Precigen (PGEN) 10-Q 10 May 16 2016 Q1 Quarterly report Financial data

Document and Entity Information

Document and Entity Information - shares	3 Months Ended
	Mar. 31, 2016	Apr. 30, 2016
Document And Entity Information [Abstract]
Document Type	10-Q
Amendment Flag	false
Document Period End Date	Mar. 31, 2016
Document Fiscal Year Focus	2,016
Document Fiscal Period Focus	Q1
Trading Symbol	XON
Entity Registrant Name	INTREXON CORP
Entity Central Index Key	1,356,090
Current Fiscal Year End Date	--12-31
Entity Filer Category	Large Accelerated Filer
Entity Common Stock, Shares Outstanding		118,164,614

Consolidated Balance Sheets

Consolidated Balance Sheets - USD ($) $ in Thousands	Mar. 31, 2016	Dec. 31, 2015
Current assets
Cash and cash equivalents	$ 145,733	$ 135,782
Short-term investments	114,659	102,528
Receivables
Trade, net	21,874	25,101
Related parties	16,019	23,597
Note, net	0	601
Other	6,707	2,995
Inventory	25,078	26,563
Prepaid expenses and other	6,469	6,634
Total current assets	336,539	323,801
Long-term investments	75,584	105,447
Equity securities	61,322	83,653
Property, plant and equipment, net	44,673	42,739
Intangible assets, net	255,460	247,535
Goodwill	164,575	165,169
Investments in affiliates	21,385	9,977
Other assets	2,890	3,725
Total assets	962,428	982,046
Current liabilities
Accounts payable	7,537	4,967
Accrued compensation and benefits	8,281	19,050
Other accrued liabilities	13,548	7,949
Deferred revenue	37,695	35,366
Lines of credit	536	561
Current portion of long term debt	893	930
Current portion of deferred consideration	9,089	6,931
Related party payables	358	150
Total current liabilities	77,937	75,904
Long term debt, net of current portion	7,613	7,598
Deferred consideration, net of current portion	6,696	8,698
Deferred revenue, net of current portion	172,543	162,363
Deferred tax liabilities	19,777	21,802
Other long term liabilities	3,030	795
Total liabilities	$ 287,596	$ 277,160
Commitments and contingencies (Note 16)
Total equity
Common stock, no par value, 200,000,000 shares authorized as of March 31, 2016 and December 31, 2015; 117,516,486 and 116,658,886 shares issued and outstanding as of March 31, 2016 and December 31, 2015, respectively	$ 0	$ 0
Additional paid-in capital	1,283,525	1,249,559
Accumulated deficit	(607,158)	(542,729)
Accumulated other comprehensive loss	(11,435)	(12,752)
Total Intrexon shareholders' equity	664,932	694,078
Noncontrolling interests	9,900	10,808
Total equity	674,832	704,886
Total liabilities and total equity	$ 962,428	$ 982,046

Consolidated Balance Sheets (Pa

Consolidated Balance Sheets (Parenthetical) - shares	Mar. 31, 2016	Dec. 31, 2015
Statement of Financial Position [Abstract]
Common stock, shares authorized	200,000,000	200,000,000
Common stock, shares issued	117,516,486	116,658,886
Common stock, shares outstanding	117,516,486	116,658,886

Consolidated Statements of Oper

Consolidated Statements of Operations - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2016	Mar. 31, 2015
Revenues
Collaboration and licensing revenues	$ 24,073	$ 14,783
Product revenues	8,555	8,933
Service revenues	10,665	9,957
Other revenues	145	176
Total revenues	43,438	33,849
Operating Expenses
Cost of products	9,562	8,675
Cost of services	5,672	5,362
Research and development	25,856	79,307
Selling, general and administrative	42,881	27,628
Total operating expenses	83,971	120,972
Operating loss	(40,533)	(87,123)
Other Income (Expense), Net
Unrealized appreciation (depreciation) in fair value of equity securities	(22,331)	115,454
Interest expense	(265)	(343)
Interest income	610	300
Other income, net	561	267
Total other income (expense), net	(21,425)	115,678
Equity in net loss of affiliates	(5,643)	(1,956)
Income (loss) before income taxes	(67,601)	26,599
Income tax benefit (expense)	2,281	(795)
Net income (loss)	(65,320)	25,804
Net loss attributable to the noncontrolling interests	891	1,293
Net income (loss) attributable to Intrexon	$ (64,429)	$ 27,097
Net income (loss) attributable to Intrexon per share, basic (in usd per share)	$ (0.55)	$ 0.26
Net income (loss) attributable to Intrexon per share, diluted (in usd per share)	$ (0.55)	$ 0.25
Weighted average shares outstanding, basic	116,861,151	106,103,848
Weighted average shares outstanding, diluted	116,861,151	108,141,734

Consolidated Statements of Comp

Consolidated Statements of Comprehensive Income (Loss) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2016	Mar. 31, 2015
Statement of Comprehensive Income [Abstract]
Net income (loss)	$ (65,320)	$ 25,804
Other comprehensive income (loss):
Unrealized gain on investments	587	27
Foreign currency translation adjustments	698	(3,120)
Comprehensive income (loss)	(64,035)	22,711
Comprehensive loss attributable to the noncontrolling interests	923	1,253
Comprehensive income (loss) attributable to Intrexon	$ (63,112)	$ 23,964

Consolidated Statements of Shar

Consolidated Statements of Shareholders' and Total Equity - 3 months ended Mar. 31, 2016 - USD ($) $ in Thousands	Total	Common Stock	Additional Paid-in Capital	Accumulated Other Comprehensive Loss	Accumulated Deficit	Total Intrexon Shareholders' Equity	Noncontrolling Interests
Balances (in shares) at Dec. 31, 2015	116,658,886	116,658,886
Balances at Dec. 31, 2015	$ 704,886		$ 1,249,559	$ (12,752)	$ (542,729)	$ 694,078	$ 10,808
Increase (Decrease) in Stockholders' Equity
Stock-based compensation expense	13,167		13,152			13,152	15
Exercises of stock options and warrants (in shares)		612,307
Exercises of stock options and warrants	13,330		13,330			13,330
Shares issued as compensation for services (in shares)		108,953
Shares issued as compensation for services	3,083		3,083			3,083
Shares issued in asset acquisition (in shares)		136,340
Shares issued in asset acquisition	4,401		4,401			4,401
Net loss	(65,320)				(64,429)	(64,429)	(891)
Other comprehensive income (loss)	$ 1,285			1,317		1,317	(32)
Balances (in shares) at Mar. 31, 2016	117,516,486	117,516,486
Balances at Mar. 31, 2016	$ 674,832		$ 1,283,525	$ (11,435)	$ (607,158)	$ 664,932	$ 9,900

Consolidated Statements of Cash

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2016	Mar. 31, 2015
Cash flows from operating activities
Net income (loss)	$ (65,320)	$ 25,804
Adjustments to reconcile net income (loss) to net cash used in operating activities:
Depreciation and amortization	5,648	3,549
Loss on disposal of property, plant and equipment	185	92
Unrealized (appreciation) depreciation on equity securities	22,331	(115,454)
Amortization of discount/premium on investments	320	124
Equity in net loss of affiliates	5,643	1,956
Stock-based compensation expense	13,188	10,259
Shares issued as compensation for services	3,083	480
Shares issued as consideration for license agreement	0	59,579
Provision for bad debts	840	393
Deferred income taxes	(2,188)	795
Other noncash items	193	264
Receivables:
Trade	3,022	(815)
Related parties	7,578	2,807
Note	(12)	(16)
Other	(168)	67
Inventory	1,485	(382)
Prepaid expenses and other	143	(292)
Other assets	839	(1,216)
Accounts payable	2,393	672
Accrued compensation and benefits	(10,773)	(297)
Other accrued liabilities	4,724	1,210
Deferred revenue	3,050	(2,621)
Related party payables	208	(156)
Other long term liabilities	(21)	157
Net cash used in operating activities	(3,609)	(13,041)
Cash flows from investing activities
Maturities of investments	18,000	24,000
Purchases of equity securities and warrants	0	(14,900)
Acquisitions of businesses, net of cash received	0	(29,559)
Acquisition of noncontrolling interest	0	(1,566)
Investments in affiliates	(2,721)	(1,491)
Cash paid in asset acquisition	(7,244)	0
Purchases of property, plant and equipment	(4,257)	(2,711)
Proceeds from sale of property, plant and equipment	102	194
Net cash provided by (used in) investing activities	3,880	(26,033)
Cash flows from financing activities
Proceeds from issuance of shares in public offerings, net of issuance costs	0	110,041
Advances from lines of credit	812	5,559
Repayments of advances from lines of credit	(837)	(7,211)
Proceeds from long term debt	0	44
Payments of long term debt	(160)	(341)
Proceeds from stock option exercises	9,777	2,567
Net cash provided by financing activities	9,592	110,659
Effect of exchange rate changes on cash and cash equivalents	88	(36)
Net increase in cash and cash equivalents	9,951	71,549
Cash and cash equivalents
Beginning of period	135,782	27,466
End of period	145,733	99,015
Supplemental disclosure of cash flow information
Cash paid during the period for interest	70	84
Significant noncash financing and investing activities
Stock received as consideration for collaboration agreements	9,333	0
Stock issued in business combinations	0	39,735
Stock issued to acquire noncontrolling interest	0	9,412
Stock issued in asset acquisition	4,401	0
Contingent consideration assumed in asset acquisition	3,660	0
Purchases of equipment included in accounts payable and other accrued liabilities	839	0
Proceeds from stock option exercises included in other receivables	$ 3,553	$ 0

Organization

Organization	3 Months Ended
	Mar. 31, 2016
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Organization	Organization Intrexon Corporation ("Intrexon"), a Virginia corporation, forms collaborations to create biologically based products and processes using synthetic biology. Intrexon's primary domestic operations are in California, Florida, Maryland, and Virginia, and its primary international operations are in Belgium and Hungary. There have been no commercialized products derived from Intrexon's collaborations to date. Trans Ova Genetics, L.C. ("Trans Ova"), a provider of bovine reproductive technologies and other genetic processes to cattle breeders and producers, is a wholly owned subsidiary of Intrexon with primary operations in Iowa, Maryland, Missouri, Oklahoma, and Texas. ViaGen, L.C. ("ViaGen"), a provider of genetic preservation and cloning technologies, and Exemplar Genetics, LLC ("Exemplar"), a provider of genetically engineered swine for medical and genetic research, are wholly owned subsidiaries with primary operations in Texas and Iowa, respectively. Intrexon Produce Holdings, Inc. ("IPHI") is a wholly owned subsidiary of Intrexon. Okanagan Specialty Fruits, Inc. ("Okanagan"), a company which developed and received regulatory approval for the world's first non-browning apple without the use of any flavor-altering chemical or antioxidant additives, is a wholly owned subsidiary of IPHI with primary operations in Canada. Fruit Orchard Holdings, Inc. ("FOHI") is a wholly owned subsidiary of IPHI with primary operations in Washington. Oxitec Limited ("Oxitec"), a pioneering company in biological insect control solutions, is a wholly owned subsidiary of Intrexon with primary operations in England and Brazil. As of March 31, 2016 , Intrexon owned approximately 63% of AquaBounty Technologies, Inc. ("AquaBounty"), a company focused on improving productivity in commercial aquaculture, and approximately 51% of Biological & Popular Culture, Inc. ("BioPop"), a company developing artwork, children's toys and novelty goods that are derived from living organisms or enabled by synthetic biology. Intrexon Corporation and its consolidated subsidiaries are hereinafter referred to as the "Company."

Summary of Significant Accounti

Summary of Significant Accounting Policies	3 Months Ended
	Mar. 31, 2016
Accounting Policies [Abstract]
Summary of Significant Accounting Policies	Summary of Significant Accounting Policies Basis of Presentation The accompanying interim consolidated financial statements are unaudited and have been prepared in accordance with accounting principles generally accepted in the United States of America ("U.S. GAAP"). Certain information and footnote disclosures normally included in the Company's annual financial statements have been condensed or omitted. These interim consolidated financial statements, in the opinion of management, reflect all normal recurring adjustments necessary for fair statement of the Company's financial position as of March 31, 2016 and results of operations and cash flows for the interim periods ended March 31, 2016 and 2015 . These interim financial results are not necessarily indicative of the results to be expected for the year ending December 31, 2016 , or for any other future annual or interim period. The accompanying interim unaudited consolidated financial statements should be read in conjunction with the audited consolidated financial statements and related notes thereto included in the Company's Annual Report on Form 10-K for the year ended December 31, 2015 . The accompanying consolidated financial statements reflect the operations of the Company and its subsidiaries. All intercompany accounts and transactions have been eliminated. Equity Method Investments The Company accounts for its investments in each of its six strategic joint ventures and for its investments in Thrive Agrobiotics, Inc. ("Thrive Agrobiotics"), Exotech Bio, Inc. ("Exotech Bio"), and Relieve Genetics, Inc. ("Relieve Genetics") using the equity method of accounting since the Company has the ability to exercise significant influence, but not control, over the operating activities of these entities. The Company's investments in these entities are included in investments in affiliates in the accompanying consolidated balance sheets. The Company determined that it had significant influence over Oragenics, Inc. ("Oragenics"), a collaborator, as of March 31, 2016 and December 31, 2015 , based on its ownership interest and other qualitative factors. The Company accounts for its investment in Oragenics using the fair value option. The fair value of the Company's equity securities of Oragenics was $10,256 and $16,601 as of March 31, 2016 and December 31, 2015 , respectively, and is included as equity securities in the accompanying consolidated balance sheets. The Company's ownership percentage of Oragenics was 30.5% and 30.7% at March 31, 2016 and December 31, 2015 , respectively. Unrealized appreciation (depreciation) in the fair value of the Company's equity securities held in Oragenics was $(6,345) and $936 for the three months ended March 31, 2016 and 2015 , respectively. Summarized unaudited financial data as of March 31, 2016 and December 31, 2015 and for the three months ended March 31, 2016 and 2015 , for the Company's equity method investments are shown in the following tables. Summarized unaudited financial data for ZIOPHARM Oncology, Inc. ("ZIOPHARM") has been included for the three months ended March 31, 2015 as the Company determined it had significant influence over ZIOPHARM until the Company distributed all of its equity securities held in ZIOPHARM to its shareholders in June 2015. March 31, December 31, Current assets $ 56,800 $ 28,123 Non-current assets 10,672 1,539 Total assets 67,472 29,662 Current liabilities 7,592 6,274 Net assets $ 59,880 $ 23,388 Three Months Ended 2016 2015 Revenues $ 282 $ 636 Operating expenses 17,660 84,069 Operating loss (17,378 ) (83,433 ) Other 3 (1 ) Net loss $ (17,375 ) $ (83,434 ) Variable Interest Entities As of March 31, 2016 and December 31, 2015 , the Company determined that certain of its collaborators and joint ventures as well as the Harvest Intrexon Enterprise Fund I, LP ("Harvest") were variable interest entities ("VIE" or "VIEs"). The Company was not the primary beneficiary for these entities since it did not have the power to direct the activities that most significantly impact the economic performance of the VIEs. The Company's aggregate investment balances of these VIEs as of March 31, 2016 and December 31, 2015 was $15,600 and $3,598 , respectively, which represents the Company's maximum risk of loss related to the identified VIEs. Net Income (Loss) per Share For the three months ended March 31, 2016 , basic net loss per share is calculated by dividing net loss attributable to common shareholders by the weighted average shares outstanding during the period, without consideration of common stock equivalents. Diluted net loss per share is calculated by adjusting weighted average shares outstanding for the dilutive effect of common stock equivalents outstanding for the period, using the treasury-stock method. For purposes of the diluted net loss per share calculation, stock options and warrants are considered to be common stock equivalents but are excluded from the calculation of diluted net loss per share because their effect would be anti-dilutive and, therefore, basic and diluted net loss per share were the same for the three months ended March 31, 2016 . For the three months ended March 31, 2015 , basic net income per share is calculated by dividing net income attributable to common shareholders by the weighted average shares outstanding during the period, without consideration of common stock equivalents. Diluted net income per share is calculated by adjusting weighted average shares outstanding for the dilutive effect of common stock equivalents outstanding for the period, using the treasury-stock method. For the purposes of the diluted net income per share calculation, stock options and warrants are considered to be common stock equivalents. Segment Information The Company has determined that it operates in one segment. The Company applies its technologies to create products and services which may be either sold directly to customers or developed through collaboration with third parties. As of March 31, 2016 and December 31, 2015 , the Company had $4,817 and $3,877 , respectively, of long-lived assets in foreign countries. The Company recognized revenues derived in foreign countries totaling $2,496 and $1,338 for the three months ended March 31, 2016 and 2015 , respectively. Use of Estimates The preparation of financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, the disclosure of contingent assets and liabilities at the date of the financial statements, and the reported amounts of revenues and expenses during the reporting periods. Actual results could differ from those estimates. Recently Issued Accounting Pronouncements In March 2016, the Financial Accounting Standards Board ("FASB") issued Accounting Standards Update ("ASU") 2016-09, Stock Compensation (Topic 718) - Improvements to Employee Share-Based Payment Accounting ("ASU 2016-09"). The provisions of ASU 2016-09 simplify various aspects of the accounting for employee share-based payment transactions, including the income tax consequences, classification of awards as either equity or liabilities, and classification on the statement of cash flows. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2016, with early adoption permitted, and is effective for the Company for the year ending December 31, 2017. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. In March 2016, the FASB issued ASU 2016-07, Investments-Equity Method and Joint Ventures (Topic 323) - Simplifying the Transition to the Equity Method of Accounting ("ASU 2016-07"). The provisions of ASU 2016-07 eliminate the requirement that when an investment qualifies for use of the equity method as a result of an increase in the level of ownership interest or degree of influence, an adjustment must be made to the investment, results of operations, and retained earnings retroactively on a step-by-step basis as if the equity method had been in effect during all previous periods that the investment had been held. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2016, with early adoption permitted, and is effective for the Company for the year ending December 31, 2017. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. In February 2016, the FASB issued ASU 2016-02, Leases (Topic 842) ("ASU 2016-02"). The provisions of ASU 2016-02 set out the principles for the recognition, measurement, presentation and disclosure of leases for both parties to a contract (i.e. lessees and lessors). The new standard requires lessees to apply a dual approach, classifying leases as either finance or operating leases based on the principle of whether or not the lease is effectively a financed purchase by the lessee. This classification will determine whether lease expense is recognized based on an effective interest method or on a straight line basis over the term of the lease, respectively. A lessee is also required to record a right-of-use asset and a lease liability for all leases with a term of greater than 12 months regardless of their classification. Leases with a term of 12 months or less will be accounted for in a similar manner as under existing guidance for operating leases today. ASU 2016-02 supersedes the previous lease standard, Topic 840 Leases . The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2018, and is effective for the Company for the year ending December 31, 2019. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. In January 2016, the FASB issued ASU 2016-01, Financial Instruments - Overall (Subtopic 825-10) - Recognition and Measurement of Financial Assets and Financial Liabilities ("ASU 2016-01"). The provisions of ASU 2016-01 make targeted improvements to enhance the reporting model for financial instruments to provide users of financial statements with more decision-useful information, including certain aspects of recognition, measurement, presentation, and disclosure of financial instruments. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2017, and is effective for the Company for the year ending December 31, 2018. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. In November 2015, the FASB issued ASU 2015-17, Income Taxes (Topic 740) - Balance Sheet Classification of Deferred Taxes ("ASU 2015-17"). The provisions of ASU 2015-17 simplify the presentation of deferred income taxes by requiring an entity to classify deferred tax liabilities and assets as noncurrent on a classified balance sheet. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2016, with early adoption permitted, and is effective for the Company for the year ending December 31, 2017. The Company elected to early adopt this guidance during the first quarter of 2016 and applied it prospectively, and there was no significant impact on the Company's consolidated financial statements. In July 2015, the FASB issued ASU 2015-11, Inventory (Topic 330) - Simplifying the Measurement of Inventory ("ASU 2015-11"). The provisions of ASU 2015-11 provide guidance for simplifying the calculation for subsequent measurement of inventory measured using the first-in-first-out or average cost methods. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2016, and is effective for the Company for the year ending December 31, 2017. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. In May 2014, the FASB issued ASU 2014-09, Revenue from Contracts with Customers ("ASU 2014-09"). The FASB issued ASU 2014-09 to clarify the principles for recognizing revenue and to develop a common revenue standard for U.S. GAAP. The standard outlines a single comprehensive model for entities to use in accounting for revenue arising from contracts with customers and supersedes the most current revenue recognition guidance. This guidance was originally effective for annual periods and interim periods within those annual periods beginning after December 15, 2016 and early adoption was not permitted. In August 2015, the FASB issued ASU 2015-14, Revenue from Contracts with Customers (Topic 606) - Deferral of the Effective Date ("ASU 2015-14"), which deferred the effective date of the guidance in ASU 2014-09 by one year to December 15, 2017 for interim and annual reporting periods beginning after that date and permitted early adoption of the standard, but not before the original effective date of December 15, 2016, and is effective for the Company for the year ending December 31, 2018. In March and April 2016, the FASB clarified the implementation guidance on principal versus agent, identifying performance obligations, and licensing by issuing ASU 2016-08, Revenue from Contracts with Customers (Topic 606) - Principal versus Agent Considerations ("ASU 2016-08") and ASU 2016-10, Revenue from Contracts with Customers (Topic 606) - Identifying Performance Obligations and Licensing ("ASU 2016-10"). The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. Reclassifications Certain insignificant reclassifications have been made to the prior interim period consolidated financial statements to conform to the current interim period presentation.

Mergers and Acquisitions

Mergers and Acquisitions	3 Months Ended
	Mar. 31, 2016
Business Combinations [Abstract]
Mergers and Acquisitions	Mergers and Acquisitions Oxitec Acquisition In September 2015, pursuant to a Stock Purchase Agreement (the "Oxitec Purchase Agreement"), the Company acquired 100% of the issued outstanding share capital of Oxitec. The aggregated consideration paid consisted of (i) 1,359,343 shares of the Company's common stock (the "Stock Consideration") and (ii) $90,199 in cash (the "Cash Consideration"), inclusive of net cash and working capital adjustments, as defined in the Oxitec Purchase Agreement, totaling $9,449 . Stock Consideration totaling 480,422 shares and Cash Consideration totaling $1,991 were withheld as escrow at closing and are issuable and payable, respectively, eighteen months after closing, subject to reduction for satisfaction of any claims for indemnification made by the Company under the Oxitec Purchase Agreement. Cash Consideration withheld is included in deferred consideration as of March 31, 2016 . The results of Oxitec's operations subsequent to the acquisition date have been included in the consolidated financial statements. The fair value of the total consideration transferred was $146,394 . The acquisition date fair value of the Stock Consideration and Cash Consideration is presented below: Cash $ 90,199 Common shares 56,195 $ 146,394 The fair value of the shares of the Company common stock issued was based on the quoted closing price of the Company's common stock as of the closing date of the acquisition. The estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown below: Cash $ 3,780 Trade receivables 125 Other receivables 7,395 Prepaid expenses and other 121 Property, plant, and equipment 1,198 Intangible assets 96,854 Total assets acquired 109,473 Accounts payable 1,187 Accrued compensation and benefits 246 Other accrued liabilities 210 Deferred revenue 120 Deferred tax liabilities 12,584 Total liabilities assumed 14,347 Net assets acquired 95,126 Goodwill 51,268 Total consideration $ 146,394 The acquired intangible assets primarily include in-process research and development, the fair value of which was determined using the multi-period excess earning method, which is a variation of the income approach that converts future cash flows to single discounted present value amounts. The in-process research and development are currently indefinite-lived intangible assets and, accordingly, are not being amortized. Goodwill, which is not expected to be deductible for tax purposes, represents the assembled workforce and the potential for future Oxitec products and technologies. The Company incurred $1,675 of acquisition-related costs which were included in selling, general and administrative expenses in the consolidated statements of operations for the related periods. Okanagan Acquisition In April 2015, pursuant to a Stock Purchase Agreement (the "Okanagan Purchase Agreement"), the Company acquired 100% of the outstanding shares of Okanagan. Pursuant to the Okanagan Purchase Agreement, the former shareholders of Okanagan received an aggregate of 707,853 shares of the Company's common stock, and $10,000 cash in exchange for all shares in Okanagan. The results of Okanagan's operations subsequent to the acquisition date have been included in the consolidated financial statements. The fair value of the total consideration transferred was $40,933 . The acquisition date fair value of each class of consideration transferred is presented below: Cash $ 10,000 Common shares 30,933 $ 40,933 The fair value of the shares of the Company's common stock issued was based on the quoted closing price of the Company's common stock as of the closing date of the acquisition. The estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown below: Cash $ 58 Trade receivables 16 Other receivables 49 Property, plant, and equipment 32 Intangible assets 36,500 Total assets acquired 36,655 Accounts payable 181 Deferred revenue 181 Deferred tax liabilities 8,847 Total liabilities assumed 9,209 Net assets acquired 27,446 Goodwill 13,487 Total consideration $ 40,933 The acquired intangible assets primarily include developed technology, patents and know-how and the fair values of the acquired assets were determined using the with-and-without method, which is a variation of the income approach that utilizes estimated cash flows with all assets in place at the valuation date and estimated cash flows with all assets in place except the intangible assets at the valuation date. The intangible assets are being amortized over a useful life of fourteen years . Goodwill, which is not expected to be deductible for tax purposes, represents potential future applications of Okanagan's technology to other fruits, including additional apple varietals, and anticipated buyer-specific synergies arising from the combination of the Company's and Okanagan's technologies. The Company incurred $341 of acquisition-related costs, of which $163 is included in selling, general and administrative expenses in the accompanying consolidated statement of operations for the three months ended March 31, 2015 . ActoGeniX Acquisition In February 2015, the Company acquired 100% of the membership interests of ActoGeniX NV ("ActoGeniX"), a European biopharmaceutical company, pursuant to a Stock Purchase Agreement (the "ActoGeniX Purchase Agreement"). ActoGeniX's platform technology complements the Company's suite of proprietary technologies available for current and future collaborators. Pursuant to the ActoGeniX Purchase Agreement, the former members of ActoGeniX received an aggregate of 965,377 shares of the Company's common stock and $32,739 in cash in exchange for all membership interests of ActoGeniX. The results of ActoGeniX's operations subsequent to the acquisition date have been included in the consolidated financial statements. The fair value of the total consideration transferred was $72,474 . The acquisition date fair value of each class of consideration transferred is presented below: Cash $ 32,739 Common shares 39,735 $ 72,474 The fair value of the shares of the Company's common stock issued was based on the quoted closing price of the Company's common stock as of the closing date of the acquisition. The estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown below: Cash $ 3,180 Other receivables 305 Prepaid expenses and other 31 Property, plant and equipment 209 Intangible assets 68,100 Other non-current assets 23 Total assets acquired 71,848 Accounts payable 230 Accrued compensation and benefits 196 Other accrued liabilities 253 Deferred revenue 732 Deferred tax liabilities 612 Total liabilities assumed 2,023 Net assets acquired 69,825 Goodwill 2,649 Total consideration $ 72,474 The acquired intangible assets primarily include in-process research and development, the fair value of which was determined using the multi-period excess earnings and with-and-without methods, which are both variations of the income approach that convert future cash flows to single discounted present value amounts. In August 2015, the Company re-evaluated the acquired in-process research and development and determined that it was placed in service as developed technology and began amortizing the original amount capitalized using a useful life of eighteen years . Goodwill, which is not expected to be deductible for tax purposes, represents the assembled workforce and anticipated buyer-specific synergies arising from the combination of the Company's and ActoGeniX's technologies. The Company incurred $418 of acquisition-related costs, of which $ 409 is included in selling, general and administrative expenses in the accompanying consolidated statement of operations for the three months ended March 31, 2015 . Unaudited Condensed Pro Forma Financial Information The results of operations of the 2015 acquisitions discussed above are included in the consolidated statements of operations beginning on the day after their respective acquisition dates. The following unaudited condensed pro forma financial information for the three months ended March 31, 2015 is presented as if the acquisitions had been consummated on January 1, 2014: Three Months Ended March 31, 2015 Pro Forma Revenues $ 34,228 Income before income taxes 20,127 Net income 20,459 Net loss attributable to the noncontrolling interests 1,293 Net income attributable to Intrexon 21,752

Investments in Joint Ventures

Investments in Joint Ventures	3 Months Ended
	Mar. 31, 2016
Equity Method Investments and Joint Ventures [Abstract]
Investments in Joint Ventures	Investments in Joint Ventures Intrexon T1D Partners In March 2016, the Company and certain investors (the "T1D Investors"), including affiliates of Third Security, LLC ("Third Security"), entered into a Limited Liability Company Agreement which governs the affairs and conduct of business of Intrexon T1D Partners, LLC ("Intrexon T1D Partners"), a joint venture formed to utilize the Company's proprietary ActoBiotics platform to develop and commercialize products to treat type 1 diabetes. The Company also entered into an ECC with Intrexon T1D Partners which provides the exclusive rights to the Company's technology for use in the field, as a result of which the Company received a technology access fee of $10,000 while retaining a 50% membership interest in Intrexon T1D Partners. The T1D Investors made initial capital contributions, totaling $10,000 in the aggregate, in exchange for pro rata membership interests in Intrexon T1D Partners totaling 50% . Intrexon has committed to make capital contributions of up to $5,000 , and the T1D Investors, as a group and pro rata in accordance with their respective membership interests in Intrexon T1D Partners, have committed to make additional capital contributions of up to $5,000 , at the request of Intrexon T1D Partners' board of managers (the "Intrexon T1D Partners Board") and subject to certain limitations. Intrexon T1D Partners is governed by the Intrexon T1D Partners Board, which has five members. Two members of the Intrexon T1D Partners Board are designated by the Company and three members are designated by a majority of the T1D Investors. The Company and the T1D Investors have the right, but not the obligation, to make additional capital contributions above these limits when and if solicited by the Intrexon T1D Partners Board. EnviroFlight In February 2016, the Company entered into a series of transactions involving EnviroFlight, LLC ("Old EnviroFlight"), Darling Ingredients Inc. ("Darling") and a newly formed venture between the Company and Darling ("New EnviroFlight"). The Company determined that the series of integrated transactions to acquire substantially all of the assets of Old EnviroFlight for cash, common stock, and contingent consideration should be accounted for as a single transaction, which constituted a business, and considered New EnviroFlight to be the accounting acquirer pursuant to Accounting Standards Codification ("ASC") 805, Business Combinations . Consideration paid to Old EnviroFlight was $4,244 in cash, 136,340 shares of the Company's common stock valued at $4,401 and contingent consideration estimated at $3,660 . Contemporaneously, all the assets acquired from Old EnviroFlight, with the exception of certain developed technology, and $3,000 of cash were contributed to New EnviroFlight in exchange for a non-controlling, 50% membership interest in New EnviroFlight. The Company's contributions to New EnviroFlight include an exclusive license to the developed technology that was retained by the Company. Darling received the remaining 50% membership interest in New EnviroFlight as consideration for terminating rights previously held in the developed technology with Old EnviroFlight. New EnviroFlight was formed to generate high-nutrition, low environmental impact animal and fish feed, as well as fertilizer products. The Company and Darling as members have each agreed to make additional capital contributions of up to $5,000 to fund ongoing operations of New EnviroFlight. All of the employees of Old EnviroFlight became employees of New EnviroFlight. The Company determined that its investment in New EnviroFlight should be accounted for using the equity method of accounting. The Company recorded an estimated fair value of $5,425 for its investment in New EnviroFlight and $9,880 for the retained developed technology intangible asset. The developed technology will be amortized over a period of twenty-one years . The contingent consideration liability payable to the members of Old EnviroFlight is considered a freestanding financial instrument in accordance with ASC 480, Distinguishing Liabilities and Equity , and will be recorded at fair value each reporting period. The value of this liability was estimated at $3,660 as of March 31, 2016 . The members of Old EnviroFlight may receive contingent consideration of up to $5,500 of additional shares of the Company's common stock if certain regulatory and commercial milestones are met prior to February 2019. The Company's investment in New EnviroFlight was $5,328 as of March 31, 2016 and is included in investments in affiliates in the accompanying consolidated balance sheet. Intrexon Energy Partners II In December 2015, the Company and certain investors (the "IEPII Investors"), including Harvest, entered into a Limited Liability Company Agreement which governs the affairs and conduct of business of Intrexon Energy Partners II, LLC ("Intrexon Energy Partners II"), a joint venture formed to utilize the Company's natural gas bioconversion platform for the production of 1,4-butanediol, an industrial chemical used to manufacture spandex, polyurethane, plastics, and polyester. The Company also entered into an ECC with Intrexon Energy Partners II which provides exclusive rights to the Company's technology for use in the field, as a result of which the Company received a technology access fee of $18,000 while retaining a 50% membership interest in Intrexon Energy Partners II. The IEPII Investors made initial capital contributions, totaling $18,000 in the aggregate, in exchange for pro rata membership interests in Intrexon Energy Partners II totaling 50% . In December 2015, the owners of Intrexon Energy Partners II made a capital contribution of $4,000 , half of which was paid by the Company. Intrexon has committed to make additional capital contributions of up to $10,000 , and the IEPII Investors, as a group and pro rata in accordance with their respective membership interests in Intrexon Energy Partners II, have committed to make additional capital contributions of up to $10,000 , at the request of Intrexon Energy Partners II's board of managers (the "Intrexon Energy Partners II Board") and subject to certain limitations. Intrexon Energy Partners II is governed by the Intrexon Energy Partners II Board which has five members. One member of the Intrexon Energy Partners II Board is designated by the Company and four members are designated by a majority of the IEPII Investors. The Company and the IEPII Investors have the right, but not the obligation, to make additional capital contributions above the initial limits when and if solicited by the Intrexon Energy Partners II Board. The Company's investment in Intrexon Energy Partners II was $1,974 and $2,000 as of March 31, 2016 and December 31, 2015 , respectively, and is included in investments in affiliates in the accompanying consolidated balance sheets. Intrexon Energy Partners In March 2014, the Company and certain investors (the "IEP Investors"), including an affiliate of Third Security, entered into a Limited Liability Company Agreement which governs the affairs and conduct of business of Intrexon Energy Partners, LLC ("Intrexon Energy Partners"), a joint venture formed to optimize and scale-up the Company's gas-to-liquid bioconversion platform for the production of certain fuels and lubricants. The Company also entered into an ECC with Intrexon Energy Partners providing exclusive rights to the Company's technology for the use in bioconversion, as a result of which the Company received a technology access fee of $25,000 while retaining a 50% membership interest in Intrexon Energy Partners. The IEP Investors made initial capital contributions, totaling $25,000 in the aggregate, in exchange for pro rata membership interests in Intrexon Energy Partners totaling 50% . In addition, Intrexon has committed to make capital contributions of up to $25,000 , and the IEP Investors, as a group and pro rata in accordance with their respective membership interests in Intrexon Energy Partners, have committed to make additional capital contributions of up to $25,000 , at the request of Intrexon Energy Partners' board of managers (the "Intrexon Energy Partners Board") and subject to certain limitations. As of March 31, 2016 , the Company's remaining commitment was $16,711 . Intrexon Energy Partners is governed by the Intrexon Energy Partners Board which has five members. Two members of the Intrexon Energy Partners Board are designated by the Company and three members are designated by a majority of the IEP Investors. The Company and the IEP Investors have the right, but not the obligation, to make additional capital contributions above the initial limits when and if solicited by the Intrexon Energy Partners Board. The Company's investment in Intrexon Energy Partners was $(984) and $(1,270) as of March 31, 2016 and December 31, 2015 , respectively, and is included in other accrued liabilities in the accompanying consolidated balance sheets. OvaXon In December 2013, the Company and OvaScience, Inc. ("OvaScience"), a life sciences company focused on the discovery, development and commercialization of new treatments for infertility, entered into a Limited Liability Company Agreement ("OvaXon LLC Agreement") to form OvaXon, LLC ("OvaXon"), a joint venture to create new applications for improving human and animal health. Both the Company and OvaScience made an initial capital contribution of $1,500 in January 2014 for a 50% membership interest in OvaXon. OvaXon is governed by the OvaXon board of managers ("OvaXon Board") which has four members, two each from the Company and OvaScience. In cases in which the OvaXon Board determines that additional capital contributions are necessary in order for OvaXon to conduct business and comply with its obligations, each of the Company and OvaScience has the right, but not the obligation, to make additional capital contributions to OvaXon subject to the OvaXon LLC Agreement. The Company's investment in OvaXon was $215 and $(144) as of March 31, 2016 and December 31, 2015 , respectively, and is included in investments in affiliates and other accrued liabilities, respectively, in the accompanying consolidated balance sheets. S & I Ophthalmic In September 2013, the Company entered into a Limited Liability Company Agreement ("Sun LLC Agreement") with Caraco Pharmaceutical Laboratories, Ltd. ("Sun Pharmaceutical Subsidiary"), an indirect subsidiary of Sun Pharmaceutical Industries Ltd. ("Sun Pharmaceutical"), an international specialty pharmaceutical company focused on chronic diseases, to form S & I Ophthalmic, LLC ("S & I Ophthalmic"). The Sun LLC Agreement governs the affairs and the conduct of business of S & I Ophthalmic. S & I Ophthalmic leverages experience and technology from both the Company and Sun Pharmaceutical. Both the Company and Sun Pharmaceutical Subsidiary made an initial capital contribution of $5,000 in October 2013 for a 50% membership interest in S & I Ophthalmic. S & I Ophthalmic is governed by a board of managers ("S & I Ophthalmic Board") which has four members, two each from the Company and Sun Pharmaceutical Subsidiary. In cases in which the S & I Ophthalmic Board determines that additional capital contributions are necessary in order for S & I Ophthalmic to conduct business and comply with its obligations, each of the Company and Sun Pharmaceutical Subsidiary has committed to making additional capital contributions to S & I Ophthalmic subject to certain limits defined in the agreement. Each has the right, but not the obligation, to make additional capital contributions above the defined limits when and if solicited by the S & I Ophthalmic Board. As of March 31, 2016 , both the Company and Sun Pharmaceutical Subsidiary have made subsequent capital contributions of $5,000 . Beginning on the seventh anniversary of the effective date of the Sun LLC Agreement, and upon the second anniversary thereafter, the Company, as well as Sun Pharmaceutical Subsidiary, may make a cash offer to purchase all of the other party's interest in S & I Ophthalmic. Upon receipt of such an offer, the other party must either agree to tender its interests at the offered price or submit a counteroffer at a price higher than the original offer. Such offer and counteroffer may continue until one party agrees to the other's price. The Company's investment in S & I Ophthalmic was $5,785 and $6,379 as of March 31, 2016 and December 31, 2015 , respectively, and is included in investments in affiliates in the accompanying consolidated balance sheets.

Collaboration and Licensing Rev

Collaboration and Licensing Revenue	3 Months Ended
	Mar. 31, 2016
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Collaboration and Licensing Revenue	Collaboration and Licensing Revenue The Company generates revenue through contractual agreements with collaborators (known as exclusive channel collaborations, "ECC" or "ECCs") and licensing agreements whereby the collaborators or the licensees obtain exclusive access to the Company's proprietary technologies for use in the research, development and commercialization of products and/or treatments in a contractually specified field of use. Upfront and milestone payments are typically deferred and recognized over the expected life of the Company's technology platform using a straight-line approach. The Company recognizes the reimbursement payments received for research and development services in the period in which the services are performed and collection is reasonably assured. The following tables summarize the amounts recorded as revenue in the consolidated statements of operations for each significant collaboration or licensing agreement for the three months ended March 31, 2016 and 2015 . Three Months Ended March 31, 2016 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 922 $ 6,059 $ 6,981 Oragenics, Inc. 263 543 806 Fibrocell Science, Inc. 605 1,252 1,857 Genopaver, LLC 69 1,509 1,578 S & I Ophthalmic, LLC — 1,186 1,186 OvaXon, LLC — 694 694 Intrexon Energy Partners, LLC 625 3,363 3,988 Persea Bio, LLC 125 199 324 Ares Trading S.A. 1,597 808 2,405 Thrive Agrobiotics, Inc. 46 388 434 Intrexon Energy Partners II, LLC 500 50 550 Other 1,020 2,250 3,270 Total $ 5,772 $ 18,301 $ 24,073 Three Months Ended March 31, 2015 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 644 $ 3,157 $ 3,801 Oragenics, Inc. 262 8 270 Fibrocell Science, Inc. 448 1,713 2,161 Genopaver, LLC 69 600 669 S & I Ophthalmic, LLC — 755 755 OvaXon, LLC — 644 644 Intrexon Energy Partners, LLC 625 2,185 2,810 Persea Bio, LLC 125 115 240 Other 858 2,575 3,433 Total $ 3,031 $ 11,752 $ 14,783 Except for the agreements discussed below, there have been no significant changes to arrangements with our collaborators and licensees in the three months ended March 31, 2016 . See Note 5 in the Company's Annual Report on Form 10-K for the year ended December 31, 2015 for additional details of the Company's existing collaboration and licensing agreements. Exotech Bio Collaboration In March 2016, the Company entered into an ECC with Exotech Bio, an affiliate of Harvest and a related party. Exotech Bio was formed for the purpose of entering into the ECC and developing and commercializing products using exosomes carrying a RNA payload designed to kill, suppress, or render immune-visible a cancer cell. Upon execution of the ECC, the Company received a technology access fee in the form of equity in Exotech Bio valued at $5,000 as upfront consideration. The Company is also entitled to up to $52,500 of potential payments for substantive and non-substantive development and commercial milestones for each product developed under the ECC. The Company receives reimbursement payments for research and development services provided pursuant to the ECC. Exotech Bio will pay the Company royalties as a percentage in the lower double-digits on the quarterly net sales of products developed under the ECC, as defined in the agreement. Exotech Bio is responsible for the development and commercialization of the product candidates. The term of the ECC commenced in March 2016 and continues until terminated pursuant to the ECC agreement. The ECC may be terminated by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by Exotech Bio upon 90 days written notice to the Company. Relieve Genetics Collaboration In March 2016, the Company entered into an ECC with Relieve Genetics, an affiliate of Harvest and a related party. Relieve Genetics was formed for the purpose of entering into the ECC and developing and commercializing products using a viral vector expressing interleukin-10 for the treatment of chronic neuropathic pain resultant from cancer in humans. Upon execution of the ECC, the Company received a technology access fee in the form of equity in Relieve Genetics valued at $4,333 as upfront consideration. The Company is also entitled to up to $52,500 of potential payments for substantive and non-substantive development and commercial milestones for each product developed under the ECC. The Company receives reimbursement payments for research and development services provided pursuant to the ECC. Relieve Genetics will pay the Company royalties as a percentage in the lower double-digits on the quarterly net sales of products developed under the ECC, as defined in the agreement. Relieve Genetics is responsible for the development and commercialization of the product candidates. The term of the ECC commenced in March 2016 and continues until terminated pursuant to the ECC agreement. The ECC may be terminated by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by Relieve Genetics upon 90 days written notice to the Company. Intrexon T1D Partners Collaboration In March 2016, the Company entered into an ECC with Intrexon T1D Partners, a related party. Pursuant to the ECC, Intrexon T1D Partners received an exclusive license to the Company's technology platform to develop and commercialize products to treat type 1 diabetes. Upon execution of the ECC, the Company received a technology access fee of $10,000 and is entitled to reimbursement of research and development services as provided for in the ECC agreement. The term of the ECC commenced in March 2016 and continues until March 2036; termination prior to that date may be initiated (i) by either party in the event of certain material breaches defined in the agreement or (ii) may be terminated Intrexon T1D Partners upon 90 days written notice to the Company. Deferred Revenue Deferred revenue primarily consists of consideration received for upfront and milestone payments in connection with the Company's collaborations and licensing agreements, prepayments for research and development services performed for collaborators and licensees, and prepayments for product and service revenues. Deferred revenue consists of the following: March 31, December 31, Upfront and milestone payments $ 194,849 $ 181,331 Prepaid research and development services 9,439 10,938 Prepaid product and service revenues 5,201 4,759 Other 749 701 Total $ 210,238 $ 197,729 Current portion of deferred revenue $ 37,695 $ 35,366 Long-term portion of deferred revenue 172,543 162,363 Total $ 210,238 $ 197,729 The following table summarizes the remaining balance of deferred revenue associated with upfront and milestone payments for each significant collaboration and licensing agreement: March 31, December 31, ZIOPHARM Oncology, Inc. $ 29,416 $ 30,338 Oragenics, Inc. 8,550 8,813 Fibrocell Science, Inc. 20,840 21,445 Genopaver, LLC 2,181 2,250 Intrexon Energy Partners, LLC 20,000 20,625 Persea Bio, LLC 4,375 4,500 Ares Trading S.A. 51,970 53,567 Thrive Agrobiotics, Inc. 1,575 1,621 Intrexon Energy Partners II, LLC 17,333 17,833 Exotech Bio, Inc. 5,000 — Relieve Genetics, Inc. 4,333 — Intrexon T1D Partners, LLC 10,000 — Other 19,276 20,339 Total $ 194,849 $ 181,331

Short-term and Long-term Invest

Short-term and Long-term Investments	3 Months Ended
	Mar. 31, 2016
Investments, Debt and Equity Securities [Abstract]
Short-term and Long-term Investments	Short-term and Long-term Investments The Company's investments are classified as available-for-sale. The following table summarizes the amortized cost, gross unrealized gains and losses and fair value of available-for-sale investments as of March 31, 2016 : Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Aggregate Fair Value U.S. government debt securities $ 189,903 $ 87 $ (19 ) $ 189,971 Certificates of deposit 272 — — 272 Total $ 190,175 $ 87 $ (19 ) $ 190,243 The following table summarizes the amortized cost, gross unrealized gains and losses and fair value of available-for-sale investments as of December 31, 2015 : Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Aggregate Fair Value U.S. government debt securities $ 208,223 $ 21 $ (540 ) $ 207,704 Certificates of deposit 271 — — 271 Total $ 208,494 $ 21 $ (540 ) $ 207,975 For more information on the Company's method for determining the fair value of its assets, see Note 2 – "Fair Value of Financial Instruments" in the Company's Annual Report on Form 10-K for the year ended December 31, 2015 . The estimated fair value of available-for-sale investments classified by their contractual maturities as of March 31, 2016 was: Due within one year $ 114,659 After one year through two years 75,584 Total $ 190,243 Changes in market interest rates and bond yields cause certain investments to fall below their cost basis, resulting in unrealized losses on investments. The unrealized losses of the Company's investments were primarily a result of unfavorable changes in interest rates subsequent to the initial purchase of these investments and have been in a loss position for less than 12 months. As of March 31, 2016 and December 31, 2015 , the Company did not consider any of its investments to be other-than-temporarily impaired. When evaluating its investments for other-than-temporary impairment, the Company reviews factors such as the length of time and extent to which fair value has been below its cost basis, the financial condition of the issuer, the Company's ability and intent to hold the security and whether it is more likely than not that it will be required to sell the investment before recovery of its cost basis.

Fair Value Measurements

Fair Value Measurements	3 Months Ended
	Mar. 31, 2016
Fair Value Disclosures [Abstract]
Fair Value Measurements	Fair Value Measurements The carrying amount of cash and cash equivalents, receivables, prepaid expenses and other current assets, accounts payable, accrued compensation and benefits, other accrued liabilities, and related party payables approximate fair value due to the short maturity of these instruments. The following table presents the placement in the fair value hierarchy of financial assets that are measured at fair value on a recurring basis, including the items for which the fair value option has been elected, at March 31, 2016 : Quoted Prices in Active Markets (Level 1) Significant Other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) March 31, Assets U.S. government debt securities $ — $ 189,971 $ — $ 189,971 Equity securities 50,189 11,133 — 61,322 Other — 399 — 399 Total $ 50,189 $ 201,503 $ — $ 251,692 The following table presents the placement in the fair value hierarchy of financial assets that are measured at fair value on a recurring basis, including the items for which the fair value option has been elected, at December 31, 2015 : Quoted Prices in Active Markets Significant Other Observable Inputs Significant Unobservable Inputs December 31, Assets U.S. government debt securities $ — $ 207,704 $ — $ 207,704 Equity securities 65,850 17,803 — 83,653 Other — 405 — 405 Total $ 65,850 $ 225,912 $ — $ 291,762 The method used to estimate the fair value of the Level 1 assets in the tables above is based on observable market data as these equity securities are publicly-traded. The method used to estimate the fair value of the Level 2 short-term and long-term investments in the tables above is based on professional pricing sources for identical or comparable instruments, rather than direct observations of quoted prices in active markets. The method used to estimate the fair value of the Level 2 equity securities in the tables above is based on the quoted market price of the publicly-traded security, adjusted for a discount for lack of marketability. There were no transfers between levels of the fair value hierarchy in the three months ended March 31, 2016 . The carrying values of the Company's long term debt approximates fair value due to the length of time to maturity and/or the existence of interest rates that approximate prevailing market rates. Significant financial liabilities measured on a recurring basis were $3,660 at March 31, 2016 . The Company accounted for the contingent consideration liability to the members of Old EnviroFlight by recording its fair value as a liability on the date of the asset acquisition (Note 4 ). At the date of the acquisition, the regulatory and commercial milestones were valued using a probability-weighted discounted cash flow model using discount rates reflecting the time value of money and additional risk inherent in meeting the milestones. These fair value measurements were based on significant inputs not observable in the market and thus represented a Level 3 measurement. The contingent consideration liability is remeasured to fair value at each reporting date until the contingency is resolved, and those changes in fair value are recognized in earnings. There were no significant changes to the fair value of this liability since the acquisition date through March 31, 2016 . Financial liabilities measured on a recurring basis were not significant at December 31, 2015 .

Inventory

Inventory	3 Months Ended
	Mar. 31, 2016
Inventory Disclosure [Abstract]
Inventory	Inventory Inventory consists of the following: March 31, December 31, Supplies, semen and embryos $ 1,287 $ 1,402 Work in process 6,112 6,290 Livestock 16,342 16,907 Feed 1,337 1,964 Total inventory $ 25,078 $ 26,563

Property, Plant and Equipment,

Property, Plant and Equipment, Net	3 Months Ended
	Mar. 31, 2016
Property, Plant and Equipment [Abstract]
Property, Plant and Equipment, Net	Property, Plant and Equipment, Net Property, plant and equipment consist of the following: March 31, December 31, Land and land improvements $ 9,352 $ 9,119 Buildings and building improvements 7,520 7,520 Furniture and fixtures 1,852 1,283 Equipment 37,372 36,016 Leasehold improvements 7,076 6,888 Computer hardware and software 6,199 5,960 Construction and other assets in progress 2,836 2,193 72,207 68,979 Less: Accumulated depreciation and amortization (27,534 ) (26,240 ) Property, plant and equipment, net $ 44,673 $ 42,739 Depreciation expense was $2,133 and $1,953 for the three months ended March 31, 2016 and 2015 , respectively.

Goodwill and Intangible Assets,

Goodwill and Intangible Assets, Net	3 Months Ended
	Mar. 31, 2016
Goodwill and Intangible Assets Disclosure [Abstract]
Goodwill and Intangible Assets, Net	Goodwill and Intangible Assets, Net The changes in the carrying amount of goodwill for the three months ended March 31, 2016 are as follows: Balance at December 31, 2015 $ 165,169 Foreign currency translation adjustments (594 ) Balance at March 31, 2016 $ 164,575 No goodwill or accumulated impairment losses existed as of March 31, 2016 and December 31, 2015 . Intangible assets consist of the following at March 31, 2016 : Weighted Average Useful Life (Years) Gross Carrying Amount Accumulated Amortization Net Patents, related technologies and know-how 15.3 $ 171,658 $ (20,759 ) $ 150,899 Customer relationships 6.5 10,700 (3,222 ) 7,478 Trademarks 9.3 6,800 (1,211 ) 5,589 Covenant not to compete 2.0 398 (215 ) 183 In-process research and development 91,311 — 91,311 Total $ 280,867 $ (25,407 ) $ 255,460 Intangible assets consist of the following at December 31, 2015 : Gross Carrying Amount Accumulated Amortization Net Patents, related technologies and know-how $ 157,411 $ (17,775 ) $ 139,636 Customer relationships 10,700 (2,739 ) 7,961 Trademarks 6,800 (1,018 ) 5,782 Covenant not to compete 384 (160 ) 224 In-process research and development 93,932 — 93,932 Total $ 269,227 $ (21,692 ) $ 247,535 Amortization expense was $3,515 and $1,596 for the three months ended March 31, 2016 and 2015 , respectively.

Lines of Credit and Long Term D

Lines of Credit and Long Term Debt	3 Months Ended
	Mar. 31, 2016
Debt Disclosure [Abstract]
Lines of Credit and Long Term Debt	Lines of Credit and Long Term Debt Lines of Credit Trans Ova has a $6,000 revolving line of credit with First National Bank of Omaha which matures on June 1, 2016. The line of credit bears interest at the greater of 2.95% above the London Interbank Offered Rate or 3.00% and, and the actual rate was 3.39% at March 31, 2016 . As of March 31, 2016 , there were no amounts outstanding. The amount available under the line of credit is based on eligible accounts receivable and inventory up to the maximum principal amount. The line of credit is collateralized by certain of Trans Ova's assets and contains certain restricted covenants that include maintaining minimum tangible net worth, maximum allowable annual capital expenditures and working capital. Trans Ova was in compliance with these covenants as of March 31, 2016. Exemplar has a $700 revolving line of credit with American State Bank which matures on November 1, 2016. The line of credit bears interest at 4.50% per annum. As of March 31, 2016 , there was an outstanding balance of $536 . Long Term Debt Long term debt consists of the following: March 31, December 31, Notes payable $ 6,363 $ 6,477 Royalty-based financing 1,945 1,807 Other 198 244 Long term debt 8,506 8,528 Less current portion 893 930 Long term debt, less current portion $ 7,613 $ 7,598 Trans Ova has a note payable to American State Bank which matures in April 2033 and has an outstanding principal balance of $5,517 as of March 31, 2016 . Trans Ova pays monthly installments of $39 , which includes interest at 3.95% . The note payable is collateralized by certain of Trans Ova's real estate and non-real estate assets. Trans Ova has a note payable to the Iowa Economic Development Authority which matures in July 2016 and has an outstanding principal balance of $366 as of March 31, 2016 . Trans Ova pays quarterly installments of $183 . The note payable is collateralized by certain of Trans Ova's real estate and project assets financed. Exemplar has notes payable with outstanding principal balances totaling $480 as of March 31, 2016 . Exemplar pays monthly installments ranging from $1 to $4 with interest rates ranging from 0% to 3.00% . These notes mature from September 2018 to May 2020 and are collateralized by certain of Exemplar's real estate or letters of credit of certain of its members. AquaBounty has a royalty-based financing grant from the Atlantic Canada Opportunities Agency ("ACOA"), a Canadian government agency, to provide funding of a research and development project. The total amount available under the award was $2,215 , which AquaBounty claimed over a five year period. All amounts claimed by AquaBounty must be repaid in the form of a 10% royalty on any products commercialized out of this research and development project until fully paid. Because the timing of commercialization is subject to additional regulatory considerations, the timing of repayment is uncertain. As of the acquisition date in March 2013, AquaBounty had claimed $1,952 of the available funds and this amount was recorded at its acquisition date fair value of $1,107 . The Company accretes the difference of $845 between the face value of amounts drawn and the acquisition date fair value over the expected period of repayment. Since the acquisition date, AquaBounty has claimed the remaining balance available under the grant, resulting in total long term debt of $1,945 as of March 31, 2016 . Future maturities of long term debt are as follows: 2016 $ 798 2017 384 2018 527 2019 342 2020 311 2021 311 Thereafter 3,888 Total $ 6,561 The AquaBounty royalty-based financing grant is not included in the table above due to the uncertainty of the timing of repayment.

Income Taxes

Income Taxes	3 Months Ended
	Mar. 31, 2016
Income Tax Disclosure [Abstract]
Income Taxes	Income Taxes Tax provisions for interim periods are calculated using an estimate of actual taxable income or loss for the respective period, rather than estimating the Company's annual effective income tax rate, as the Company is currently unable to reliably estimate its income for the full year. For the three months ended March 31, 2016 , the Company had U.S. taxable loss of approximately $9,900 , for which no income tax benefit was recognized. For the three months ended March 31, 2016 , the Company recognized $93 of current foreign income tax benefit. For the three months ended March 31, 2015 , the Company had U.S. taxable loss of approximately $26,600 , and no income tax benefit was recognized. For the three months ended March 31, 2016 , the Company recorded deferred tax benefit of $2,188 . There was $795 of deferred tax expense for the three months ended March 31, 2015 . The Company's net deferred tax assets, excluding certain deferred tax liabilities totaling $19,777 , are offset by a valuation allowance due to the Company's history of net losses combined with an inability to confirm recovery of the tax benefits of the Company's losses and other net deferred tax assets. In assessing the realizability of deferred tax assets, management considers whether it is more likely than not that some portion or all of the deferred tax assets will not be realized. The ultimate realization of deferred tax assets is dependent upon the generation of future taxable income during the periods in which those temporary differences become deductible. Management considers the scheduled reversal of deferred tax liabilities, projected future taxable income and tax planning strategies in making this assessment. At March 31, 2016 , the Company has loss carryforwards for U.S. federal income tax purposes of approximately $258,600 available to offset future taxable income and federal and state research and development tax credits of approximately $6,770 , prior to consideration of annual limitations that may be imposed under Section 382. These carryforwards will begin to expire in 2022 . Of these loss carryforwards, approximately $32,100 relates to benefits from stock compensation deductions that will be recorded as a component of paid-in capital when realized. The Company's direct foreign subsidiaries have foreign loss carryforwards of approximately $118,800 , most of which do not expire.

Shareholders' Equity

Shareholders' Equity	3 Months Ended
	Mar. 31, 2016
Equity [Abstract]
Shareholders' Equity	Shareholders' Equity Components of Accumulated Other Comprehensive Loss The components of accumulated other comprehensive loss are as follows: March 31, December 31, Unrealized gain (loss) on investments $ 68 $ (519 ) Foreign currency translation adjustments (11,503 ) (12,233 ) Total accumulated other comprehensive loss $ (11,435 ) $ (12,752 )

Share-Based Payments

Share-Based Payments	3 Months Ended
	Mar. 31, 2016
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Share-Based Payments	Share-Based Payments The Company records the fair value of stock options issued to employees and non-employees as of the grant date as stock-based compensation expense. Stock-based compensation expense for employees and non-employees is recognized over the requisite service period, which is typically the vesting period. Stock-based compensation costs included in the consolidated statements of operations are presented below: Three Months Ended 2016 2015 Cost of products $ 20 $ 34 Cost of services 68 98 Research and development 2,565 1,769 Selling, general and administrative 10,535 8,358 Total $ 13,188 $ 10,259 Intrexon Stock Option Plans In April 2008, Intrexon adopted the 2008 Equity Incentive Plan (the "2008 Plan") for employees and nonemployees pursuant to which Intrexon's Board of Directors may grant share based awards, including stock options, to officers, key employees and nonemployees. Upon the effectiveness of the 2013 Omnibus Incentive Plan (the "2013 Plan"), no new awards may be granted under the 2008 Plan. As of March 31, 2016 , there were 1,154,315 stock options outstanding under the 2008 Plan. Intrexon adopted the 2013 Plan for employees and nonemployees pursuant to which Intrexon's Board of Directors may grant share based awards, including stock options and shares of common stock, to employees, officers, consultants, advisors and nonemployee directors. The 2013 Plan became effective upon the closing of the Company's initial public offering in August 2013, and as of March 31, 2016 , there were 13,000,000 shares authorized for issuance under the 2013 Plan, of which 9,355,773 stock options were outstanding and 2,421,499 shares were available for grant. In April 2016, Intrexon's Board of Directors approved, subject to shareholder approval at Intrexon's annual meeting in June 2016, an increase of 3,000,000 shares of common stock to be reserved for issuance under the 2013 Plan. Stock option activity under Intrexon's award plans was as follows: Number of Shares Weighted Average Exercise Price Weighted Average Remaining Contractual Term (Years) Balances at December 31, 2015 11,043,528 $ 32.66 8.49 Granted 848,360 32.50 Exercised (537,307 ) (24.81 ) Forfeited (841,002 ) (35.31 ) Expired (3,491 ) (29.68 ) Balances at March 31, 2016 10,510,088 32.84 8.13 Exercisable at March 31, 2016 3,147,589 22.12 6.16 Vested and Expected to Vest at March 31, 2016(1) 8,906,749 31.86 7.95 (1) The number of stock options expected to vest takes into account an estimate of expected forfeitures. Total unrecognized compensation costs related to unvested awards at March 31, 2016 and December 31, 2015 were $103,746 and $113,655 , respectively, and are expected to be recognized over a weighted-average period of approximately three years . Intrexon currently uses authorized and unissued shares to satisfy share award exercises. In October 2015, the Compensation Committee and the independent members of Intrexon's Board of Directors approved a compensation arrangement whereby the Company's Chief Executive Officer ("CEO") would receive a monthly salary. Previously, the CEO did not receive compensation for his services as an employee of the Company other than through his participation in the Company's Annual Executive Incentive Plan which became effective January 1, 2015. Pursuant to the compensation agreement, the CEO receives a base salary of $200 per month payable in fully vested shares of Intrexon common stock with such shares subject to a three -year lock-up on resale. The monthly number of shares of common stock is calculated based on the closing price on the last trading day of each month and the shares are issued pursuant to the terms of a Restricted Stock Unit Agreement (the "RSU Agreement") which was executed between Intrexon and the CEO pursuant to the terms of the 2013 Plan. The RSU Agreement became effective in November 2015, has an initial term of 12 months , and is renewable annually at the discretion of Intrexon's Board of Directors. The fair value of the shares issued as compensation for services is included in selling, general and administrative expenses in the Company's consolidated statement of operations for the three months ended March 31, 2016 and totaled $ 471 . Other Plans As of March 31, 2016 , there were 5,607,000 options, which are exercisable into shares of AquaBounty common stock, outstanding under the AquaBounty 2006 Equity Incentive Plan ("AquaBounty Plan") at a weighted average exercise price of $0.26 per share of which 5,090,791 were exercisable. As of December 31, 2015 , there were 5,382,000 options outstanding under the AquaBounty Plan at a weighted average exercise price of $0.26 per share of which 4,320,333 were exercisable.

License Agreement

License Agreement	3 Months Ended
	Mar. 31, 2016
License Agreement [Abstract]
License Agreement	License Agreement In January 2015, the Company and ZIOPHARM jointly entered into a license agreement with the University of Texas System Board of Regents on behalf of the University of Texas MD Anderson Cancer Center ("MD Anderson") whereby the Company received an exclusive license to certain research and development technologies owned and licensed by MD Anderson, including technologies relating to novel chimeric antigen receptor (CAR) T-cell therapies, as well as co-licenses and non-exclusive licenses to certain other related technologies. ZIOPHARM received access to these technologies pursuant to the terms of the Company's ECC with ZIOPHARM. The Company issued 2,100,085 shares of its common stock valued at $59,579 to MD Anderson as consideration, which is included in research and development expenses in the accompanying consolidated statement of operations for the three months ended March 31, 2015 . Subject to certain exceptions, the license agreement expires on the last to occur of (i) the expiration of all patents licensed thereunder, or (ii) the twentieth anniversary of the date of the license agreement. In connection with the license agreement, the Company, ZIOPHARM, and MD Anderson entered into a research and development agreement which governs certain operational activities between the parties and pursuant to which ZIOPHARM will provide funding for certain research and development activities of MD Anderson for a period of three years , in an amount between $15,000 and $20,000 per year. The Company and ZIOPHARM reimburse MD Anderson for out of pocket expenses for maintaining patents covering the licensed technologies.

Commitments and Contingencies

Commitments and Contingencies	3 Months Ended
	Mar. 31, 2016
Commitments and Contingencies Disclosure [Abstract]
Commitments and Contingencies	Commitments and Contingencies Operating Leases The Company leases certain facilities and equipment under noncancelable operating leases. The equipment leases are renewable at the option of the Company. At March 31, 2016 , future minimum lease payments under operating leases having initial or remaining noncancelable lease terms in excess of one year are as follows: 2016 $ 2,459 2017 3,775 2018 2,312 2019 2,127 2020 2,179 2021 1,604 Total $ 14,456 Rent expense, including other facility expenses, was $2,032 and $2,134 for the three months ended March 31, 2016 and 2015 , respectively. The Company maintains subleases for certain of its facilities. Rental income under sublease agreements was $335 and $425 for the three months ended March 31, 2016 and 2015 , respectively. Future rental income is expected to be $210 for 2016 and $36 for 2017 . Contingencies In March 2012, Trans Ova was named as a defendant in a licensing and patent infringement suit brought by XY, LLC alleging that certain of Trans Ova's activities breach a licensing agreement and infringe on patents that XY, LLC allegedly owns. Trans Ova filed a number of counterclaims in the case. The matter proceeded to a jury trial in January 2016, and in February 2016, the jury determined that XY, LLC and Trans Ova had each breached the licensing agreement and that Trans Ova had infringed the intellectual property of XY, LLC. In April 2016, the court issued its order, entering a jury award of damages to Trans Ova in the amount of $528 and a jury award of damages to XY, LLC in the amount of $6,066 , each with prejudgment interest. The order provides for the continuation of Trans Ova's license to XY, LLC's technology, subject to an ongoing royalty for Trans Ova which is subject to a post-judgment motion and potential appeals therefrom. Since the inception of the license, Trans Ova has remitted payments to XY, LLC pursuant to the terms of the original license agreement and has recorded these payments in cost of services in the consolidated statements of operations for the respective periods. For the period from inception of the agreement through March 31, 2016, aggregate royalty and license payments were $3,420 , of which $3,009 had not yet been deposited by XY, LLC. For the three months ended March 31, 2016, the Company recorded litigation settlement expense of $4,228 , which is included in selling, general and administrative expenses on the accompanying consolidated statement of operations and represents the excess of the net damages awarded to XY, LLC, including prejudgment interest, over the liability previously recorded by Trans Ova for uncashed checks previously remitted to XY, LLC. The Company and Trans Ova believe they have compelling grounds to overturn the adverse rulings of the order through appellate actions and that, as a result, the amount of damages could be reduced or eliminated. No assurances can be given, however, that such matters will ultimately be ruled in Trans Ova's favor, and XY, LLC may also elect to appeal aspects of the ruling that were in Trans Ova's favor. Moreover, Trans Ova and the Company could elect to enter into a settlement agreement in order to avoid the further costs and uncertainties of litigation, to modify the license to XY, LLC's technologies, or to recover monetary damages related to Trans Ova's antitrust counterclaims. The Company may become subject to other claims and assessments from time to time in the ordinary course of business. Such matters are subject to many uncertainties and outcomes are not predictable with assurance. The Company accrues liabilities for such matters when it is probable that future expenditures will be made and such expenditures can be reasonably estimated. As of March 31, 2016 and December 31, 2015 , the Company does not believe that any such matters, individually or in the aggregate, will have a material adverse effect on the Company's business, financial condition, results of operations, or cash flows.

Related Party Transactions

Related Party Transactions	3 Months Ended
	Mar. 31, 2016
Related Party Transactions [Abstract]
Related Party Transactions	Related Party Transactions Third Security and Affiliates The Company's CEO and Chairman of the Board of Directors of the Company is also the manager of Third Security. In November 2015, Intrexon's Board of Directors approved the execution of a Services Agreement ("Services Agreement") with Third Security pursuant to which Third Security provides the Company with certain professional, legal, financial, administrative, and other support services necessary to support the Company and its CEO. As consideration for providing these services, Third Security is entitled to a fee of $800 per month to be paid in the form of fully vested shares of the Company's common stock. The number of shares of common stock is calculated based on the closing price of the Company's common stock on the 15th day of each month. The payments made by the Company under the Services Agreement constitute, in the aggregate, an award under the 2013 Plan and are subject to the terms of the 2013 Plan (Note 14 ). The Services Agreement has a term of one year , can be terminated by the Company at any time, and may be extended only by agreement of the parties, including approval of a majority of the independent members of Intrexon's Board of Directors. For the three months ended March 31, 2016 , the Company issued 79,870 shares with a value of $2,267 to Third Security as payment for services pursuant to the Services Agreement. In addition to the foregoing Services Agreement, the Company reimburses Third Security for certain out-of-pocket expenses incurred on the Company's behalf and the total expenses incurred by the Company under this arrangement was $46 and $41 for the three months ended March 31, 2016 and 2015 , respectively. See also Note 14 regarding compensation arrangements between the Company and its CEO. Transactions with ECC Parties In addition to entities controlled by Third Security, any entity in which the Company holds equity securities, including securities received as upfront or milestone consideration, and which also are party to a collaboration with the Company are considered to be related parties. In conjunction with the ECC with Oragenics, the Company is entitled to, at its election, purchase up to 30% of securities offerings that may be conducted by Oragenics in the future, subject to certain conditions and limitations. In connection with the Company's third ECC with Oragenics ("Oragenics ECC 3") in June 2015, the Company agreed to purchase additional common stock in a qualified financing, as defined in the agreement, during the sixteen months following the effective date of the Oragenics ECC 3 in an amount up to the lesser of (i) the amount that is the proportion of such financing equal to the Company's pro rata equity holdings in Oragenics as of the effective date and (ii) $10,000 , subject to certain conditions. The Company recognized $19,999 and $12,796 of collaboration revenues from related parties in the three months ended March 31, 2016 and 2015 , respectively. Other Related Parties In June 2015, the Company entered into an agreement with Harvest, an investment fund sponsored by Harvest Capital Strategies, LLC, and a related party based on ownership in the fund by affiliates of Third Security. Harvest was established to invest in life science research and development opportunities that the Company offers to Harvest. These will be investment proposals that are suitable for pursuit by a start-up venture, characterized by the agreement as "start-up opportunities." For such start-up opportunities, the Company will provide Harvest with exclusive rights of first-look and first negotiation. For any opportunities it decides to pursue, Harvest would establish new collaboration entities which would enter into an ECC with the Company in a designated field. The terms of such ECCs would be negotiated between the Company and Harvest. In addition, the agreement provides the Company the right to present to Harvest the opportunity to invest in other ventures, including investment opportunities with respect to the Company's existing collaborations. Any such opportunities would be presented at the Company's discretion on a non-exclusive basis. The agreement with Harvest does not limit the Company's ability to execute other collaborations and joint ventures with third parties. As consideration for providing exclusive rights of first-look and first negotiation for start-up opportunities, the Company receives a portion of the management fee collected by the fund sponsor of Harvest. These fees are included in other income in the accompanying consolidated statements of operations and totaled $645 for the three months ended March 31, 2016 .

Net Income (Loss) per Share

Net Income (Loss) per Share	3 Months Ended
	Mar. 31, 2016
Earnings Per Share [Abstract]
Net Income (Loss) per Share	Net Income (Loss) per Share The following table presents the computation of basic and diluted net income (loss) per share for the three months ended March 31, 2016 and 2015 : Three Months Ended 2016 2015 Historical net income (loss) per share: Numerator: Net income (loss) attributable to Intrexon $ (64,429 ) $ 27,097 Denominator: Weighted average shares outstanding, basic 116,861,151 106,103,848 Weighted average effect of dilutive stock options and warrants — 2,037,886 Weighted average shares outstanding, diluted 116,861,151 108,141,734 Net income (loss) attributable to Intrexon per share, basic $ (0.55 ) $ 0.26 Net income (loss) attributable to Intrexon per share, diluted $ (0.55 ) $ 0.25 The following potentially dilutive securities as of March 31, 2016 and 2015 , have been excluded from the above computations of diluted weighted average shares outstanding for the three months then ended, as they would have been anti-dilutive: March 31, 2016 2015 Options 10,510,088 4,719,991 Warrants 117,702 — Total 10,627,790 4,719,991

Subsequent Events

Subsequent Events	3 Months Ended
	Mar. 31, 2016
Subsequent Events [Abstract]
Subsequent Events	Subsequent Events In May 2016, two purported shareholder class action lawsuits, captioned Hoffman v. Intrexon Corporation et al. and Gibrall v. Intrexon Corporation et al. , were filed in the U.S. District Court for the Northern District of California on behalf of purchasers of the Company's common stock between May 12, 2015 and April 20, 2016 (the "Class Period"). The complaints name as defendants the Company and certain current Company officers (the "Defendants"). The complaints allege, among other things, that, in violation of the federal securities laws, the Defendants made materially false and/or misleading statements in its periodic reports on Forms 10-K and 10-Q filed during the Class Period with respect to the Company's business, operations and prospects. The basis for the plaintiffs' claims derives from the April 21, 2016 report published on the Seeking Alpha financial blog. The plaintiffs seek compensatory damages, interest and an award of reasonable attorneys' fees and costs. The Company believes that these putative class action lawsuits are without merit and intends to defend the lawsuits vigorously; however, there can be no assurance regarding the ultimate outcome of these lawsuits.

Summary of Significant Accoun27

Summary of Significant Accounting Policies (Policies)	3 Months Ended
	Mar. 31, 2016
Accounting Policies [Abstract]
Basis of Presentation	Basis of Presentation The accompanying interim consolidated financial statements are unaudited and have been prepared in accordance with accounting principles generally accepted in the United States of America ("U.S. GAAP"). Certain information and footnote disclosures normally included in the Company's annual financial statements have been condensed or omitted. These interim consolidated financial statements, in the opinion of management, reflect all normal recurring adjustments necessary for fair statement of the Company's financial position as of March 31, 2016 and results of operations and cash flows for the interim periods ended March 31, 2016 and 2015 . These interim financial results are not necessarily indicative of the results to be expected for the year ending December 31, 2016 , or for any other future annual or interim period. The accompanying interim unaudited consolidated financial statements should be read in conjunction with the audited consolidated financial statements and related notes thereto included in the Company's Annual Report on Form 10-K for the year ended December 31, 2015 .
Consolidation	The accompanying consolidated financial statements reflect the operations of the Company and its subsidiaries. All intercompany accounts and transactions have been eliminated.
Equity Method Investments	Equity Method Investments The Company accounts for its investments in each of its six strategic joint ventures and for its investments in Thrive Agrobiotics, Inc. ("Thrive Agrobiotics"), Exotech Bio, Inc. ("Exotech Bio"), and Relieve Genetics, Inc. ("Relieve Genetics") using the equity method of accounting since the Company has the ability to exercise significant influence, but not control, over the operating activities of these entities. The Company's investments in these entities are included in investments in affiliates in the accompanying consolidated balance sheets.
Net Income (Loss) per Share	Net Income (Loss) per Share For the three months ended March 31, 2016 , basic net loss per share is calculated by dividing net loss attributable to common shareholders by the weighted average shares outstanding during the period, without consideration of common stock equivalents. Diluted net loss per share is calculated by adjusting weighted average shares outstanding for the dilutive effect of common stock equivalents outstanding for the period, using the treasury-stock method. For purposes of the diluted net loss per share calculation, stock options and warrants are considered to be common stock equivalents but are excluded from the calculation of diluted net loss per share because their effect would be anti-dilutive and, therefore, basic and diluted net loss per share were the same for the three months ended March 31, 2016 . For the three months ended March 31, 2015 , basic net income per share is calculated by dividing net income attributable to common shareholders by the weighted average shares outstanding during the period, without consideration of common stock equivalents. Diluted net income per share is calculated by adjusting weighted average shares outstanding for the dilutive effect of common stock equivalents outstanding for the period, using the treasury-stock method. For the purposes of the diluted net income per share calculation, stock options and warrants are considered to be common stock equivalents.
Segment Information	Segment Information The Company has determined that it operates in one segment. The Company applies its technologies to create products and services which may be either sold directly to customers or developed through collaboration with third parties.
Use of Estimates	Use of Estimates The preparation of financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, the disclosure of contingent assets and liabilities at the date of the financial statements, and the reported amounts of revenues and expenses during the reporting periods. Actual results could differ from those estimates.
Recently Issued Accounting Pronouncements	Recently Issued Accounting Pronouncements In March 2016, the Financial Accounting Standards Board ("FASB") issued Accounting Standards Update ("ASU") 2016-09, Stock Compensation (Topic 718) - Improvements to Employee Share-Based Payment Accounting ("ASU 2016-09"). The provisions of ASU 2016-09 simplify various aspects of the accounting for employee share-based payment transactions, including the income tax consequences, classification of awards as either equity or liabilities, and classification on the statement of cash flows. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2016, with early adoption permitted, and is effective for the Company for the year ending December 31, 2017. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. In March 2016, the FASB issued ASU 2016-07, Investments-Equity Method and Joint Ventures (Topic 323) - Simplifying the Transition to the Equity Method of Accounting ("ASU 2016-07"). The provisions of ASU 2016-07 eliminate the requirement that when an investment qualifies for use of the equity method as a result of an increase in the level of ownership interest or degree of influence, an adjustment must be made to the investment, results of operations, and retained earnings retroactively on a step-by-step basis as if the equity method had been in effect during all previous periods that the investment had been held. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2016, with early adoption permitted, and is effective for the Company for the year ending December 31, 2017. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. In February 2016, the FASB issued ASU 2016-02, Leases (Topic 842) ("ASU 2016-02"). The provisions of ASU 2016-02 set out the principles for the recognition, measurement, presentation and disclosure of leases for both parties to a contract (i.e. lessees and lessors). The new standard requires lessees to apply a dual approach, classifying leases as either finance or operating leases based on the principle of whether or not the lease is effectively a financed purchase by the lessee. This classification will determine whether lease expense is recognized based on an effective interest method or on a straight line basis over the term of the lease, respectively. A lessee is also required to record a right-of-use asset and a lease liability for all leases with a term of greater than 12 months regardless of their classification. Leases with a term of 12 months or less will be accounted for in a similar manner as under existing guidance for operating leases today. ASU 2016-02 supersedes the previous lease standard, Topic 840 Leases . The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2018, and is effective for the Company for the year ending December 31, 2019. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. In January 2016, the FASB issued ASU 2016-01, Financial Instruments - Overall (Subtopic 825-10) - Recognition and Measurement of Financial Assets and Financial Liabilities ("ASU 2016-01"). The provisions of ASU 2016-01 make targeted improvements to enhance the reporting model for financial instruments to provide users of financial statements with more decision-useful information, including certain aspects of recognition, measurement, presentation, and disclosure of financial instruments. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2017, and is effective for the Company for the year ending December 31, 2018. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. In November 2015, the FASB issued ASU 2015-17, Income Taxes (Topic 740) - Balance Sheet Classification of Deferred Taxes ("ASU 2015-17"). The provisions of ASU 2015-17 simplify the presentation of deferred income taxes by requiring an entity to classify deferred tax liabilities and assets as noncurrent on a classified balance sheet. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2016, with early adoption permitted, and is effective for the Company for the year ending December 31, 2017. The Company elected to early adopt this guidance during the first quarter of 2016 and applied it prospectively, and there was no significant impact on the Company's consolidated financial statements. In July 2015, the FASB issued ASU 2015-11, Inventory (Topic 330) - Simplifying the Measurement of Inventory ("ASU 2015-11"). The provisions of ASU 2015-11 provide guidance for simplifying the calculation for subsequent measurement of inventory measured using the first-in-first-out or average cost methods. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2016, and is effective for the Company for the year ending December 31, 2017. The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements. In May 2014, the FASB issued ASU 2014-09, Revenue from Contracts with Customers ("ASU 2014-09"). The FASB issued ASU 2014-09 to clarify the principles for recognizing revenue and to develop a common revenue standard for U.S. GAAP. The standard outlines a single comprehensive model for entities to use in accounting for revenue arising from contracts with customers and supersedes the most current revenue recognition guidance. This guidance was originally effective for annual periods and interim periods within those annual periods beginning after December 15, 2016 and early adoption was not permitted. In August 2015, the FASB issued ASU 2015-14, Revenue from Contracts with Customers (Topic 606) - Deferral of the Effective Date ("ASU 2015-14"), which deferred the effective date of the guidance in ASU 2014-09 by one year to December 15, 2017 for interim and annual reporting periods beginning after that date and permitted early adoption of the standard, but not before the original effective date of December 15, 2016, and is effective for the Company for the year ending December 31, 2018. In March and April 2016, the FASB clarified the implementation guidance on principal versus agent, identifying performance obligations, and licensing by issuing ASU 2016-08, Revenue from Contracts with Customers (Topic 606) - Principal versus Agent Considerations ("ASU 2016-08") and ASU 2016-10, Revenue from Contracts with Customers (Topic 606) - Identifying Performance Obligations and Licensing ("ASU 2016-10"). The Company is currently evaluating the impact that the implementation of this standard will have on the Company's consolidated financial statements.
Reclassifications	Reclassifications Certain insignificant reclassifications have been made to the prior interim period consolidated financial statements to conform to the current interim period presentation.

Summary of Significant Accoun28

Summary of Significant Accounting Policies (Tables)	3 Months Ended
	Mar. 31, 2016
Accounting Policies [Abstract]
Summarized Unaudited Financial Information for the Equity Method Investments	Summarized unaudited financial data as of March 31, 2016 and December 31, 2015 and for the three months ended March 31, 2016 and 2015 , for the Company's equity method investments are shown in the following tables. Summarized unaudited financial data for ZIOPHARM Oncology, Inc. ("ZIOPHARM") has been included for the three months ended March 31, 2015 as the Company determined it had significant influence over ZIOPHARM until the Company distributed all of its equity securities held in ZIOPHARM to its shareholders in June 2015. March 31, December 31, Current assets $ 56,800 $ 28,123 Non-current assets 10,672 1,539 Total assets 67,472 29,662 Current liabilities 7,592 6,274 Net assets $ 59,880 $ 23,388 Three Months Ended 2016 2015 Revenues $ 282 $ 636 Operating expenses 17,660 84,069 Operating loss (17,378 ) (83,433 ) Other 3 (1 ) Net loss $ (17,375 ) $ (83,434 )

Mergers and Acquisitions (Table

Mergers and Acquisitions (Tables)	3 Months Ended
	Mar. 31, 2016
Oxitec Limited
Business Acquisition [Line Items]
Fair Value of Consideration Transferred	The fair value of the total consideration transferred was $146,394 . The acquisition date fair value of the Stock Consideration and Cash Consideration is presented below: Cash $ 90,199 Common shares 56,195 $ 146,394
Fair Value of Assets Acquired and Liabilities Assumed	The estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown below: Cash $ 3,780 Trade receivables 125 Other receivables 7,395 Prepaid expenses and other 121 Property, plant, and equipment 1,198 Intangible assets 96,854 Total assets acquired 109,473 Accounts payable 1,187 Accrued compensation and benefits 246 Other accrued liabilities 210 Deferred revenue 120 Deferred tax liabilities 12,584 Total liabilities assumed 14,347 Net assets acquired 95,126 Goodwill 51,268 Total consideration $ 146,394
Okanagan Specialty Fruits Inc
Business Acquisition [Line Items]
Fair Value of Consideration Transferred	The fair value of the total consideration transferred was $40,933 . The acquisition date fair value of each class of consideration transferred is presented below: Cash $ 10,000 Common shares 30,933 $ 40,933
Fair Value of Assets Acquired and Liabilities Assumed	The estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown below: Cash $ 58 Trade receivables 16 Other receivables 49 Property, plant, and equipment 32 Intangible assets 36,500 Total assets acquired 36,655 Accounts payable 181 Deferred revenue 181 Deferred tax liabilities 8,847 Total liabilities assumed 9,209 Net assets acquired 27,446 Goodwill 13,487 Total consideration $ 40,933
ActoGeniX NV
Business Acquisition [Line Items]
Fair Value of Consideration Transferred	The fair value of the total consideration transferred was $72,474 . The acquisition date fair value of each class of consideration transferred is presented below: Cash $ 32,739 Common shares 39,735 $ 72,474
Fair Value of Assets Acquired and Liabilities Assumed	The estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown below: Cash $ 3,180 Other receivables 305 Prepaid expenses and other 31 Property, plant and equipment 209 Intangible assets 68,100 Other non-current assets 23 Total assets acquired 71,848 Accounts payable 230 Accrued compensation and benefits 196 Other accrued liabilities 253 Deferred revenue 732 Deferred tax liabilities 612 Total liabilities assumed 2,023 Net assets acquired 69,825 Goodwill 2,649 Total consideration $ 72,474
2015 Business Acquisitions
Business Acquisition [Line Items]
Pro forma Financial Information	The following unaudited condensed pro forma financial information for the three months ended March 31, 2015 is presented as if the acquisitions had been consummated on January 1, 2014: Three Months Ended March 31, 2015 Pro Forma Revenues $ 34,228 Income before income taxes 20,127 Net income 20,459 Net loss attributable to the noncontrolling interests 1,293 Net income attributable to Intrexon 21,752

Collaboration and Licensing R30

Collaboration and Licensing Revenue (Tables)	3 Months Ended
	Mar. 31, 2016
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Summarized Collaboration and Licensing Revenues	The following tables summarize the amounts recorded as revenue in the consolidated statements of operations for each significant collaboration or licensing agreement for the three months ended March 31, 2016 and 2015 . Three Months Ended March 31, 2016 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 922 $ 6,059 $ 6,981 Oragenics, Inc. 263 543 806 Fibrocell Science, Inc. 605 1,252 1,857 Genopaver, LLC 69 1,509 1,578 S & I Ophthalmic, LLC — 1,186 1,186 OvaXon, LLC — 694 694 Intrexon Energy Partners, LLC 625 3,363 3,988 Persea Bio, LLC 125 199 324 Ares Trading S.A. 1,597 808 2,405 Thrive Agrobiotics, Inc. 46 388 434 Intrexon Energy Partners II, LLC 500 50 550 Other 1,020 2,250 3,270 Total $ 5,772 $ 18,301 $ 24,073 Three Months Ended March 31, 2015 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 644 $ 3,157 $ 3,801 Oragenics, Inc. 262 8 270 Fibrocell Science, Inc. 448 1,713 2,161 Genopaver, LLC 69 600 669 S & I Ophthalmic, LLC — 755 755 OvaXon, LLC — 644 644 Intrexon Energy Partners, LLC 625 2,185 2,810 Persea Bio, LLC 125 115 240 Other 858 2,575 3,433 Total $ 3,031 $ 11,752 $ 14,783
Summary of Deferred Revenue	Deferred revenue consists of the following: March 31, December 31, Upfront and milestone payments $ 194,849 $ 181,331 Prepaid research and development services 9,439 10,938 Prepaid product and service revenues 5,201 4,759 Other 749 701 Total $ 210,238 $ 197,729 Current portion of deferred revenue $ 37,695 $ 35,366 Long-term portion of deferred revenue 172,543 162,363 Total $ 210,238 $ 197,729
Summary of Deferred Revenue by Collaborator	The following table summarizes the remaining balance of deferred revenue associated with upfront and milestone payments for each significant collaboration and licensing agreement: March 31, December 31, ZIOPHARM Oncology, Inc. $ 29,416 $ 30,338 Oragenics, Inc. 8,550 8,813 Fibrocell Science, Inc. 20,840 21,445 Genopaver, LLC 2,181 2,250 Intrexon Energy Partners, LLC 20,000 20,625 Persea Bio, LLC 4,375 4,500 Ares Trading S.A. 51,970 53,567 Thrive Agrobiotics, Inc. 1,575 1,621 Intrexon Energy Partners II, LLC 17,333 17,833 Exotech Bio, Inc. 5,000 — Relieve Genetics, Inc. 4,333 — Intrexon T1D Partners, LLC 10,000 — Other 19,276 20,339 Total $ 194,849 $ 181,331

Short-term and Long-term Inve31

Short-term and Long-term Investments (Tables)	3 Months Ended
	Mar. 31, 2016
Investments, Debt and Equity Securities [Abstract]
Summary of Amortized Cost, Gross Unrealized Gains and Losses, and Fair Value of Investments	The following table summarizes the amortized cost, gross unrealized gains and losses and fair value of available-for-sale investments as of March 31, 2016 : Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Aggregate Fair Value U.S. government debt securities $ 189,903 $ 87 $ (19 ) $ 189,971 Certificates of deposit 272 — — 272 Total $ 190,175 $ 87 $ (19 ) $ 190,243 The following table summarizes the amortized cost, gross unrealized gains and losses and fair value of available-for-sale investments as of December 31, 2015 : Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Aggregate Fair Value U.S. government debt securities $ 208,223 $ 21 $ (540 ) $ 207,704 Certificates of deposit 271 — — 271 Total $ 208,494 $ 21 $ (540 ) $ 207,975
Summary of Estimated Fair Value of Available-for-Sale Investments Classified by Contractual Maturities	The estimated fair value of available-for-sale investments classified by their contractual maturities as of March 31, 2016 was: Due within one year $ 114,659 After one year through two years 75,584 Total $ 190,243

Fair Value Measurements (Tables

Fair Value Measurements (Tables)	3 Months Ended
	Mar. 31, 2016
Fair Value Disclosures [Abstract]
Summary of Placement in the Fair Value Hierarchy of Financial Assets that are Measured at Fair Value on a Recurring Basis	The following table presents the placement in the fair value hierarchy of financial assets that are measured at fair value on a recurring basis, including the items for which the fair value option has been elected, at March 31, 2016 : Quoted Prices in Active Markets (Level 1) Significant Other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) March 31, Assets U.S. government debt securities $ — $ 189,971 $ — $ 189,971 Equity securities 50,189 11,133 — 61,322 Other — 399 — 399 Total $ 50,189 $ 201,503 $ — $ 251,692 The following table presents the placement in the fair value hierarchy of financial assets that are measured at fair value on a recurring basis, including the items for which the fair value option has been elected, at December 31, 2015 : Quoted Prices in Active Markets Significant Other Observable Inputs Significant Unobservable Inputs December 31, Assets U.S. government debt securities $ — $ 207,704 $ — $ 207,704 Equity securities 65,850 17,803 — 83,653 Other — 405 — 405 Total $ 65,850 $ 225,912 $ — $ 291,762

Inventory (Tables)

Inventory (Tables)	3 Months Ended
	Mar. 31, 2016
Inventory Disclosure [Abstract]
Schedule of Inventory	Inventory consists of the following: March 31, December 31, Supplies, semen and embryos $ 1,287 $ 1,402 Work in process 6,112 6,290 Livestock 16,342 16,907 Feed 1,337 1,964 Total inventory $ 25,078 $ 26,563

Property, Plant and Equipment34

Property, Plant and Equipment, Net (Tables)	3 Months Ended
	Mar. 31, 2016
Property, Plant and Equipment [Abstract]
Schedule of Property, Plant and Equipment	Property, plant and equipment consist of the following: March 31, December 31, Land and land improvements $ 9,352 $ 9,119 Buildings and building improvements 7,520 7,520 Furniture and fixtures 1,852 1,283 Equipment 37,372 36,016 Leasehold improvements 7,076 6,888 Computer hardware and software 6,199 5,960 Construction and other assets in progress 2,836 2,193 72,207 68,979 Less: Accumulated depreciation and amortization (27,534 ) (26,240 ) Property, plant and equipment, net $ 44,673 $ 42,739

Goodwill and Intangible Asset35

Goodwill and Intangible Assets, Net (Tables)	3 Months Ended
	Mar. 31, 2016
Goodwill and Intangible Assets Disclosure [Abstract]
Schedule of Changes in Carrying Amount of Goodwill	The changes in the carrying amount of goodwill for the three months ended March 31, 2016 are as follows: Balance at December 31, 2015 $ 165,169 Foreign currency translation adjustments (594 ) Balance at March 31, 2016 $ 164,575
Schedule of Intangible Assets	Intangible assets consist of the following at March 31, 2016 : Weighted Average Useful Life (Years) Gross Carrying Amount Accumulated Amortization Net Patents, related technologies and know-how 15.3 $ 171,658 $ (20,759 ) $ 150,899 Customer relationships 6.5 10,700 (3,222 ) 7,478 Trademarks 9.3 6,800 (1,211 ) 5,589 Covenant not to compete 2.0 398 (215 ) 183 In-process research and development 91,311 — 91,311 Total $ 280,867 $ (25,407 ) $ 255,460 Intangible assets consist of the following at December 31, 2015 : Gross Carrying Amount Accumulated Amortization Net Patents, related technologies and know-how $ 157,411 $ (17,775 ) $ 139,636 Customer relationships 10,700 (2,739 ) 7,961 Trademarks 6,800 (1,018 ) 5,782 Covenant not to compete 384 (160 ) 224 In-process research and development 93,932 — 93,932 Total $ 269,227 $ (21,692 ) $ 247,535

Lines of Credit and Long Term36

Lines of Credit and Long Term Debt (Tables)	3 Months Ended
	Mar. 31, 2016
Debt Disclosure [Abstract]
Schedule of Long Term Debt Instruments	Long term debt consists of the following: March 31, December 31, Notes payable $ 6,363 $ 6,477 Royalty-based financing 1,945 1,807 Other 198 244 Long term debt 8,506 8,528 Less current portion 893 930 Long term debt, less current portion $ 7,613 $ 7,598
Schedule of Future Maturities of Long Term Debt	Future maturities of long term debt are as follows: 2016 $ 798 2017 384 2018 527 2019 342 2020 311 2021 311 Thereafter 3,888 Total $ 6,561

Shareholders' Equity (Tables)

Shareholders' Equity (Tables)	3 Months Ended
	Mar. 31, 2016
Equity [Abstract]
Components of Accumulated Other Comprehensive Loss	The components of accumulated other comprehensive loss are as follows: March 31, December 31, Unrealized gain (loss) on investments $ 68 $ (519 ) Foreign currency translation adjustments (11,503 ) (12,233 ) Total accumulated other comprehensive loss $ (11,435 ) $ (12,752 )

Share-Based Payments (Tables)

Share-Based Payments (Tables)	3 Months Ended
	Mar. 31, 2016
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Schedule of Stock-Based Compensation Costs	Stock-based compensation costs included in the consolidated statements of operations are presented below: Three Months Ended 2016 2015 Cost of products $ 20 $ 34 Cost of services 68 98 Research and development 2,565 1,769 Selling, general and administrative 10,535 8,358 Total $ 13,188 $ 10,259
Schedule of Stock Option Activity	Stock option activity under Intrexon's award plans was as follows: Number of Shares Weighted Average Exercise Price Weighted Average Remaining Contractual Term (Years) Balances at December 31, 2015 11,043,528 $ 32.66 8.49 Granted 848,360 32.50 Exercised (537,307 ) (24.81 ) Forfeited (841,002 ) (35.31 ) Expired (3,491 ) (29.68 ) Balances at March 31, 2016 10,510,088 32.84 8.13 Exercisable at March 31, 2016 3,147,589 22.12 6.16 Vested and Expected to Vest at March 31, 2016(1) 8,906,749 31.86 7.95 (1) The number of stock options expected to vest takes into account an estimate of expected forfeitures.

Commitments and Contingencies (

Commitments and Contingencies (Tables)	3 Months Ended
	Mar. 31, 2016
Commitments and Contingencies Disclosure [Abstract]
Future Minimum Lease Payments Under Noncancelable Operating Leases	At March 31, 2016 , future minimum lease payments under operating leases having initial or remaining noncancelable lease terms in excess of one year are as follows: 2016 $ 2,459 2017 3,775 2018 2,312 2019 2,127 2020 2,179 2021 1,604 Total $ 14,456

Net Income (Loss) per Share (Ta

Net Income (Loss) per Share (Tables)	3 Months Ended
	Mar. 31, 2016
Earnings Per Share [Abstract]
Computation of Basic and Diluted Net Income (Loss) per Share	The following table presents the computation of basic and diluted net income (loss) per share for the three months ended March 31, 2016 and 2015 : Three Months Ended 2016 2015 Historical net income (loss) per share: Numerator: Net income (loss) attributable to Intrexon $ (64,429 ) $ 27,097 Denominator: Weighted average shares outstanding, basic 116,861,151 106,103,848 Weighted average effect of dilutive stock options and warrants — 2,037,886 Weighted average shares outstanding, diluted 116,861,151 108,141,734 Net income (loss) attributable to Intrexon per share, basic $ (0.55 ) $ 0.26 Net income (loss) attributable to Intrexon per share, diluted $ (0.55 ) $ 0.25
Schedule of Antidilutive Securities Excluded from Computation of Net Income (Loss) per Share	The following potentially dilutive securities as of March 31, 2016 and 2015 , have been excluded from the above computations of diluted weighted average shares outstanding for the three months then ended, as they would have been anti-dilutive: March 31, 2016 2015 Options 10,510,088 4,719,991 Warrants 117,702 — Total 10,627,790 4,719,991

Organization (Details)

Organization (Details)	Mar. 31, 2016
AquaBounty Technologies, Inc.
Organization, Consolidation and Presentation of Financial Statements Disclosure [Line Items]
Parent ownership interest	63.00%
Biological & Popular Culture, Inc.
Organization, Consolidation and Presentation of Financial Statements Disclosure [Line Items]
Parent ownership interest	51.00%

Summary of Significant Accoun42

Summary of Significant Accounting Policies - Additional Information (Details) $ in Thousands	3 Months Ended
	Mar. 31, 2016USD ($)segmentjoint_venture	Mar. 31, 2015USD ($)	Dec. 31, 2015USD ($)
Organization And Significant Accounting Policies [Line Items]
Number of strategic joint ventures | joint_venture	6
Fair value of financial assets measured at fair value on a recurring basis	$ 251,692		$ 291,762
Unrealized appreciation (depreciation) in fair value of equity securities	(22,331)	$ 115,454
Maximum risk of loss related to the identified VIEs	$ 15,600		3,598
Number of segments | segment	1
Property, plant and equipment, net	$ 44,673		42,739
Revenues	43,438	33,849
Foreign Countries
Organization And Significant Accounting Policies [Line Items]
Property, plant and equipment, net	4,817		3,877
Revenues	2,496	1,338
Equity securities
Organization And Significant Accounting Policies [Line Items]
Fair value of financial assets measured at fair value on a recurring basis	$ 61,322		$ 83,653
Oragenics, Inc.
Organization And Significant Accounting Policies [Line Items]
Company's ownership percentage	30.50%		30.70%
Oragenics, Inc. | Equity securities
Organization And Significant Accounting Policies [Line Items]
Fair value of financial assets measured at fair value on a recurring basis	$ 10,256		$ 16,601
Unrealized appreciation (depreciation) in fair value of equity securities	$ (6,345)	$ 936

Summary of Significant Accoun43

Summary of Significant Accounting Policies - Summarized Unaudited Financial Information for the Equity Method Investments (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2016	Mar. 31, 2015	Dec. 31, 2015
Schedule of Equity Method Investments [Line Items]
Operating expenses	$ 83,971	$ 120,972
Operating loss	(40,533)	(87,123)
Other	(21,425)	115,678
Equity Method Investments
Schedule of Equity Method Investments [Line Items]
Current assets	56,800		$ 28,123
Non-current assets	10,672		1,539
Total assets	67,472		29,662
Current liabilities	7,592		6,274
Net assets	59,880		$ 23,388
Revenues	282	636
Operating expenses	17,660	84,069
Operating loss	(17,378)	(83,433)
Other	3	(1)
Net loss	$ (17,375)	$ (83,434)

Mergers and Acquisitions - Oxit

Mergers and Acquisitions - Oxitec - Additional Information (Details) - Oxitec Limited - USD ($) $ in Thousands	1 Months Ended	3 Months Ended
	Sep. 30, 2015	Mar. 31, 2016
Business Acquisition [Line Items]
Percentage of outstanding common stock acquired	100.00%
Consideration transferred, shares issued or issuable	1,359,343
Cash	$ 90,199
Consideration transferred, cash and working capital adjustments	$ 9,449
Equity interest issued or issuable, number of shares withheld as escrow	480,422
Cash consideration withheld as escrow	$ 1,991
Consideration withheld as escrow, transfer period after closing	18 months
Consideration transferred	$ 146,394
Acquisition related costs		$ 1,675

Mergers and Acquisitions - Ox45

Mergers and Acquisitions - Oxitec - Fair Value of Consideration Transferred (Details) - Oxitec Limited $ in Thousands	1 Months Ended
	Sep. 30, 2015USD ($)
Business Acquisition [Line Items]
Cash	$ 90,199
Common shares	56,195
Total consideration transferred	$ 146,394

Mergers and Acquisitions - Ox46

Mergers and Acquisitions - Oxitec - Fair Value of Assets Acquired and Liabilities Assumed (Details) - USD ($) $ in Thousands	Mar. 31, 2016	Dec. 31, 2015	Sep. 30, 2015
Business Acquisition [Line Items]
Goodwill	$ 164,575	$ 165,169
Oxitec Limited
Business Acquisition [Line Items]
Cash			$ 3,780
Trade receivables			125
Other receivables			7,395
Prepaid expenses and other			121
Property, plant and equipment			1,198
Intangible assets			96,854
Total assets acquired			109,473
Accounts payable			1,187
Accrued compensation and benefits			246
Other accrued liabilities			210
Deferred revenue			120
Deferred tax liabilities			12,584
Total liabilities assumed			14,347
Net assets acquired			95,126
Goodwill			51,268
Total consideration			$ 146,394

Mergers and Acquisitions - Okan

Mergers and Acquisitions - Okanagan - Additional Information (Details) - Okanagan Specialty Fruits Inc - USD ($) $ in Thousands	1 Months Ended	3 Months Ended
	Apr. 30, 2015	Mar. 31, 2016	Mar. 31, 2015
Business Acquisition [Line Items]
Percentage of outstanding common stock acquired	100.00%
Consideration transferred, shares issued or issuable	707,853
Cash	$ 10,000
Consideration transferred	$ 40,933
Expected useful life of intangible asset	14 years
Acquisition related costs		$ 341
Selling, general and administrative
Business Acquisition [Line Items]
Acquisition related costs			$ 163

Mergers and Acquisitions - Ok48

Mergers and Acquisitions - Okanagan - Fair Value of Consideration Transferred (Details) - Okanagan Specialty Fruits Inc $ in Thousands	1 Months Ended
	Apr. 30, 2015USD ($)
Business Acquisition [Line Items]
Cash	$ 10,000
Common shares	30,933
Total consideration transferred	$ 40,933

Mergers and Acquisitions - Ok49

Mergers and Acquisitions - Okanagan - Fair Value of Assets Acquired and Liabilities Assumed (Details) - USD ($) $ in Thousands	Mar. 31, 2016	Dec. 31, 2015	Apr. 30, 2015
Business Acquisition [Line Items]
Goodwill	$ 164,575	$ 165,169
Okanagan Specialty Fruits Inc
Business Acquisition [Line Items]
Cash			$ 58
Trade receivables			16
Other receivables			49
Property, plant and equipment			32
Intangible assets			36,500
Total assets acquired			36,655
Accounts payable			181
Deferred revenue			181
Deferred tax liabilities			8,847
Total liabilities assumed			9,209
Net assets acquired			27,446
Goodwill			13,487
Total consideration			$ 40,933

Mergers and Acquisitions - Acto

Mergers and Acquisitions - ActoGeniX - Additional Information (Details) - ActoGeniX NV - USD ($) $ in Thousands	1 Months Ended		3 Months Ended
	Aug. 31, 2015	Feb. 28, 2015	Mar. 31, 2016	Mar. 31, 2015
Business Acquisition [Line Items]
Percentage of outstanding common stock acquired		100.00%
Consideration transferred, shares issued or issuable		965,377
Cash		$ 32,739
Consideration transferred		$ 72,474
Expected useful life of intangible asset	18 years
Acquisition related costs			$ 418
Selling, general and administrative
Business Acquisition [Line Items]
Acquisition related costs				$ 409

Mergers and Acquisitions - Ac51

Mergers and Acquisitions - ActoGeniX - Fair Value of Consideration Transferred (Details) - ActoGeniX NV $ in Thousands	1 Months Ended
	Feb. 28, 2015USD ($)
Business Acquisition [Line Items]
Cash	$ 32,739
Common shares	39,735
Total consideration transferred	$ 72,474

Mergers and Acquisitions - Ac52

Mergers and Acquisitions - ActoGeniX - Fair Value of Assets Acquired and Liabilities Assumed (Details) - USD ($) $ in Thousands	Mar. 31, 2016	Dec. 31, 2015	Feb. 28, 2015
Business Acquisition [Line Items]
Goodwill	$ 164,575	$ 165,169
ActoGeniX NV
Business Acquisition [Line Items]
Cash			$ 3,180
Other receivables			305
Prepaid expenses and other			31
Property, plant and equipment			209
Intangible assets			68,100
Other non-current assets			23
Total assets acquired			71,848
Accounts payable			230
Accrued compensation and benefits			196
Other accrued liabilities			253
Deferred revenue			732
Deferred tax liabilities			612
Total liabilities assumed			2,023
Net assets acquired			69,825
Goodwill			2,649
Total consideration			$ 72,474

Mergers and Acquisitions - 2015

Mergers and Acquisitions - 2015 Acquisitions - Pro Forma Financial Information (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2016	Mar. 31, 2015
Business Acquisition, Pro Forma Information, Nonrecurring Adjustment [Line Items]
Income before income taxes	$ (67,601)	$ 26,599
Net income (loss)	(65,320)	25,804
Net loss attributable to the noncontrolling interests	$ 891	1,293
2015 Business Acquisitions | Pro Forma
Business Acquisition, Pro Forma Information, Nonrecurring Adjustment [Line Items]
Revenues		34,228
Income before income taxes		20,127
Net income (loss)		20,459
Net loss attributable to the noncontrolling interests		1,293
Net income attributable to Intrexon		$ 21,752

Investments in Joint Ventures -

Investments in Joint Ventures - Intrexon T1D Partners - Additional Information (Details) - Intrexon T1D Partners, LLC	1 Months Ended
	Mar. 31, 2016USD ($)board_seat
Schedule Of Investments In Joint Venture [Line Items]
Membership interest	50.00%
Maximum additional capital contribution committed	$ 5,000,000
Number of board members designated by the Company | board_seat	2
Number of board members not designated by the Company | board_seat	3
Investors
Schedule Of Investments In Joint Venture [Line Items]
Membership interest	50.00%
Capital contributions	$ 10,000,000
Maximum additional capital contribution committed	5,000,000
Upfront | Upfront and Milestone Payments
Schedule Of Investments In Joint Venture [Line Items]
Collaborative arrangement consideration received, value	$ 10,000,000

Investments in Joint Ventures55

Investments in Joint Ventures - EnviroFlight - Additional Information (Details) - USD ($)	1 Months Ended	3 Months Ended
	Feb. 29, 2016	Mar. 31, 2016	Mar. 31, 2015	Dec. 31, 2015
Schedule Of Investments In Joint Venture [Line Items]
Cash paid in asset acquisition		$ 7,244,000	$ 0
Shares issued in asset acquisition		4,401,000	0
Contingent consideration assumed in asset acquisition		3,660,000	$ 0
Investment		21,385,000		$ 9,977,000
Significant Unobservable Inputs (Level 3)
Schedule Of Investments In Joint Venture [Line Items]
Fair value of financial liabilities measured at fair value on a recurring basis		3,660,000
EnviroFlight, LLC
Schedule Of Investments In Joint Venture [Line Items]
Capital contributions	$ 3,000,000
Membership interest	50.00%
Maximum additional capital contribution committed	$ 5,000,000
Estimated fair value of investment	$ 5,425,000
EnviroFlight, LLC | Investments In Affiliates
Schedule Of Investments In Joint Venture [Line Items]
Investment		5,328,000
EnviroFlight, LLC | Investors
Schedule Of Investments In Joint Venture [Line Items]
Membership interest	50.00%
Maximum additional capital contribution committed	$ 5,000,000
EnviroFlight, LLC
Schedule Of Investments In Joint Venture [Line Items]
Cash paid in asset acquisition	$ 4,244,000
Shares issued in asset acquisition (in shares)	136,340
Shares issued in asset acquisition	$ 4,401,000
Contingent consideration assumed in asset acquisition	3,660,000
Contingent consideration payable in common stock, maximum	5,500,000
EnviroFlight, LLC | Significant Unobservable Inputs (Level 3)
Schedule Of Investments In Joint Venture [Line Items]
Fair value of financial liabilities measured at fair value on a recurring basis		$ 3,660,000
EnviroFlight, LLC | Patents, related technologies and know-how
Schedule Of Investments In Joint Venture [Line Items]
Estimated fair value of developed technology acquired	$ 9,880,000
Expected useful life of intangible asset	21 years

Investments in Joint Ventures56

Investments in Joint Ventures - Intrexon Energy Partners II - Additional Information (Details)	1 Months Ended
	Dec. 31, 2015USD ($)	Mar. 31, 2016USD ($)board_seat
Schedule Of Investments In Joint Venture [Line Items]
Investment	$ 9,977,000	$ 21,385,000
Intrexon Energy Partners II, LLC
Schedule Of Investments In Joint Venture [Line Items]
Membership interest	50.00%
Maximum additional capital contribution committed	$ 10,000,000
Number of board members designated by the Company | board_seat		1
Number of board members not designated by the Company | board_seat		4
Intrexon Energy Partners II, LLC | Investments In Affiliates
Schedule Of Investments In Joint Venture [Line Items]
Investment	$ 2,000,000	$ 1,974,000
Intrexon Energy Partners II, LLC | Investors
Schedule Of Investments In Joint Venture [Line Items]
Membership interest	50.00%
Capital contributions	$ 18,000,000
Maximum additional capital contribution committed	10,000,000
Intrexon Energy Partners II, LLC | All Investors
Schedule Of Investments In Joint Venture [Line Items]
Capital contributions	4,000,000
Intrexon Energy Partners II, LLC | Upfront and Milestone Payments | Upfront
Schedule Of Investments In Joint Venture [Line Items]
Collaborative arrangement consideration received, value	$ 18,000,000

Investments in Joint Ventures57

Investments in Joint Ventures - Intrexon Energy Partners - Additional Information (Details)	1 Months Ended
	Mar. 31, 2014USD ($)	Mar. 31, 2016USD ($)board_seat	Dec. 31, 2015USD ($)
Schedule Of Investments In Joint Venture [Line Items]
Investment		$ 21,385,000	$ 9,977,000
Intrexon Energy Partners, LLC
Schedule Of Investments In Joint Venture [Line Items]
Membership interest	50.00%
Maximum additional capital contribution committed	$ 25,000,000
Additional capital contributions committed, remaining commitment		$ 16,711,000
Number of board members designated by the Company | board_seat		2
Number of board members not designated by the Company | board_seat		3
Intrexon Energy Partners, LLC | Other Accrued Liabilities
Schedule Of Investments In Joint Venture [Line Items]
Investment		$ (984,000)	$ (1,270,000)
Intrexon Energy Partners, LLC | Investors
Schedule Of Investments In Joint Venture [Line Items]
Membership interest	50.00%
Capital contributions	$ 25,000,000
Maximum additional capital contribution committed	25,000,000
Intrexon Energy Partners, LLC | Upfront and Milestone Payments | Upfront
Schedule Of Investments In Joint Venture [Line Items]
Collaborative arrangement consideration received, value	$ 25,000,000

Investments in Joint Ventures58

Investments in Joint Ventures - OvaXon - Additional Information (Details)	1 Months Ended
	Jan. 31, 2014USD ($)	Mar. 31, 2016USD ($)board_seat	Dec. 31, 2015USD ($)
Schedule Of Investments In Joint Venture [Line Items]
Investment		$ 21,385,000	$ 9,977,000
OvaXon, LLC
Schedule Of Investments In Joint Venture [Line Items]
Capital contributions	$ 1,500,000
Membership interest	50.00%
Number of board members not designated by the Company | board_seat		2
Number of board members designated by the Company | board_seat		2
OvaXon, LLC | Investments In Affiliates
Schedule Of Investments In Joint Venture [Line Items]
Investment		$ 215,000
OvaXon, LLC | Other Accrued Liabilities
Schedule Of Investments In Joint Venture [Line Items]
Investment			$ (144,000)
OvaXon, LLC | Investors
Schedule Of Investments In Joint Venture [Line Items]
Capital contributions	$ 1,500,000
Membership interest	50.00%

Investments in Joint Ventures59

Investments in Joint Ventures - S & I Ophthalmic - Additional Information (Details)	1 Months Ended	30 Months Ended
	Oct. 31, 2013USD ($)	Mar. 31, 2016USD ($)board_seat	Dec. 31, 2015USD ($)
Schedule Of Investments In Joint Venture [Line Items]
Investment		$ 21,385,000	$ 9,977,000
S & I Ophthalmic, LLC
Schedule Of Investments In Joint Venture [Line Items]
Capital contributions	$ 5,000,000	$ 5,000,000
Membership interest	50.00%
Number of board members designated by the Company | board_seat		2
Number of board members not designated by the Company | board_seat		2
S & I Ophthalmic, LLC | Investments In Affiliates
Schedule Of Investments In Joint Venture [Line Items]
Investment		$ 5,785,000	$ 6,379,000
S & I Ophthalmic, LLC | Investors
Schedule Of Investments In Joint Venture [Line Items]
Capital contributions	$ 5,000,000	$ 5,000,000
Membership interest	50.00%

Collaboration and Licensing R60

Collaboration and Licensing Revenue - Summarized Collaboration and Licensing Revenues (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2016	Mar. 31, 2015
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	$ 24,073	$ 14,783
ZIOPHARM Oncology, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	6,981	3,801
Oragenics, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	806	270
Fibrocell Science, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,857	2,161
Genopaver, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,578	669
S & I Ophthalmic, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,186	755
OvaXon, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	694	644
Intrexon Energy Partners, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	3,988	2,810
Persea Bio, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	324	240
Ares Trading S.A.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	2,405
Thrive Agrobiotics, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	434
Intrexon Energy Partners II, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	550
Other
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	3,270	3,433
Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	5,772	3,031
Upfront and Milestone Payments | ZIOPHARM Oncology, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	922	644
Upfront and Milestone Payments | Oragenics, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	263	262
Upfront and Milestone Payments | Fibrocell Science, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	605	448
Upfront and Milestone Payments | Genopaver, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	69	69
Upfront and Milestone Payments | S & I Ophthalmic, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	0	0
Upfront and Milestone Payments | OvaXon, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	0	0
Upfront and Milestone Payments | Intrexon Energy Partners, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	625	625
Upfront and Milestone Payments | Persea Bio, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	125	125
Upfront and Milestone Payments | Ares Trading S.A.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,597
Upfront and Milestone Payments | Thrive Agrobiotics, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	46
Upfront and Milestone Payments | Intrexon Energy Partners II, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	500
Upfront and Milestone Payments | Other
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,020	858
Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	18,301	11,752
Research and Development Services | ZIOPHARM Oncology, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	6,059	3,157
Research and Development Services | Oragenics, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	543	8
Research and Development Services | Fibrocell Science, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,252	1,713
Research and Development Services | Genopaver, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,509	600
Research and Development Services | S & I Ophthalmic, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,186	755
Research and Development Services | OvaXon, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	694	644
Research and Development Services | Intrexon Energy Partners, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	3,363	2,185
Research and Development Services | Persea Bio, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	199	115
Research and Development Services | Ares Trading S.A.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	808
Research and Development Services | Thrive Agrobiotics, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	388
Research and Development Services | Intrexon Energy Partners II, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	50
Research and Development Services | Other
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	$ 2,250	$ 2,575

Collaboration and Licensing R61

Collaboration and Licensing Revenue - Additional Information (Details)	1 Months Ended
	Mar. 31, 2016USD ($)
Exotech Bio, Inc.
Collaboration and Licensing Agreements [Line Items]
Maximum milestone payments required upon successful achievement, per product	$ 52,500,000
Required notice period for voluntary termination of collaborative agreement	90 days
Exotech Bio, Inc. | Upfront | Upfront and Milestone Payments
Collaboration and Licensing Agreements [Line Items]
Collaborative arrangement consideration received, value	$ 5,000,000
Relieve Genetics, Inc.
Collaboration and Licensing Agreements [Line Items]
Maximum milestone payments required upon successful achievement, per product	$ 52,500,000
Required notice period for voluntary termination of collaborative agreement	90 days
Relieve Genetics, Inc. | Upfront | Upfront and Milestone Payments
Collaboration and Licensing Agreements [Line Items]
Collaborative arrangement consideration received, value	$ 4,333,000
Intrexon T1D Partners, LLC
Collaboration and Licensing Agreements [Line Items]
Required notice period for voluntary termination of collaborative agreement	90 days
Intrexon T1D Partners, LLC | Upfront | Upfront and Milestone Payments
Collaboration and Licensing Agreements [Line Items]
Collaborative arrangement consideration received, value	$ 10,000,000

Collaboration and Licensing R62

Collaboration and Licensing Revenue - Summary of Deferred Revenue (Details) - USD ($) $ in Thousands	Mar. 31, 2016	Dec. 31, 2015
Deferred Revenue Arrangement [Line Items]
Deferred revenue	$ 210,238	$ 197,729
Current portion of deferred revenue	37,695	35,366
Long-term portion of deferred revenue	172,543	162,363
Upfront and Milestone Payments
Deferred Revenue Arrangement [Line Items]
Deferred revenue	194,849	181,331
Prepaid Research and Development Services
Deferred Revenue Arrangement [Line Items]
Deferred revenue	9,439	10,938
Prepaid Product and Service Revenues
Deferred Revenue Arrangement [Line Items]
Deferred revenue	5,201	4,759
Other
Deferred Revenue Arrangement [Line Items]
Deferred revenue	$ 749	$ 701

Collaboration and Licensing R63

Collaboration and Licensing Revenue - Summary of Deferred Revenue by Collaborator (Details) - USD ($) $ in Thousands	Mar. 31, 2016	Dec. 31, 2015
Deferred Revenue Arrangement [Line Items]
Deferred revenue	$ 210,238	$ 197,729
Upfront and Milestone Payments
Deferred Revenue Arrangement [Line Items]
Deferred revenue	194,849	181,331
Upfront and Milestone Payments | ZIOPHARM Oncology, Inc.
Deferred Revenue Arrangement [Line Items]
Deferred revenue	29,416	30,338
Upfront and Milestone Payments | Oragenics, Inc.
Deferred Revenue Arrangement [Line Items]
Deferred revenue	8,550	8,813
Upfront and Milestone Payments | Fibrocell Science, Inc.
Deferred Revenue Arrangement [Line Items]
Deferred revenue	20,840	21,445
Upfront and Milestone Payments | Genopaver, LLC
Deferred Revenue Arrangement [Line Items]
Deferred revenue	2,181	2,250
Upfront and Milestone Payments | Intrexon Energy Partners, LLC
Deferred Revenue Arrangement [Line Items]
Deferred revenue	20,000	20,625
Upfront and Milestone Payments | Persea Bio, LLC
Deferred Revenue Arrangement [Line Items]
Deferred revenue	4,375	4,500
Upfront and Milestone Payments | Ares Trading S.A.
Deferred Revenue Arrangement [Line Items]
Deferred revenue	51,970	53,567
Upfront and Milestone Payments | Thrive Agrobiotics, Inc.
Deferred Revenue Arrangement [Line Items]
Deferred revenue	1,575	1,621
Upfront and Milestone Payments | Intrexon Energy Partners II, LLC
Deferred Revenue Arrangement [Line Items]
Deferred revenue	17,333	17,833
Upfront and Milestone Payments | Exotech Bio, Inc.
Deferred Revenue Arrangement [Line Items]
Deferred revenue	5,000	0
Upfront and Milestone Payments | Relieve Genetics, Inc.
Deferred Revenue Arrangement [Line Items]
Deferred revenue	4,333	0
Upfront and Milestone Payments | Intrexon T1D Partners, LLC
Deferred Revenue Arrangement [Line Items]
Deferred revenue	10,000	0
Upfront and Milestone Payments | Other
Deferred Revenue Arrangement [Line Items]
Deferred revenue	$ 19,276	$ 20,339

Short-term and Long-term Inve64

Short-term and Long-term Investments - Summary of Amortized Cost, Gross Unrealized Gains and Losses, and Fair Value of Short-term and Long-term Investments (Details) - USD ($) $ in Thousands	Mar. 31, 2016	Dec. 31, 2015
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	$ 190,175	$ 208,494
Gross Unrealized Gains	87	21
Gross Unrealized Losses	(19)	(540)
Aggregate Fair Value	190,243	207,975
U.S. government debt securities
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	189,903	208,223
Gross Unrealized Gains	87	21
Gross Unrealized Losses	(19)	(540)
Aggregate Fair Value	189,971	207,704
Certificates of deposit
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	272	271
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Aggregate Fair Value	$ 272	$ 271

Short-term and Long-term Inve65

Short-term and Long-term Investments - Summary of Estimated Fair Value of Available-for-Sale Investments Classified by Contractual Maturities (Details) - USD ($) $ in Thousands	Mar. 31, 2016	Dec. 31, 2015
Investments, Debt and Equity Securities [Abstract]
Due within one year	$ 114,659
After one year through two years	75,584
Total	$ 190,243	$ 207,975

Fair Value Measurements - Summa

Fair Value Measurements - Summary of Placement in the Fair Value Hierarchy of Financial Assets that are Measured at Fair Value on a Recurring Basis (Details) - USD ($) $ in Thousands	Mar. 31, 2016	Dec. 31, 2015
Assets
Fair value of financial assets measured at fair value on a recurring basis	$ 251,692	$ 291,762
U.S. government debt securities
Assets
Fair value of financial assets measured at fair value on a recurring basis	189,971	207,704
Equity securities
Assets
Fair value of financial assets measured at fair value on a recurring basis	61,322	83,653
Other
Assets
Fair value of financial assets measured at fair value on a recurring basis	399	405
Quoted Prices in Active Markets (Level 1)
Assets
Fair value of financial assets measured at fair value on a recurring basis	50,189	65,850
Quoted Prices in Active Markets (Level 1) | U.S. government debt securities
Assets
Fair value of financial assets measured at fair value on a recurring basis	0	0
Quoted Prices in Active Markets (Level 1) | Equity securities
Assets
Fair value of financial assets measured at fair value on a recurring basis	50,189	65,850
Quoted Prices in Active Markets (Level 1) | Other
Assets
Fair value of financial assets measured at fair value on a recurring basis	0	0
Significant Other Observable Inputs (Level 2)
Assets
Fair value of financial assets measured at fair value on a recurring basis	201,503	225,912
Significant Other Observable Inputs (Level 2) | U.S. government debt securities
Assets
Fair value of financial assets measured at fair value on a recurring basis	189,971	207,704
Significant Other Observable Inputs (Level 2) | Equity securities
Assets
Fair value of financial assets measured at fair value on a recurring basis	11,133	17,803
Significant Other Observable Inputs (Level 2) | Other
Assets
Fair value of financial assets measured at fair value on a recurring basis	399	405
Significant Unobservable Inputs (Level 3)
Assets
Fair value of financial assets measured at fair value on a recurring basis	0	0
Significant Unobservable Inputs (Level 3) | U.S. government debt securities
Assets
Fair value of financial assets measured at fair value on a recurring basis	0	0
Significant Unobservable Inputs (Level 3) | Equity securities
Assets
Fair value of financial assets measured at fair value on a recurring basis	0	0
Significant Unobservable Inputs (Level 3) | Other
Assets
Fair value of financial assets measured at fair value on a recurring basis	$ 0	$ 0

Fair Value Measurements - Addit

Fair Value Measurements - Additional Information (Details)	3 Months Ended
	Mar. 31, 2016USD ($)
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Transfers between levels of the fair value hierarchy	$ 0
Significant Unobservable Inputs (Level 3)
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of financial liabilities measured at fair value on a recurring basis	$ 3,660,000

Inventory - Schedule of Invento

Inventory - Schedule of Inventory (Details) - USD ($) $ in Thousands	Mar. 31, 2016	Dec. 31, 2015
Inventory [Line Items]
Inventory	$ 25,078	$ 26,563
Supplies, semen and embryos
Inventory [Line Items]
Inventory	1,287	1,402
Work in process
Inventory [Line Items]
Inventory	6,112	6,290
Livestock
Inventory [Line Items]
Inventory	16,342	16,907
Feed
Inventory [Line Items]
Inventory	$ 1,337	$ 1,964

Property, Plant and Equipment69

Property, Plant and Equipment, Net - Schedule of Property, Plant and Equipment (Details) - USD ($) $ in Thousands	Mar. 31, 2016	Dec. 31, 2015
Property, Plant and Equipment [Abstract]
Land and land improvements	$ 9,352	$ 9,119
Buildings and building improvements	7,520	7,520
Furniture and fixtures	1,852	1,283
Equipment	37,372	36,016
Leasehold improvements	7,076	6,888
Computer hardware and software	6,199	5,960
Construction and other assets in progress	2,836	2,193
Property, plant and equipment, gross	72,207	68,979
Less: Accumulated depreciation and amortization	(27,534)	(26,240)
Property, plant and equipment, net	$ 44,673	$ 42,739

Property, Plant and Equipment70

Property, Plant and Equipment, Net - Additional Information (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2016	Mar. 31, 2015
Property, Plant and Equipment [Abstract]
Depreciation expense	$ 2,133	$ 1,953

Goodwill and Intangible Asset71

Goodwill and Intangible Assets, Net - Schedule of Changes in Carrying Amount of Goodwill (Details) $ in Thousands	3 Months Ended
	Mar. 31, 2016USD ($)
Goodwill
Beginning balance	$ 165,169
Foreign currency translation adjustments	(594)
Ending balance	$ 164,575

Goodwill and Intangible Asset72

Goodwill and Intangible Assets, Net - Additional Information (Details) - USD ($)	3 Months Ended
	Mar. 31, 2016	Mar. 31, 2015	Dec. 31, 2015
Goodwill and Intangible Assets Disclosure [Abstract]
Goodwill accumulated impairment losses	$ 0		$ 0
Amortization expense	$ 3,515,000	$ 1,596,000

Goodwill and Intangible Asset73

Goodwill and Intangible Assets, Net - Schedule of Intangible Assets (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2016	Dec. 31, 2015
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	$ 280,867	$ 269,227
Accumulated Amortization	(25,407)	(21,692)
Net	255,460	247,535
Patents, related technologies and know-how
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	171,658	157,411
Accumulated Amortization	(20,759)	(17,775)
Net	150,899	139,636
Customer relationships
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	10,700	10,700
Accumulated Amortization	(3,222)	(2,739)
Net	7,478	7,961
Trademarks
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	6,800	6,800
Accumulated Amortization	(1,211)	(1,018)
Net	5,589	5,782
Covenant not to compete
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	398	384
Accumulated Amortization	(215)	(160)
Net	183	224
In-process research and development
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	91,311	93,932
Accumulated Amortization	0	0
Net	$ 91,311	$ 93,932
Weighted Average | Patents, related technologies and know-how
Finite-Lived Intangible Assets [Line Items]
Weighted Average Useful Life (Years)	15 years 3 months 18 days
Weighted Average | Customer relationships
Finite-Lived Intangible Assets [Line Items]
Weighted Average Useful Life (Years)	6 years 6 months
Weighted Average | Trademarks
Finite-Lived Intangible Assets [Line Items]
Weighted Average Useful Life (Years)	9 years 3 months 18 days
Weighted Average | Covenant not to compete
Finite-Lived Intangible Assets [Line Items]
Weighted Average Useful Life (Years)	2 years

Lines of Credit and Long Term74

Lines of Credit and Long Term Debt - Lines of Credit - Additional Information (Details) - Revolving Line of Credit	3 Months Ended
	Mar. 31, 2016USD ($)
Trans Ova Genetics, LC | First National Bank of Omaha
Line of Credit Facility [Line Items]
Line of credit facility, maximum borrowing capacity	$ 6,000,000
Line of credit facility, interest rate at period end	3.39%
Line of credit facility, outstanding balance	$ 0
Trans Ova Genetics, LC | First National Bank of Omaha | Minimum
Line of Credit Facility [Line Items]
Debt instrument, interest rate, stated percentage	3.00%
Trans Ova Genetics, LC | First National Bank of Omaha | London Interbank Offered Rate (LIBOR)
Line of Credit Facility [Line Items]
Line of credit facility, basis spread on variable rate	2.95%
Exemplar Genetics, LLC | American State Bank
Line of Credit Facility [Line Items]
Line of credit facility, maximum borrowing capacity	$ 700,000
Debt instrument, interest rate, stated percentage	4.50%
Line of credit facility, outstanding balance	$ 536,000

Lines of Credit and Long Term75

Lines of Credit and Long Term Debt - Schedule of Long Term Debt Instruments (Details) - USD ($) $ in Thousands	Mar. 31, 2016	Dec. 31, 2015
Debt Instrument [Line Items]
Long term debt	$ 8,506	$ 8,528
Less current portion	893	930
Long term debt, net of current portion	7,613	7,598
Notes payable
Debt Instrument [Line Items]
Long term debt	6,363	6,477
Royalty-based financing
Debt Instrument [Line Items]
Long term debt	1,945	1,807
Other
Debt Instrument [Line Items]
Long term debt	$ 198	$ 244

Lines of Credit and Long Term76

Lines of Credit and Long Term Debt - Long Term Debt - Additional Information (Details) - USD ($)	3 Months Ended
	Mar. 31, 2016	Dec. 31, 2015	Mar. 15, 2013
Debt Instrument [Line Items]
Long term debt	$ 8,506,000	$ 8,528,000
Notes payable to banks | Trans Ova Genetics, LC | American State Bank
Debt Instrument [Line Items]
Long term debt	5,517,000
Debt instrument, periodic payment	$ 39,000
Debt instrument, interest rate, stated percentage	3.95%
Notes payable
Debt Instrument [Line Items]
Long term debt	$ 6,363,000	6,477,000
Notes payable | Trans Ova Genetics, LC | Iowa Economic Development Authority
Debt Instrument [Line Items]
Long term debt	366,000
Debt instrument, periodic principal payment	183,000
Notes payable | Exemplar Genetics, LLC
Debt Instrument [Line Items]
Long term debt	480,000
Notes payable | Exemplar Genetics, LLC | Minimum
Debt Instrument [Line Items]
Debt instrument, periodic payment	$ 1,000
Debt instrument, interest rate, stated percentage	0.00%
Notes payable | Exemplar Genetics, LLC | Maximum
Debt Instrument [Line Items]
Debt instrument, periodic payment	$ 4,000
Debt instrument, interest rate, stated percentage	3.00%
Royalty-based financing
Debt Instrument [Line Items]
Long term debt	$ 1,945,000	$ 1,807,000
Royalty-based financing | AquaBounty Technologies, Inc. | Atlantic Canada Opportunities Agency
Debt Instrument [Line Items]
Long term debt	1,945,000
Amount available under the grant for research and development	$ 2,215,000
Claims period	5 years
Royalty on products	10.00%
Amount claimed			$ 1,952,000
Long term debt			1,107,000
Accreted difference between face value of amount drawn and acquisition date fair value			$ 845,000

Lines of Credit and Long Term77

Lines of Credit and Long Term Debt - Schedule of Future Maturities of Long Term Debt (Details) $ in Thousands	Mar. 31, 2016USD ($)
Maturities of Long-term Debt [Abstract]
2,016	$ 798
2,017	384
2,018	527
2,019	342
2,020	311
2,021	311
Thereafter	3,888
Total	$ 6,561

Income Taxes (Details)

Income Taxes (Details) - USD ($)	3 Months Ended
	Mar. 31, 2016	Mar. 31, 2015
Operating Loss Carryforwards [Line Items]
Deferred income tax expense (benefit)	$ (2,188,000)	$ 795,000
Deferred tax liabilities	19,777,000
Domestic Tax Authority
Operating Loss Carryforwards [Line Items]
Taxable loss	9,900,000	26,600,000
Current income tax benefit	0	$ 0
Operating loss carryforwards	258,600,000
Federal and state research and development tax credits	$ 6,770,000
Expiration date of U.S. federal income tax loss carryforwards	2,022
Domestic Tax Authority | Stock Compensation Deductions
Operating Loss Carryforwards [Line Items]
Operating loss carryforwards	$ 32,100,000
Foreign Tax Authority
Operating Loss Carryforwards [Line Items]
Current income tax benefit	93,000
Operating loss carryforwards	$ 118,800,000

Shareholders' Equity - Componen

Shareholders' Equity - Components of Accumulated Other Comprehensive Loss (Details) - USD ($) $ in Thousands	Mar. 31, 2016	Dec. 31, 2015
Accumulated Other Comprehensive Income (Loss) [Line Items]
Total accumulated other comprehensive loss	$ (11,435)	$ (12,752)
Unrealized gain (loss) on investments
Accumulated Other Comprehensive Income (Loss) [Line Items]
Total accumulated other comprehensive loss	68	(519)
Foreign currency translation adjustments
Accumulated Other Comprehensive Income (Loss) [Line Items]
Total accumulated other comprehensive loss	$ (11,503)	$ (12,233)

Share-Based Payments - Schedule

Share-Based Payments - Schedule of Stock-Based Compensation Expense (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2016	Mar. 31, 2015
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation expense	$ 13,188	$ 10,259
Cost of products
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation expense	20	34
Cost of services
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation expense	68	98
Research and development
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation expense	2,565	1,769
Selling, general and administrative
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation expense	$ 10,535	$ 8,358

Share-Based Payments - Addition

Share-Based Payments - Additional Information (Details) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended	3 Months Ended	12 Months Ended
	Apr. 30, 2016	Mar. 31, 2016	Dec. 31, 2015	Aug. 31, 2013
Chief Executive Officer
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Monthly compensation, in the form of equity		$ 200
Lock-up period		3 years
Initial term of compensation arrangement		12 months
Chief Executive Officer | Selling, general and administrative
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Fair value of shares issued		$ 471
Intrexon Stock Option Plan - 2008 Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Remaining shares available to grant				0
Options outstanding (in shares)		1,154,315
Intrexon Stock Option Plan - 2013 Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Remaining shares available to grant		2,421,499
Options outstanding (in shares)		9,355,773
Number of shares authorized for issuance		13,000,000
Intrexon Stock Option Plan - 2013 Plan | Subsequent Event
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Additional shares to be authorized, approved by Board of Directors, subject to shareholder approval	3,000,000
Intrexon Stock Option Plans
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Options outstanding (in shares)		10,510,088	11,043,528
Unrecognized compensation costs related to nonvested awards		$ 103,746	$ 113,655
Recognized over weighted-average period		3 years	3 years
Weighted average exercise price of option (in usd per share)		$ 32.84	$ 32.66
Shares exercisable at end of period		3,147,589
AquaBounty Stock Option Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Options outstanding (in shares)		5,607,000	5,382,000
Weighted average exercise price of option (in usd per share)		$ 0.26	$ 0.26
Shares exercisable at end of period		5,090,791	4,320,333

Share-Based Payments - Schedu82

Share-Based Payments - Schedule of Stock Option Activity (Details) - Intrexon Stock Option Plans - $ / shares		3 Months Ended	12 Months Ended
		Mar. 31, 2016	Dec. 31, 2015
Number of Shares
Balances at beginning of period (in shares)		11,043,528
Granted (in shares)		848,360
Exercised (in shares)		(537,307)
Forfeited (in shares)		(841,002)
Expired (in shares)		(3,491)
Balances at end of period (in shares)		10,510,088	11,043,528
Exercisable at end of period (in shares)		3,147,589
Vested and Expected to Vest at end of period (in shares)	[1]	8,906,749
Weighted Average Exercise Price
Balances at beginning of period (in usd per share)		$ 32.66
Granted (in usd per share)		32.50
Exercised (in usd per share)		(24.81)
Forfeited (in usd per share)		(35.31)
Expired (in usd per share)		(29.68)
Balances at period end (in usd per share)		32.84	$ 32.66
Exercisable, weighted average exercise price, at end of period (in usd per share)		22.12
Vested and Expected to Vest, weighted average exercise price at end of period (in usd per share)	[1]	$ 31.86
Weighted average remaining contractual term
Balances, weighted average remaining contractual period		8 years 1 month 17 days	8 years 5 months 27 days
Exercisable at period end, weighted average remaining contractual period		6 years 1 month 28 days
Vested and Expected to Vest at period end, weighted average remaining contractual period	[1]	7 years 11 months 12 days
[1]	The number of stock options expected to vest takes into account an estimate of expected forfeitures.

License Agreement (Details)

License Agreement (Details)	1 Months Ended
	Jan. 31, 2015USD ($)shares
License Agreement [Abstract]
Shares issued as consideration of license agreement | shares	2,100,085
ZIOPHARM Oncology, Inc.
Other Commitments [Line Items]
Annual funding commitment, term	3 years
ZIOPHARM Oncology, Inc. | Minimum
Other Commitments [Line Items]
Annual funding commitment, amount	$ 15,000,000
ZIOPHARM Oncology, Inc. | Maximum
Other Commitments [Line Items]
Annual funding commitment, amount	20,000,000
Research and development
Other Commitments [Line Items]
Payment of license fees	$ 59,579,000

Commitments and Contingencies -

Commitments and Contingencies - Future Minimum Lease Payments Under Noncancelable Operating Leases (Details) $ in Thousands	Mar. 31, 2016USD ($)
Future Minimum Lease Payments
2,016	$ 2,459
2,017	3,775
2,018	2,312
2,019	2,127
2,020	2,179
2,021	1,604
Total	$ 14,456

Commitments and Contingencies85

Commitments and Contingencies - Operating Leases - Additional Information (Details) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2016	Mar. 31, 2015
Commitments and Contingencies Disclosure [Abstract]
Rent expense	$ 2,032	$ 2,134
Rental income under sublease agreement	335	$ 425
Future rental income under sublease agreements, 2016	210
Future rental income under sublease agreements, 2017	$ 36

Commitments and Contingencies86

Commitments and Contingencies - Contingencies - Additional Information (Details) - Licensing and patent infringement suit - USD ($) $ in Thousands	1 Months Ended	3 Months Ended	49 Months Ended
	Apr. 30, 2016	Mar. 31, 2016	Mar. 31, 2016
Loss Contingencies [Line Items]
Cumulative payments for royalties and licenses			$ 3,420
Royalties and license payments not yet deposited		$ 3,009	$ 3,009
Selling, general and administrative
Loss Contingencies [Line Items]
Litigation settlement expense		$ 4,228
Subsequent Event
Loss Contingencies [Line Items]
Damages awarded to (against) Trans Ova	$ 528
Subsequent Event | XY, LLC
Loss Contingencies [Line Items]
Damages awarded to (against) Trans Ova	$ (6,066)

Related Party Transactions (Det

Related Party Transactions (Details) - USD ($)	1 Months Ended		3 Months Ended
	Nov. 30, 2015	Jun. 30, 2015	Mar. 31, 2016	Mar. 31, 2015
Related Party Transaction [Line Items]
Shares issued as compensation for services			$ 3,083,000
Collaboration and licensing revenues			24,073,000	$ 14,783,000
Third Security, LLC
Related Party Transaction [Line Items]
Expense for services			$ 46,000	41,000
Initial term of services agreement	1 year
Shares issued as compensation for services (in shares)			79,870
Shares issued as compensation for services			$ 2,267,000
Third Security, LLC | Common Stock
Related Party Transaction [Line Items]
Expense for services	$ 800,000
Oragenics, Inc.
Related Party Transaction [Line Items]
Maximum percentage of shares of future securities offerings of collaborative partners to which the entity is entitled to purchase			30.00%
Oragenics, Inc. | Maximum
Related Party Transaction [Line Items]
Common stock purchase commitment			$ 10,000
Oragenics ECC 3
Related Party Transaction [Line Items]
Commitment period for purchase of additional common stock after effective date		16 months
Related Parties, Aggregated
Related Party Transaction [Line Items]
Collaboration and licensing revenues			19,999,000	$ 12,796,000
Harvest Intrexon Enterprise Fund I, LP | Other nonoperating income
Related Party Transaction [Line Items]
Management fees revenue			$ 645,000

Net Income (Loss) per Share - C

Net Income (Loss) per Share - Computation of Basic and Diluted Net Income (Loss) Per Share (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended
	Mar. 31, 2016	Mar. 31, 2015
Numerator:
Net income (loss) attributable to Intrexon	$ (64,429)	$ 27,097
Denominator:
Weighted average shares outstanding, basic	116,861,151	106,103,848
Weighted average effect of dilutive stock options and warrants (in shares)	0	2,037,886
Weighted average shares outstanding, diluted	116,861,151	108,141,734
Net income (loss) attributable to Intrexon per share, basic (in usd per share)	$ (0.55)	$ 0.26
Net income (loss) attributable to Intrexon per share, diluted (in usd per share)	$ (0.55)	$ 0.25

Net Income (Loss) per Share - S

Net Income (Loss) per Share - Schedule of Antidilutive Securities Excluded from Calculation of Net Income (Loss) per Share (Details) - shares	3 Months Ended
	Mar. 31, 2016	Mar. 31, 2015
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of net income (loss) per share (in shares)	10,627,790	4,719,991
Options
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of net income (loss) per share (in shares)	10,510,088	4,719,991
Warrants
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of net income (loss) per share (in shares)	117,702	0