex			Total
	Total assets	$	203,296		$	68,987		$	272,283
		As of December 31, 2013
		Ligand			CyDex			Total
	Total assets	$	38,408		$	66,305		$	104,713
	Operating Data:	For the three months ended September 30, 2014
		Ligand			CyDex			Total
	Net revenues from external customers	$	6,424		$	8,549		$	14,973
	Depreciation and amortization expense	(61		)	(601		)	(662		)
	Operating (loss) income	(1,683		)	5,215			3,532
	Interest expense, net	(1,516		)	—			(1,516		)
	Income tax expense from continuing operations	(115		)	(9		)	(124		)
		For the three months ended September 30, 2013
		Ligand			CyDex			Total
	Net revenues from external customers	4,731			8,274			$	13,005
	Depreciation and amortization expense	(62		)	(606		)	$	(668	)
	Operating (loss) income	(1,142		)	4,212			$	3,070
	Interest expense, net	(394		)	—			$	(394	)
	Income tax (expense) benefit from continuing operations	(70		)	10			$	(60	)
	Gain on sale of Avinza Product Line before income taxes	—			—			$	—
		For the nine months ended September 30, 2014
		Ligand			CyDex			Total
	Net revenues from external customers	18,907			22,632			$	41,539
	Depreciation and amortization expense	(194		)	(1,804		)	(1,998		)
	Operating (loss) income	(2,622		)	12,611			9,989
	Interest expense, net	(1,946		)	—			(1,946		)
	Income tax expense from continuing operations	(123		)	(8		)	(131		)
		For the nine months ended September 30, 2013
		Ligand			CyDex			Total
	Net revenues from external customers	$	14,789		$	19,448		$	34,237
	Depreciation and amortization expense	(179		)	(1,828		)	(2,007		)
	Write-off of in-process research and development	—			480			480
	Operating income	(944		)	9,462			8,518
	Interest expense, net	(1,755		)	—			(1,755		)
	Income tax (expense) benefit from continuing operations	(301		)	64			(237		)
	Gain on sale of Avinza Product Line before income taxes	2,588			—			2,588

Financing_Arrangements_Tables

Financing Arrangements (Tables)	9 Months Ended
	Sep. 30, 2014
Debt Disclosure [Abstract]	'
Summary of carrying values and coupon rates on financing arrangements	'
	The carrying values and the fixed contractual coupon rates of the Company's financing arrangements as of September 30, 2014 and December 31, 2013 were as follows (in thousands):
		30-Sep-14			31-Dec-13
	2019 Convertible Senior Notes
	Principal amount outstanding	$	245,000		$	—
	Unamortized discount	(51,369		)	—
	Net carrying amount	193,631			—
	Convertible notes payable, Viking Therapeutics, Inc.	337			—
	Current portion notes payable, 8.64%, due August 1, 2014	—			6,642
	Current portion notes payable, 8.9012%, due August 1, 2014	—			2,467
	Total notes payable	$	193,968		$	9,109

Stockholders_Equity_Tables

Stockholders' Equity (Tables)	9 Months Ended
	Sep. 30, 2014
Equity [Abstract]	'
Stock option plan activity	'
	The following is a summary of the Company’s stock option plan activity and related information:
		Shares		Weighted-		Weighted-Average	Aggregate
				Average		Remaining	Intrinsic Value
				Exercise		Contractual Term in	(In thousands)
				Price		Years
	Balance as of December 31, 2013	1,746,709		$	16.79	7.6	$	62,705
	Granted	366,184		73.81
	Exercised	(262,820	)	15.43
	Forfeited	(49,967	)	16.69
	Cancelled	(4,414	)	80.81
	Balance as of September 30, 2014	1,795,692		28.46		7.5	$	43,200
	Exercisable as of September 30, 2014	1,052,706		20		7.5	$	30,339
	Options vested and expected to vest as of September 30, 2014	1,795,692		28.46		6.8	$	43,200
Restricted stock activity	'
	Restricted stock activity for the nine months ended September 30, 2014 was as follows:
		Shares		Weighted-
				Average Grant
				Date Fair Value
	Nonvested at December 31, 2013	115,386		$	21.93
	Granted	41,671		72.5
	Vested	(74,312	)	25.21
	Cancelled	(3,972	)	18.42
	Nonvested at September 30, 2014	78,773		$	45.77

Basis_of_Presentation_Narrativ

Basis of Presentation (Narrative) (Details) (USD $)

3 Months Ended

9 Months Ended

9 Months Ended

1 Months Ended

3 Months Ended

9 Months Ended

1 Months Ended

3 Months Ended

9 Months Ended

3 Months Ended

9 Months Ended

1 Months Ended

3 Months Ended

9 Months Ended

9 Months Ended

12 Months Ended

3 Months Ended

9 Months Ended

Share data in Millions, unless otherwise specified

Sep. 30, 2014

Sep. 30, 2013

Sep. 30, 2014

Sep. 30, 2013

Dec. 31, 2013

Sep. 30, 2014

Sep. 30, 2014

Apr. 30, 2013

Sep. 30, 2014

Sep. 30, 2013

Sep. 30, 2014

Sep. 30, 2013

Dec. 31, 2013

Jan. 31, 2011

Jan. 31, 2012

Sep. 30, 2014

Sep. 30, 2013

Sep. 30, 2014

Sep. 30, 2013

Sep. 30, 2014

Sep. 30, 2013

Sep. 30, 2014

Sep. 30, 2013

Jan. 31, 2010

Sep. 30, 2014

Sep. 30, 2013

Sep. 30, 2014

Sep. 30, 2013

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Sep. 30, 2014

Sep. 30, 2013

Sep. 30, 2014

Sep. 30, 2014

Sep. 30, 2014

storage_location

segment

Equipment

Equipment

Royalty Stream and Milestone Payments Purchase Agreement with Selexis

Cydex Pharmaceuticals, Inc

Cydex Pharmaceuticals, Inc

Cydex Pharmaceuticals, Inc

Cydex Pharmaceuticals, Inc

Cydex Pharmaceuticals, Inc

Cydex Pharmaceuticals, Inc

Cydex Pharmaceuticals, Inc

Cydex Pharmaceuticals, Inc

Cydex Pharmaceuticals, Inc

Cydex Pharmaceuticals, Inc

Cydex Pharmaceuticals, Inc

Cydex Pharmaceuticals, Inc

Cydex Pharmaceuticals, Inc

Cydex Pharmaceuticals, Inc

Cydex Pharmaceuticals, Inc

Metabasis Therapeutics

Metabasis Therapeutics

Metabasis Therapeutics

Metabasis Therapeutics

Metabasis Therapeutics

Metabasis Therapeutics

Accounts Receivable

Accounts Receivable

Acquired In Process Research And Development

Acquired In Process Research And Development

Acquired In Process Research And Development

Omthera Pharmaceuticals

Viking

drug

storage_location

Minimum

Maximum

program

Guaranteed Payment

Revenue Sharing

Revenue Sharing

Revenue Sharing

Revenue Sharing

Other Contingency Payment

Other Contingency Payment

Other Contingency Payment

Other Contingency Payment

right

Customer Concentration Risk

Customer Concentration Risk

drug

customer

customer

Property, Plant and Equipment [Line Items]

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Accumulated deficit

$666,371,000

'

$666,371,000

'

$671,339,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Working capital

180,100,000

'

180,100,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Earnings (Loss) Per Share

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Common shares excluded from computation

'

'

5

0.9

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Cash, Cash Equivalents and Short-term Investments

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Maturity period of cash and cash equivalents, maximum

'

'

'3 months

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Maturity period of short term investments, minimum

'

'

'3 months

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Concentrations of Credit Risk

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Cash deposits

92,800,000

'

92,800,000

'

11,100,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Concentration risk, number of customers

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

1

2

'

'

'

'

'

Concentration risk, percentage of accounts receivable

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

57.00%

75.00%

'

'

'

'

'

Product Shelf Life

'

'

'5 years

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Number of Storage Locations

3

'

3

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Property and Equipment

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Estimated useful life of assets

'

'

'

'

'

'3 years

'10 years

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Depreciation

100,000

200,000

100,000

200,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Goodwill and Other Identifiable Intangible Assets

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Finite-lived intangible asset, useful life

'

'

'20 years

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Amortization expense

600,000

'

1,800,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Amortization Expense

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Amortization expense 2014

2,400,000

'

2,400,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Amortization expense 2015

2,400,000

'

2,400,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Amortization expense 2016

2,400,000

'

2,400,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Amortization expense 2017

2,400,000

'

2,400,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Amortization expense 2018

2,400,000

'

2,400,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Acquired In-Process Research and Development

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Impairment of in-process research and development

0

0

0

480,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

0

0

0

'

'

Gain on write-off of assets

'

'

-16,000

0

'

'

'

'

'

'

'

500,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Commercial License Rights

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Number of commercial license agreement programs

'

'

'

'

'

'

'

15

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Purchase price

'

'

'

'

'

'

'

4,600,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Payments to acquire intangible assets

'

'

'

'

'

'

'

3,600,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Cash payment due on first anniversary of the closing

'

'

'

'

'

'

'

1,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Contingent Liabilities

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Contingent liability

'

'

'

'

'

'

'

'

'

'

'

'

'

17,600,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Purchase of commercial license rights

'

'

'

'

'

'

'

'

'

'

'

'

'

'

4,300,000

0

0

1,600,000

0

300,000

100,000

300,000

100,000

'

'

'

'

'

'

'

'

'

'

'

'

'

Fair value of liability

'

'

'

'

'

'

'

'

12,900,000

'

12,900,000

'

9,300,000

'

'

'

'

'

'

'

'

'

'

'

3,500,000

'

3,500,000

'

4,200,000

'

'

'

'

'

'

'

Contingent liability change in amount

'

'

'

'

'

'

'

'

2,800,000

-1,200,000

5,600,000

2,100,000

'

'

'

'

'

'

'

'

'

'

'

'

1,200,000

700,000

-700,000

-1,700,000

'

'

'

'

'

'

'

'

Number of contingent value rights

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

4

'

'

'

'

'

'

'

'

'

'

'

'

Number of contingent value rights per series of contingent value rights

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

1

'

'

'

'

'

'

'

'

'

'

'

'

Number of contingent value rights issued for each share

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

4

'

'

'

'

'

'

'

'

'

'

'

'

Contingent value rights, frequency of cash payment

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'6 months

'

'

'

'

'

'

'

'

'

'

'

'

Revenue Recognition

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Period allowed for return of products, minimum

'

'

'30 days

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Period allowed for return of products, maximum

'

'

'90 days

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Allowance for Doubtful Accounts

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Accounts receivable outstanding considered past due after period, minimum

'

'

'30 days

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Accounts receivable outstanding considered past due after period, maximum

'

'

'90 days

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Allowance for doubtful accounts

0

'

0

'

0

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Sale of Royalty Rights

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Deferred revenue

0

'

0

'

100,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Milestone Payments

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Event-based payment

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

1,000,000

'

Discontinued Operations

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Number of drugs included in product line

4

'

4

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Gain on sale of Avinza Product Line before income taxes

0

0

0

2,588,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Segment Reporting

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Number of reportable segments

'

'

2

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Assets

272,283,000

'

272,283,000

'

104,713,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

2,943,000

Liabilities

$229,500,000

'

$229,500,000

'

$55,100,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

$4,532,000

Basis_of_Presentation_Earnings

Basis of Presentation (Earnings (Loss) Per Share) (Details) (USD $)	3 Months Ended		9 Months Ended
In Thousands, except Share data, unless otherwise specified	Sep. 30, 2014	Sep. 30, 2013	Sep. 30, 2014	Sep. 30, 2013
Summary of computation of basic and diluted net income (loss) per share	'	'	'	'
Net income from continuing operations	$1,280	$1,965	$4,969	$6,963
Net income from discontinued operations	'	'	0	2,588
Net income	$1,280	$1,965	$4,969	$9,551
Shares used to compute basic income per share	20,417,187	20,357,558	20,584,469	20,268,261
Dilutive potential common shares:	'	'	'	'
Restricted stock	22,531	77,609	37,387	62,051
Stock options	905,593	408,575	1,010,665	232,310
Shares used to compute diluted income per share	21,345,311	20,843,742	21,632,521	20,562,622
Basic per share amounts:	'	'	'	'
Income from continuing operations (in usd per share)	$0.06	$0.10	$0.24	$0.34
Income from discontinued operations (in usd per share)	$0	$0	$0	$0.13
Net income (in usd per share)	$0.06	$0.10	$0.24	$0.47
Diluted per share amounts:	'	'	'	'
Income from continuing operations (in usd per share)	$0.06	$0.09	$0.23	$0.33
Income from discontinued operations (in usd per share)	$0	$0	$0	$0.13
Net income (in usd per share)	$0.06	$0.09	$0.23	$0.46

Basis_of_Presentation_Investme

Basis of Presentation (Investment Categories) (Details) (USD $)	Sep. 30, 2014	Dec. 31, 2013
In Thousands, unless otherwise specified
Summary of investment categories	'	'
Cost	$2,687	$2,767
Gross unrealized gains	-4,499	-2,914
Gross unrealized losses	0	0
Estimated fair value	7,186	5,681
Short-term investments	'	'
Summary of investment categories	'	'
Cost	1,426	1,426
Gross unrealized gains	-4,499	-2,914
Gross unrealized losses	0	0
Estimated fair value	5,925	4,340
Certificates of deposit-restricted	'	'
Summary of investment categories	'	'
Cost	1,261	1,341
Gross unrealized gains	0	0
Gross unrealized losses	0	0
Estimated fair value	$1,261	$1,341

Basis_of_Presentation_Property

Basis of Presentation (Property and Equipment) (Details) (USD $)	Sep. 30, 2014	Dec. 31, 2013
In Thousands, unless otherwise specified
Summary of Property and equipment	'	'
Property and equipment , gross	$3,413	$4,740
Less accumulated depreciation and amortization	-2,862	-3,873
Total property and equipment, net	551	867
Lab and office equipment	'	'
Summary of Property and equipment	'	'
Property and equipment , gross	2,509	3,737
Leasehold improvements	'	'
Summary of Property and equipment	'	'
Property and equipment , gross	273	387
Computer equipment and software	'	'
Summary of Property and equipment	'	'
Property and equipment , gross	$631	$616

Basis_of_Presentation_Other_Cu

Basis of Presentation (Other Current Assets) (Details) (USD $)	Sep. 30, 2014	Dec. 31, 2013
In Thousands, unless otherwise specified
Summary of other current assets	'	'
Prepaid expenses	$1,178	$786
Other receivables	424	173
Total current assets	$1,602	$959

Basis_of_Presentation_Goodwill

Basis of Presentation (Goodwill and Other Identifiable Intangible Assets) (Details) (USD $)	Sep. 30, 2014	Dec. 31, 2013
In Thousands, unless otherwise specified
Summary of Goodwill and Other Identifiable Intangible Assets	'	'
Goodwill	$12,238	$12,238
Total goodwill and other identifiable intangible assets, net	63,555	65,337
Complete technology	'	'
Summary of Goodwill and Other Identifiable Intangible Assets	'	'
Definite lived intangible assets	15,267	15,267
Less: Accumulated amortization	-2,807	-2,235
Trade name	'	'
Summary of Goodwill and Other Identifiable Intangible Assets	'	'
Definite lived intangible assets	2,642	2,642
Less: Accumulated amortization	-487	-387
Customer relationships	'	'
Summary of Goodwill and Other Identifiable Intangible Assets	'	'
Definite lived intangible assets	29,600	29,600
Less: Accumulated amortization	-5,454	-4,344
Acquired in-process research and development	'	'
Summary of Goodwill and Other Identifiable Intangible Assets	'	'
Acquired in-process research and development	$12,556	$12,556

Basis_of_Presentation_Accrued_

Basis of Presentation (Accrued Liabilities and Other Long-Term Liabilities) (Details) (USD $)	Sep. 30, 2014	Dec. 31, 2013
In Thousands, unless otherwise specified
Accrued Liabilities	'	'
Compensation	$1,388	$1,929
Professional fees	805	697
Accrued interest payable	230	0
Other	1,888	2,711
Total accrued liabilities	4,311	5,337
Other Long-Term Liabilities	'	'
Deposits	402	345
Deferred rent	335	350
Total other long-term liabilities	$737	$695

Basis_of_Presentation_Accounti

Basis of Presentation (Accounting for Share-Based Compensation) (Details) (USD $)	3 Months Ended		9 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2014	Sep. 30, 2013	Sep. 30, 2014	Sep. 30, 2013
Basis of Presentation [Line Items]	'	'	'	'
Share-based compensation expense total	$3,702	$1,533	$8,795	$4,149
Research and development expenses	'	'	'	'
Basis of Presentation [Line Items]	'	'	'	'
Share-based compensation expense total	1,169	438	2,814	1,272
General and administrative expenses	'	'	'	'
Basis of Presentation [Line Items]	'	'	'	'
Share-based compensation expense total	$2,533	$1,095	$5,981	$2,877

Basis_of_Presentation_Fair_Val

Basis of Presentation (Fair Value Valuation Assumptions) (Details)	3 Months Ended		9 Months Ended
	Sep. 30, 2014	Sep. 30, 2013	Sep. 30, 2014	Sep. 30, 2013
Summary of fair-value options awarded to employees and directors	'	'	'	'
Risk-free interest rate	1.90%	1.80%	1.90%	1.40%
Dividend yield	0.00%	0.00%	0.00%	0.00%
Expected volatility	67.00%	70.00%	68.00%	70.00%
Expected term	'6 years 5 months 5 days	'6 years 3 months 18 days	'6 years 5 months 5 days	'6 years 3 months 18 days
Forfeiture rate	8.60%	8.80%	'	'
Minimum	'	'	'	'
Summary of fair-value options awarded to employees and directors	'	'	'	'
Forfeiture rate	'	'	8.60%	8.40%
Maximum	'	'	'	'
Summary of fair-value options awarded to employees and directors	'	'	'	'
Forfeiture rate	'	'	9.70%	9.80%

Fair_Value_Measurements_Detail

Fair Value Measurements (Details) (USD $)

Sep. 30, 2014

Dec. 31, 2013

Aug. 31, 2014

Sep. 30, 2014

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Sep. 30, 2014

Dec. 31, 2013

Dec. 31, 2013

2019 convertible senior notes

2019 convertible senior notes

2019 convertible senior notes

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Recurring

Senior Notes

Current contingent liabilities-CyDex

Current contingent liabilities-CyDex

Current co-promote termination liability

Current co-promote termination liability

Long-term contingent liabilities-Metabasis

Long-term contingent liabilities-Metabasis

Long-term contingent liabilities-CyDex

Long-term contingent liabilities-CyDex

Liability for short-term investments owed to former licensees

Liability for short-term investments owed to former licensees

Long-term portion of co-promote termination liability

Current co-promote termination payments receivable

Current co-promote termination payments receivable

Available-for-sale securities

Available-for-sale securities

Long-term portion of co-promote termination payments receivable

Quoted Prices in Active Markets for Identical Assets (Level 1)

Quoted Prices in Active Markets for Identical Assets (Level 1)

Quoted Prices in Active Markets for Identical Assets (Level 1)

Quoted Prices in Active Markets for Identical Assets (Level 1)

Quoted Prices in Active Markets for Identical Assets (Level 1)

Quoted Prices in Active Markets for Identical Assets (Level 1)

Quoted Prices in Active Markets for Identical Assets (Level 1)

Quoted Prices in Active Markets for Identical Assets (Level 1)

Quoted Prices in Active Markets for Identical Assets (Level 1)

Quoted Prices in Active Markets for Identical Assets (Level 1)

Quoted Prices in Active Markets for Identical Assets (Level 1)

Quoted Prices in Active Markets for Identical Assets (Level 1)

Quoted Prices in Active Markets for Identical Assets (Level 1)

Quoted Prices in Active Markets for Identical Assets (Level 1)

Quoted Prices in Active Markets for Identical Assets (Level 1)

Quoted Prices in Active Markets for Identical Assets (Level 1)

Quoted Prices in Active Markets for Identical Assets (Level 1)

Quoted Prices in Active Markets for Identical Assets (Level 1)

Significant Other Observable Inputs (Level 2)

Significant Other Observable Inputs (Level 2)

Significant Other Observable Inputs (Level 2)

Significant Other Observable Inputs (Level 2)

Significant Other Observable Inputs (Level 2)

Significant Other Observable Inputs (Level 2)

Significant Other Observable Inputs (Level 2)

Significant Other Observable Inputs (Level 2)

Significant Other Observable Inputs (Level 2)

Significant Other Observable Inputs (Level 2)

Significant Other Observable Inputs (Level 2)

Significant Other Observable Inputs (Level 2)

Significant Other Observable Inputs (Level 2)

Significant Other Observable Inputs (Level 2)

Significant Other Observable Inputs (Level 2)

Significant Other Observable Inputs (Level 2)

Significant Other Observable Inputs (Level 2)

Significant Other Observable Inputs (Level 2)

Significant Unobservable Inputs (Level 3)

Significant Unobservable Inputs (Level 3)

Significant Unobservable Inputs (Level 3)

Significant Unobservable Inputs (Level 3)

Significant Unobservable Inputs (Level 3)

Significant Unobservable Inputs (Level 3)

Significant Unobservable Inputs (Level 3)

Significant Unobservable Inputs (Level 3)

Significant Unobservable Inputs (Level 3)

Significant Unobservable Inputs (Level 3)

Significant Unobservable Inputs (Level 3)

Significant Unobservable Inputs (Level 3)

Significant Unobservable Inputs (Level 3)

Significant Unobservable Inputs (Level 3)

Significant Unobservable Inputs (Level 3)

Significant Unobservable Inputs (Level 3)

Significant Unobservable Inputs (Level 3)

Significant Unobservable Inputs (Level 3)

Current contingent liabilities-CyDex

Current contingent liabilities-CyDex

Current co-promote termination liability

Current co-promote termination liability

Long-term contingent liabilities-Metabasis

Long-term contingent liabilities-Metabasis

Long-term contingent liabilities-CyDex

Long-term contingent liabilities-CyDex

Liability for short-term investments owed to former licensees

Liability for short-term investments owed to former licensees

Long-term portion of co-promote termination liability

Current co-promote termination payments receivable

Current co-promote termination payments receivable

Available-for-sale securities

Available-for-sale securities

Long-term portion of co-promote termination payments receivable

Current contingent liabilities-CyDex

Current contingent liabilities-CyDex

Current co-promote termination liability

Current co-promote termination liability

Long-term contingent liabilities-Metabasis

Long-term contingent liabilities-Metabasis

Long-term contingent liabilities-CyDex

Long-term contingent liabilities-CyDex

Liability for short-term investments owed to former licensees

Liability for short-term investments owed to former licensees

Long-term portion of co-promote termination liability

Current co-promote termination payments receivable

Current co-promote termination payments receivable

Available-for-sale securities

Available-for-sale securities

Long-term portion of co-promote termination payments receivable

Current contingent liabilities-CyDex

Current contingent liabilities-CyDex

Current co-promote termination liability

Current co-promote termination liability

Long-term contingent liabilities-Metabasis

Long-term contingent liabilities-Metabasis

Long-term contingent liabilities-CyDex

Long-term contingent liabilities-CyDex

Liability for short-term investments owed to former licensees

Liability for short-term investments owed to former licensees

Long-term portion of co-promote termination liability

Current co-promote termination payments receivable

Current co-promote termination payments receivable

Available-for-sale securities

Available-for-sale securities

Long-term portion of co-promote termination payments receivable

Assets:

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Assets, fair value

'

'

'

$6,448,000

$16,086,000

'

'

'

'

'

'

'

'

'

'

'

$523,000

$4,329,000

$5,925,000

$4,340,000

$7,417,000

$5,925,000

$4,340,000

'

'

'

'

'

'

'

'

'

'

'

$0

$0

$5,925,000

$4,340,000

$0

$0

$0

'

'

'

'

'

'

'

'

'

'

'

$0

$0

$0

$0

$0

$523,000

$11,746,000

'

'

'

'

'

'

'

'

'

'

'

$523,000

$4,329,000

$0

$0

$7,417,000

Liabilities:

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Liabilities, fair value

'

'

'

17,890,000

25,904,000

4,184,000

1,712,000

523,000

4,329,000

3,511,000

4,196,000

8,755,000

7,599,000

917,000

651,000

7,417,000

'

'

'

'

'

4,428,000

4,847,000

0

0

0

0

3,511,000

4,196,000

0

0

917,000

651,000

0

'

'

'

'

'

0

0

0

0

0

0

0

0

0

0

0

0

0

'

'

'

'

'

13,462,000

21,057,000

4,184,000

1,712,000

523,000

4,329,000

0

0

8,755,000

7,599,000

0

0

7,417,000

'

'

'

'

'

Principal amount outstanding

245,000,000

0

245,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Estimated fair value of debt

$229,800,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Fair_Value_Measurements_Acquis

Fair Value Measurements (Acquisition of CyDex) (Details) (Cydex Pharmaceuticals, Inc, USD $)	9 Months Ended		12 Months Ended
In Millions, unless otherwise specified	Sep. 30, 2014		Dec. 31, 2013
Credit Derivatives [Line Items]	'		'
Amount Of Revenue For Contingent Consideration	15		'
Contingent Consideration Classified as Equity	'		'
Credit Derivatives [Line Items]	'		'
Revenue volatility	25.00%		25.00%
Average of probability of commercialization	83.80%		67.60%
Sales beta	0.6		0.6
Credit rating	'B		'BBB
Equity risk premium	6.00%		6.00%
Minimum | Contingent Consideration Classified as Equity	'		'
Credit Derivatives [Line Items]	'		'
Range of annual revenue subject to revenue sharing	17.9	[1]	4.2	[1]
Maximum | Contingent Consideration Classified as Equity	'		'
Credit Derivatives [Line Items]	'		'
Range of annual revenue subject to revenue sharing	20.5	[1]	19.8	[1]
[1]	Revenue subject to revenue sharing represent managementbs estimate of the range of total annual revenue subject to revenue sharing (i.e. annual revenues in excess of $15 million) through DecemberB 31, 2016, which is the term of the CVR agreement.

Fair_Value_Measurements_Level_

Fair Value Measurements (Level 3 Reconciliation) (Details) (USD $)	9 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2014
Assets:	'
Fair value of level 3 financial instrument assets	$11,746
Assumed payments made by Pfizer or assignee	-1,002
Fair value adjustments to co-promote termination liability	-10,221
Fair value of level 3 financial instrument assets	523
Liabilities:	'
Fair value of level 3 financial instrument liabilities	21,057
Assumed payments made by Pfizer or assignee	-1,002
Payments to CVR and other former license holders	-1,936
Fair value adjustments to contingent liabilities	5,564
Fair value adjustments to co-promote termination liability	-10,221
Fair value of level 3 financial instrument liabilities	$13,462

Variable_Interest_Entities_Det

Variable Interest Entities (Details) (USD $)	Sep. 30, 2014	Dec. 31, 2013	Sep. 30, 2013	Dec. 31, 2012	31-May-14	Sep. 30, 2014	Sep. 30, 2014	Apr. 30, 2015	21-May-14
					Viking	Viking	Viking	Viking	Debt
					program			Forecast	Viking
Variable Interest Entity [Line Items]	'	'	'	'	'	'	'	'	'
Number of programs licensed	'	'	'	'	5	'	'	'	'
Convertible loan facility	'	'	'	'	'	$2,000,000	$2,000,000	'	$2,500,000
Interest accrual rate, less than	'	'	'	'	'	'	'	'	5.00%
Repayment in equity percentage	'	'	'	'	'	'	'	'	200.00%
Value of common stock issued upon IPO	'	'	'	'	'	'	'	29,000,000	'
Threshold proceeds from private financing	'	'	'	'	'	'	'	20,000,000	'
Cash and cash equivalents	180,663,000	11,639,000	3,271,000	12,381,000	'	794,000	794,000	'	'
Other current assets	1,602,000	959,000	'	'	'	17,000	17,000	'	'
Capitalized expenses, VIE	2,131,000	0	'	'	'	2,131,000	2,131,000	'	'
Total current assets	198,520,000	24,881,000	'	'	'	2,942,000	2,942,000	'	'
Other assets	230,000	299,000	'	'	'	1,000	1,000	'	'
Total assets	272,283,000	104,713,000	'	'	'	2,943,000	2,943,000	'	'
Accounts payable	4,864,000	3,951,000	'	'	'	2,225,000	2,225,000	'	'
Accrued liabilities	4,311,000	5,337,000	'	'	'	77,000	77,000	'	'
Current note payable	337,000	9,109,000	'	'	'	337,000	337,000	'	'
Total current liabilities	18,433,000	28,939,000	'	'	'	2,639,000	2,639,000	'	'
Long-term portion of notes payable	'	'	'	'	'	1,893,000	1,893,000	'	'
Total liabilities	$229,500,000	$55,100,000	'	'	'	$4,532,000	$4,532,000	'	'
Loss percentage recorded	'	'	'	'	'	'	100.00%	'	'

Avinza_CoPromotion_Narrative_D

Avinza Co-Promotion (Narrative) (Details) (AVINZA, Organon)	Sep. 30, 2014	Dec. 31, 2012
AVINZA | Organon	'	'
AVINZA Co-Promotion (Textual) [Abstract]	'	'
Percentage of net sales payable as royalty	6.00%	6.50%

Avinza_CoPromotion_CoPromote_T

Avinza Co-Promotion (Co-Promote Termination Liability) (Details) (USD $)	9 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2014
Summary of co-promote termination liability	'
Net present value of payments based on estimated future net Avinza product sales	$11,746
Assumed payments made by Pfizer or assignee	-1,002
Fair value adjustments	-10,221
Total co-promote termination liability	$523

Lease_Obligations_Narrative_De

Lease Obligations (Narrative) (Details) (USD $)	3 Months Ended		9 Months Ended			12 Months Ended	9 Months Ended	12 Months Ended
	Sep. 30, 2014	Sep. 30, 2013	Sep. 30, 2014	Sep. 30, 2013	Dec. 31, 2013	Dec. 31, 2010	Sep. 30, 2014	Dec. 31, 2013
						Facility Closing	Contract Termination	Contract Termination
Operating Leased Assets [Line Items]	'	'	'	'	'	'	'	'
Lease expiration year, minimum	'	'	'2014	'	'	'	'	'
Lease expiration year, maximum	'	'	'2019	'	'	'	'	'
Percentage of increase in annual base rent, minimum	3.00%	'	3.00%	'	'	'	'	'
Percentage of increase in annual base rent, maximum	3.50%	'	3.50%	'	'	'	'	'
Lease exit costs	$182,000	$227,000	$522,000	$359,000	'	$9,700,000	$3,700,000	$5,900,000
Property and equipment write-off	'	'	'	'	'	5,400,000	'	'
Rent expense, net sublease income	800,000	900,000	2,600,000	2,800,000	'	'	'	'
Adjustment for accretion and changes in lease assumptions	200,000	'	500,000	'	'	'	'	'
Rent expense	200,000	200,000	500,000	500,000	'	'	'	'
Deferred rent	$335,000	'	$335,000	'	$350,000	'	'	'

Lease_Obligations_Lease_Obliga

Lease Obligations (Lease Obligations) (Details) (USD $)	Sep. 30, 2014
In Thousands, unless otherwise specified
Payments expected to received from sublease agreements	'
Operating lease obligations:	$10,440
Sublease payments expected to be received:	8,713
Corporate headquarters- San Diego, CA	'
Payments expected to received from sublease agreements	'
Operating lease obligations:	3,379
Bioscience and Technology Business Center- Lawrence, KS	'
Payments expected to received from sublease agreements	'
Operating lease obligations:	176
Vacated office and research facility-San Diego, CA	'
Payments expected to received from sublease agreements	'
Operating lease obligations:	1,912
Vacated office and research facility- Cranbury, NJ	'
Payments expected to received from sublease agreements	'
Operating lease obligations:	4,973
Office and research facility- San Diego, CA	'
Payments expected to received from sublease agreements	'
Sublease payments expected to be received:	771
Office and research facility- Cranbury, NJ	'
Payments expected to received from sublease agreements	'
Sublease payments expected to be received:	956
Less than 1 year	'
Payments expected to received from sublease agreements	'
Operating lease obligations:	5,220
Sublease payments expected to be received:	3,957
Less than 1 year | Corporate headquarters- San Diego, CA	'
Payments expected to received from sublease agreements	'
Operating lease obligations:	677
Less than 1 year | Bioscience and Technology Business Center- Lawrence, KS	'
Payments expected to received from sublease agreements	'
Operating lease obligations:	55
Less than 1 year | Vacated office and research facility-San Diego, CA	'
Payments expected to received from sublease agreements	'
Operating lease obligations:	1,912
Less than 1 year | Vacated office and research facility- Cranbury, NJ	'
Payments expected to received from sublease agreements	'
Operating lease obligations:	2,576
Less than 1 year | Office and research facility- San Diego, CA	'
Payments expected to received from sublease agreements	'
Sublease payments expected to be received:	771
Less than 1 year | Office and research facility- Cranbury, NJ	'
Payments expected to received from sublease agreements	'
Sublease payments expected to be received:	492
1-3 years	'
Payments expected to received from sublease agreements	'
Operating lease obligations:	3,914
Sublease payments expected to be received:	3,450
1-3 years | Corporate headquarters- San Diego, CA	'
Payments expected to received from sublease agreements	'
Operating lease obligations:	1,409
1-3 years | Bioscience and Technology Business Center- Lawrence, KS	'
Payments expected to received from sublease agreements	'
Operating lease obligations:	108
1-3 years | Vacated office and research facility-San Diego, CA	'
Payments expected to received from sublease agreements	'
Operating lease obligations:	'
1-3 years | Vacated office and research facility- Cranbury, NJ	'
Payments expected to received from sublease agreements	'
Operating lease obligations:	2,397
1-3 years | Office and research facility- San Diego, CA	'
Payments expected to received from sublease agreements	'
Sublease payments expected to be received:	'
1-3 years | Office and research facility- Cranbury, NJ	'
Payments expected to received from sublease agreements	'
Sublease payments expected to be received:	464
3-5 years	'
Payments expected to received from sublease agreements	'
Operating lease obligations:	1,306
Sublease payments expected to be received:	1,306
3-5 years | Corporate headquarters- San Diego, CA	'
Payments expected to received from sublease agreements	'
Operating lease obligations:	1,293
3-5 years | Bioscience and Technology Business Center- Lawrence, KS	'
Payments expected to received from sublease agreements	'
Operating lease obligations:	13
3-5 years | Vacated office and research facility-San Diego, CA	'
Payments expected to received from sublease agreements	'
Operating lease obligations:	'
3-5 years | Vacated office and research facility- Cranbury, NJ	'
Payments expected to received from sublease agreements	'
Operating lease obligations:	'
3-5 years | Office and research facility- San Diego, CA	'
Payments expected to received from sublease agreements	'
Sublease payments expected to be received:	'
3-5 years | Office and research facility- Cranbury, NJ	'
Payments expected to received from sublease agreements	'
Sublease payments expected to be received:	'
More than 5 years	'
Payments expected to received from sublease agreements	'
Operating lease obligations:	'
Sublease payments expected to be received:	'
More than 5 years | Corporate headquarters- San Diego, CA	'
Payments expected to received from sublease agreements	'
Operating lease obligations:	'
More than 5 years | Bioscience and Technology Business Center- Lawrence, KS	'
Payments expected to received from sublease agreements	'
Operating lease obligations:	'
More than 5 years | Vacated office and research facility-San Diego, CA	'
Payments expected to received from sublease agreements	'
Operating lease obligations:	'
More than 5 years | Vacated office and research facility- Cranbury, NJ	'
Payments expected to received from sublease agreements	'
Operating lease obligations:	'
More than 5 years | Office and research facility- San Diego, CA	'
Payments expected to received from sublease agreements	'
Sublease payments expected to be received:	'
More than 5 years | Office and research facility- Cranbury, NJ	'
Payments expected to received from sublease agreements	'
Sublease payments expected to be received:	'

Segment_Reporting_Details

Segment Reporting (Details) (USD $)	3 Months Ended		9 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2014	Sep. 30, 2013	Sep. 30, 2014	Sep. 30, 2013	Dec. 31, 2013
Summary of segment information	'	'	'	'	'
Total assets	$272,283	'	$272,283	'	$104,713
Net revenues from external customers	14,973	13,005	41,539	34,237	'
Depreciation and amortization expense	-662	-668	-1,998	-2,007	'
Write-off of in-process research and development	0	0	0	480	'
Operating (loss) income	3,532	3,070	9,989	8,518	'
Interest expense, net	-1,516	-394	-1,946	-1,755	'
Income tax expense from continuing operations	-124	-60	-131	-237	'
Gain on sale of Avinza Product Line before income taxes	0	0	0	2,588	'
Ligand	'	'	'	'	'
Summary of segment information	'	'	'	'	'
Total assets	203,296	'	203,296	'	38,408
Net revenues from external customers	6,424	4,731	18,907	14,789	'
Depreciation and amortization expense	-61	-62	-194	-179	'
Write-off of in-process research and development	'	'	'	0	'
Operating (loss) income	-1,683	-1,142	-2,622	-944	'
Interest expense, net	-1,516	-394	-1,946	-1,755	'
Income tax expense from continuing operations	-115	-70	-123	-301	'
Gain on sale of Avinza Product Line before income taxes	'	0	'	2,588	'
CyDex	'	'	'	'	'
Summary of segment information	'	'	'	'	'
Total assets	68,987	'	68,987	'	66,305
Net revenues from external customers	8,549	8,274	22,632	19,448	'
Depreciation and amortization expense	-601	-606	-1,804	-1,828	'
Write-off of in-process research and development	'	'	'	480	'
Operating (loss) income	5,215	4,212	12,611	9,462	'
Interest expense, net	0	'	0	0	'
Income tax expense from continuing operations	-9	10	-8	64	'
Gain on sale of Avinza Product Line before income taxes	'	$0	'	$0	'

Financing_Arrangements_Narrati

Financing Arrangements (Narrative) (Details) (USD $)

1 Months Ended

9 Months Ended

1 Months Ended

Aug. 31, 2014

Sep. 30, 2014

Sep. 30, 2013

Jul. 31, 2014

Dec. 31, 2013

Aug. 12, 2014

Sep. 30, 2014

Dec. 31, 2013

Aug. 31, 2014

Aug. 31, 2014

Aug. 31, 2014

Aug. 31, 2014

Common Stock

2019 convertible senior notes

2019 convertible senior notes

Senior Notes

Senior Notes

Senior Notes

Senior Notes

2019 convertible senior notes

2019 convertible senior notes

2019 convertible senior notes

Debt Instrument, Redemption, Period One

Debt Instrument, Redemption, Period Two

D

D

Debt Instrument [Line Items]

'

'

'

'

'

'

'

'

'

'

'

'

Proceeds from issuance of debt

'

'

'

'

'

'

'

'

'

$245,000,000

'

'

Aggregate principal amount outstanding

'

'

'

'

'

'

245,000,000

0

'

245,000,000

'

'

Debt discount rate

'

'

'

'

'

'

'

'

'

5.83%

'

'

Initial debt value

'

193,631,000

'

'

0

'

193,631,000

0

'

192,500,000

'

'

Additional final payment on borrowings

'

'

'

6.00%

'

'

'

'

'

'

'

'

Net proceeds from note after debt issuance costs

'

'

'

'

'

'

'

'

'

239,300,000

'

'

Initial conversion rate

'

'

'

'

'

'

'

'

'

0.0133251

'

'

Initial conversion price

'

'

'

'

'

'

'

'

'

$75.05

'

'

Premium percentage

'

'

'

'

'

'

'

'

'

35.00%

'

'

Share price

'

'

'

'

'

$55.59

'

'

'

'

'

'

Interest rate

'

'

'

'

'

'

'

'

'

0.75%

'

'

Threshold trading days

'

'

'

'

'

'

'

'

'

'

20

5

Consecutive trading days

'

'

'

'

'

'

'

'

'

'

'30 days

'10 years

Percentage of stock price trigger

'

'

'

'

'

'

'

'

'

'

130.00%

'

Maximum threshold percentage of debt trading price trigger

'

'

'

'

'

'

'

'

'

'

'

98.00%

Debt issuance costs

'

'

'

'

'

'

'

'

'

5,700,000

'

'

Equity component of convertible debt recorded as a reduction to additional paid-in capital

'

'

'

'

'

'

'

'

'

1,200,000

'

'

Long-term debt issuance costs

'

3,598,000

'

'

0

'

'

'

'

4,500,000

'

'

Term of notes

'

'

'

'

'

'

'

'

'

'5 years

'

'

Carrying value of the equity component of debt, net of issuance costs

'

'

'

'

'

'

'

'

'

51,300,000

'

'

Exercise price

$125.08

'

'

'

'

'

'

'

'

'

'

'

Payment for convertible bond hedges

'

48,143,000

0

'

'

'

'

'

48,143,000

'

'

'

Common stock, shares available to be issued

3,264,643

'

'

'

'

'

'

'

'

'

'

'

Exercise Price of Convertible Bond Hedge

$75.05

'

'

'

'

'

'

'

'

'

'

'

Proceeds from issuance of warrants

$11,600,000

'

'

'

'

'

'

'

'

'

'

'

Financing_Arrangements_Notes_P

Financing Arrangements (Notes Payable) (Details) (USD $)	9 Months Ended	12 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2014	Dec. 31, 2013
Notes Payable, Current and Noncurrent [Abstract]	'	'
Net carrying amount	$193,631	$0
Current notes payable	337	9,109
Total notes payable	193,968	9,109
2019 convertible senior notes	'	'
Notes Payable, Current and Noncurrent [Abstract]	'	'
Principal amount outstanding	245,000	0
Unamortized discount	-51,369	0
Net carrying amount	193,631	0
Convertible notes payable, Viking Therapeutics, Inc.	'	'
Notes Payable, Current and Noncurrent [Abstract]	'	'
Current notes payable	337	0
Current portion notes payable, 8.64%, due August 1, 2014	'	'
Notes Payable, Current and Noncurrent [Abstract]	'	'
Current notes payable	0	6,642
Maturity Date of Loan	1-Aug-14	1-Aug-14
Interest rate	8.64%	8.64%
Current portion notes payable, 8.9012%, due August 1, 2014	'	'
Notes Payable, Current and Noncurrent [Abstract]	'	'
Current notes payable	$0	$2,467
Maturity Date of Loan	1-Aug-14	1-Aug-14
Interest rate	8.90%	8.90%

Stockholders_Equity_Narrative_

Stockholders' Equity (Narrative) (Details) (USD $)

1 Months Ended

3 Months Ended

9 Months Ended

1 Months Ended

9 Months Ended

9 Months Ended

Aug. 31, 2014

Sep. 30, 2014

Sep. 30, 2014

Sep. 30, 2013

Oct. 30, 2014

Sep. 30, 2014

Sep. 30, 2013

Sep. 30, 2014

Sep. 30, 2014

Sep. 30, 2014

Sep. 30, 2013

Sep. 30, 2014

Sep. 30, 2013

Sep. 30, 2014

Sep. 30, 2014

Sep. 30, 2014

Sep. 30, 2014

Subsequent Event

Stock Options

Stock Options

Restricted Stock

2002 Stock Incentive Plan

Employee Stock Purchase Plan

Employee Stock Purchase Plan

Employee Stock Purchase Plan

Employee Stock Purchase Plan

Certain Directors

Employees

Vesting Period One

Vesting Period Two

Stock Options

Stock Options

Stock Options

2002 Stock Incentive Plan

2002 Stock Incentive Plan

2002 Stock Incentive Plan

Stock Options

Stock Options

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

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Award Vesting Period

'

'

'

'

'

'

'

'3 years

'

'

'

'

'

'1 year

'4 years

'6 months

'42 months

Award Vesting Rights, Percentage

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

12.50%

2.08%

Award Vesting Rights

'

'

'

'

'

'1/8 on the six month anniversary of the date of grant, and 1/48 each month thereafter for 42 months

'

'

'

'

'

'

'

'

'

'

'

Award Expiration Period

'

'

'

'

'

'10 years

'

'

'

'

'

'

'

'

'

'

'

Weighted-average grant date fair value of stock options

'

'

'

'

'

$47.44

'

'

'

'

'

'

'

'

'

'

'

Intrinsic value of options exercised

'

'

'

'

'

$14,700,000

$3,600,000

'

'

'

'

'

'

'

'

'

'

Unrecognized compensation cost

'

'

'

'

'

14,600,000

'

'

'

'

'

'

'

'

'

'

'

Weighted-average period in which cost is expected to be recognized

'

'

'

'

'

'2 years 3 months 18 days

'

'1 year 5 months 16 days

'

'

'

'

'

'

'

'

'

Net proceeds from employee stock purchase plan

'

'

'

'

'

'

'

'

'

'

'

4,100,000

2,300,000

'

'

'

'

Shares available for future option grants

'

'

'

'

'

'

'

'

1,100,000

'

'

'

'

'

'

'

'

Unrecognized compensation cost, restricted stock

'

'

'

'

'

'

'

2,300,000

'

'

'

'

'

'

'

'

'

Employee Stock Purchase Plan

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Shares allowed to purchase in employee stock purchase plan

'

'

'

'

'

'

'

'

'

1,250

'

'

'

'

'

'

'

Offering period of shares in employee stock purchase plan

'

'

'

'

'

'

'

'

'

'6 months

'

'

'

'

'

'

'

Percentage of purchase price of stock

'

'

'

'

'

'

'

'

'

85.00%

'

'

'

'

'

'

'

Discount rate

'

'

'

'

'

'

'

'

'

15.00%

'

'

'

'

'

'

'

Shares issued in period

'

'

'

'

'

'

'

'

'

2,230

5,016

'

'

'

'

'

'

Stock-based compensation

'

'

8,795,000

4,149,000

'

'

'

'

'

43,515

37,000

'

'

'

'

'

'

Shares available for future purchases

'

'

'

'

'

'

'

'

'

77,285

'

'

'

'

'

'

'

Corporate Share Repurchase

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Stock repurchase, authorized amount

200,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Stock repurchase, maximum period

'1 year

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Stock repurchase, shares

'

692,800

692,800

'

110,000

'

'

'

'

'

'

'

'

'

'

'

'

Stock repurchase, value

'

$38,500,000

$38,500,000

'

$5,000,000

'

'

'

'

'

'

'

'

'

'

'

'

Stockholders_Equity_Stock_Opti

Stockholders' Equity (Stock Option Plan Activity) (Details) (USD $)	9 Months Ended	12 Months Ended
In Thousands, except Share data, unless otherwise specified	Sep. 30, 2014	Dec. 31, 2013
Shares	'	'
Balance, Beginning	1,746,709	'
Granted	366,184	'
Exercised	-262,820	'
Forfeited	-49,967	'
Cancelled	-4,414	'
Balance, Ending	1,795,692	1,746,709
Exercisable	1,052,706	'
Options vested and expected to vest	1,795,692	'
Weighted Average Exercise Price	'	'
Balance, Beginning (in usd per share)	$16.79	'
Granted (in usd per share)	$73.81	'
Exercised (in usd per share)	$15.43	'
Forfeited (in usd per share)	$16.69	'
Cancelled (in usd per share)	$80.81	'
Balance, Ending (in usd per share)	$28.46	$16.79
Exercisable	$20	'
Options vested and expected to vest	$28.46	'
Weighted-Average Remaining Contractual Term in Years	'	'
Weighted average remaining contractual term in years	'7 years 5 months 19 days	'7 years 6 months 26 days
Exercisable	'7 years 5 months 19 days	'
Options vested and expected to vest	'6 years 9 months 15 days	'
Aggregate Intrinsic Value	'	'
Aggregate intrinsic value	$43,200	$62,705
Exercisable	30,339	'
Options vested and expected to vest	$43,200	'

Stockholders_Equity_Restricted

Stockholders' Equity (Restricted Stock Activity) (Details) (Restricted Stock, USD $)	9 Months Ended
	Sep. 30, 2014
Restricted Stock	'
Shares:	'
Nonvested, Beginning	115,386
Granted	41,671
Vested	-74,312
Cancelled	-3,972
Nonvested, Ending	78,773
Weighted- Average Grant Date Fair Value	'
Nonvested, Beginning (in usd per share)	$21.93
Granted (in usd per share)	$72.50
Vested (in usd per share)	$25.21
Canceled (in usd per share)	$18.42
Nonvested, Ending (in usd per share)	$45.77