Precigen (PGEN) 10-Q 9 Aug 16 2016 Q2 Quarterly report Financial data

Document and Entity Information

Document and Entity Information - shares	6 Months Ended
	Jun. 30, 2016	Jul. 31, 2016
Document And Entity Information [Abstract]
Document Type	10-Q
Amendment Flag	false
Document Period End Date	Jun. 30, 2016
Document Fiscal Year Focus	2,016
Document Fiscal Period Focus	Q2
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		118,325,697

Consolidated Balance Sheets

Consolidated Balance Sheets - USD ($) $ in Thousands	Jun. 30, 2016	Dec. 31, 2015
Current assets
Cash and cash equivalents	$ 155,081	$ 135,782
Short-term investments	115,667	102,528
Receivables
Trade, net	27,028	25,101
Related parties	14,394	23,597
Note, net	0	601
Other	2,294	2,995
Inventory	24,492	26,563
Prepaid expenses and other	6,701	6,634
Total current assets	345,657	323,801
Long-term investments	50,463	105,447
Equity securities	39,020	83,653
Investment in preferred stock	120,000	0
Property, plant and equipment, net	46,659	42,739
Intangible assets, net	244,314	247,535
Goodwill	161,257	165,169
Investments in affiliates	22,714	9,977
Other assets	1,028	3,725
Total assets	1,031,112	982,046
Current liabilities
Accounts payable	8,204	4,967
Accrued compensation and benefits	9,474	19,050
Other accrued liabilities	13,295	7,949
Deferred revenue	53,863	35,366
Lines of credit	461	561
Current portion of long term debt	491	930
Current portion of deferred consideration	9,255	6,931
Related party payables	456	150
Total current liabilities	95,499	75,904
Long term debt, net of current portion	7,530	7,598
Deferred consideration, net of current portion	6,689	8,698
Deferred revenue, net of current portion	271,376	162,363
Deferred tax liabilities	18,680	21,802
Other long term liabilities	3,157	795
Total liabilities	402,931	277,160
Commitments and contingencies (Note 17)
Total equity
Common stock, no par value, 200,000,000 shares authorized as of June 30, 2016 and December 31, 2015; 118,269,920 and 116,658,886 shares issued and outstanding as of June 30, 2016 and December 31, 2015, respectively	0	0
Additional paid-in capital	1,297,103	1,249,559
Accumulated deficit	(656,222)	(542,729)
Accumulated other comprehensive loss	(21,651)	(12,752)
Total Intrexon shareholders' equity	619,230	694,078
Noncontrolling interests	8,951	10,808
Total equity	628,181	704,886
Total liabilities and total equity	$ 1,031,112	$ 982,046

Consolidated Balance Sheets (Pa

Consolidated Balance Sheets (Parenthetical) - shares	Jun. 30, 2016	Dec. 31, 2015
Statement of Financial Position [Abstract]
Common stock, shares authorized	200,000,000	200,000,000
Common stock, shares issued	118,269,920	116,658,886
Common stock, shares outstanding	118,269,920	116,658,886

Consolidated Statements of Oper

Consolidated Statements of Operations - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Revenues
Collaboration and licensing revenues	$ 27,481	$ 17,181	$ 51,554	$ 31,964
Product revenues	10,884	14,266	19,439	23,199
Service revenues	13,927	13,255	24,592	23,212
Other revenues	209	189	354	365
Total revenues	52,501	44,891	95,939	78,740
Operating Expenses
Cost of products	10,753	11,764	20,315	20,439
Cost of services	6,332	6,503	12,004	11,865
Research and development	28,375	20,381	54,231	99,688
Selling, general and administrative	30,263	23,673	73,144	51,301
Total operating expenses	75,723	62,321	159,694	183,293
Operating loss	(23,222)	(17,430)	(63,755)	(104,553)
Other Income (Expense), Net
Unrealized and realized appreciation (depreciation) in fair value of equity securities	(23,469)	(20,609)	(45,800)	94,845
Interest expense	(267)	(359)	(532)	(702)
Interest income	713	344	1,323	644
Other income (expense), net	676	(326)	1,237	(59)
Total other income (expense), net	(22,347)	(20,950)	(43,772)	94,728
Equity in net loss of affiliates	(5,053)	(2,180)	(10,696)	(4,136)
Loss before income taxes	(50,622)	(40,560)	(118,223)	(13,961)
Income tax benefit (expense)	591	(934)	2,872	(1,729)
Net loss	(50,031)	(41,494)	(115,351)	(15,690)
Net loss attributable to the noncontrolling interests	967	831	1,858	2,124
Net loss attributable to Intrexon	$ (49,064)	$ (40,663)	$ (113,493)	$ (13,566)
Net loss attributable to Intrexon per share, basic and diluted (in usd per share)	$ (0.42)	$ (0.37)	$ (0.97)	$ (0.13)
Weighted average shares outstanding, basic and diluted	118,141,377	109,318,471	117,501,264	107,720,040

Consolidated Statements of Comp

Consolidated Statements of Comprehensive Loss - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Statement of Comprehensive Income [Abstract]
Net loss	$ (50,031)	$ (41,494)	$ (115,351)	$ (15,690)
Other comprehensive income (loss):
Unrealized gain (loss) on investments	152	(8)	739	19
Foreign currency translation adjustments	(10,370)	848	(9,672)	(2,272)
Comprehensive loss	(60,249)	(40,654)	(124,284)	(17,943)
Comprehensive loss attributable to the noncontrolling interests	969	843	1,892	2,096
Comprehensive loss attributable to Intrexon	$ (59,280)	$ (39,811)	$ (122,392)	$ (15,847)

Consolidated Statements of Shar

Consolidated Statements of Shareholders' and Total Equity - 6 months ended Jun. 30, 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	19,818		19,783			19,783	35
Exercises of stock options and warrants (in shares)		1,258,327
Exercises of stock options and warrants	17,671		17,671			17,671
Shares issued as payment for services (in shares)		216,367
Shares issued as payment for services	5,689		5,689			5,689
Shares issued in asset acquisition (in shares)		136,340
Shares issued in asset acquisition	4,401		4,401			4,401
Net loss	(115,351)				(113,493)	(113,493)	(1,858)
Other comprehensive loss	$ (8,933)			(8,899)		(8,899)	(34)
Balances (in shares) at Jun. 30, 2016	118,269,920	118,269,920
Balances at Jun. 30, 2016	$ 628,181		$ 1,297,103	$ (21,651)	$ (656,222)	$ 619,230	$ 8,951

Consolidated Statements of Cash

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015
Cash flows from operating activities
Net loss	$ (115,351)	$ (15,690)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	11,674	7,358
Loss on disposal of property, plant and equipment	225	201
Unrealized and realized (appreciation) depreciation on equity securities	45,800	(94,845)
Amortization of discount/premium on investments	598	196
Equity in net loss of affiliates	10,696	4,136
Stock-based compensation expense	19,839	18,139
Shares issued as payment for services	5,689	480
Shares issued as consideration for license agreement	0	59,579
Provision for bad debts	1,183	984
Deferred income taxes	(2,659)	952
Other noncash items	391	542
Receivables:
Trade	(2,463)	(127,516)
Related parties	9,203	213
Note	(24)	(20)
Other	626	210
Inventory	2,071	(1,212)
Prepaid expenses and other	1,299	(1,669)
Other assets	2,697	(4,876)
Accounts payable	2,834	(125)
Accrued compensation and benefits	(9,543)	4,099
Other accrued liabilities	4,807	839
Deferred revenue	(6,078)	60,909
Related party payables	331	57,370
Other long term liabilities	106	188
Net cash used in operating activities	(16,049)	(29,558)
Cash flows from investing activities
Maturities of investments	41,987	48,000
Purchases of equity securities and warrants	(1,167)	(14,900)
Acquisitions of businesses, net of cash received	0	(39,501)
Acquisition of noncontrolling interest	0	(1,566)
Investments in affiliates	(5,054)	(3,334)
Cash paid in asset acquisition	(7,244)	0
Purchases of property, plant and equipment	(10,038)	(6,740)
Proceeds from sale of property, plant and equipment	140	233
Net cash provided by (used in) investing activities	18,624	(17,808)
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	1,540	11,680
Repayments of advances from lines of credit	(1,640)	(13,080)
Proceeds from long term debt	0	44
Payments of long term debt	(685)	(678)
Proceeds from stock option exercises	17,671	10,382
Net cash provided by financing activities	16,886	118,389
Effect of exchange rate changes on cash and cash equivalents	(162)	410
Net increase in cash and cash equivalents	19,299	71,433
Cash and cash equivalents
Beginning of period	135,782	27,466
End of period	155,081	98,899
Supplemental disclosure of cash flow information
Cash paid during the period for interest	140	99
Significant noncash financing and investing activities
Note receivable as consideration for collaboration agreement	0	5,000
Stock received as consideration for collaboration agreements	13,666	0
Preferred stock received as consideration for collaboration amendments	120,000	0
Stock issued in business combinations	0	70,668
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
Noncash dividend to shareholders	0	172,419
Purchases of equipment included in accounts payable and other accrued liabilities	$ 1,118	$ 1,064

Organization

Organization	6 Months Ended
	Jun. 30, 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 June 30, 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	6 Months Ended
	Jun. 30, 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 June 30, 2016 and results of operations and cash flows for the interim periods ended June 30, 2016 and 2015 . The year-end consolidated balance sheet data was derived from the Company's audited financial statements but does not include all disclosures required by U.S. GAAP. 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. Investment in Preferred Stock The Company holds preferred stock received from one of its collaborators, ZIOPHARM Oncology, Inc. ("ZIOPHARM"), which may be converted to common stock upon the occurrence of certain events in the future (Note 7 ). The Company elected the fair value option to account for its investment in preferred stock whereby the value of preferred stock is adjusted to fair value as of each reporting date and unrealized gains and losses are reported in the consolidated statement of operations. This investment is subject to fluctuation in the future due to, among other things, the likelihood and timing of conversion of the preferred stock into common stock, the volatility of ZIOPHARM's common stock, and changes in general economic and financial conditions of ZIOPHARM. The investment is classified as noncurrent in the consolidated balance sheet because the Company does not intend to sell the investment or expect it to be converted into shares of common stock within one year. The Company is entitled to a monthly dividend payable in additional shares of preferred stock. Equity Method Investments The Company accounts for its investments in each of its joint ventures and for its investments in start-up entities backed by the Harvest Intrexon Enterprise Fund I, LP ("Harvest") (Note 18 ) using the equity method of accounting because 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 June 30, 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 $6,626 and $16,601 as of June 30, 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 29.5% and 30.7% at June 30, 2016 and December 31, 2015 , respectively. Unrealized appreciation (depreciation) in the fair value of these securities was $(4,797) and $2,943 for the three months ended June 30, 2016 and 2015 , respectively, and $(11,142) and $3,879 for the six months ended June 30, 2016 and 2015 , respectively. Summarized unaudited financial data as of June 30, 2016 and December 31, 2015 and for the three and six months ended June 30, 2016 and 2015 , for the Company's equity method investments are shown in the following tables. Summarized unaudited financial data for ZIOPHARM has been included for the three and six months ended June 30, 2015 as the Company determined it had significant influence over ZIOPHARM until the Company distributed all of its common stock held in ZIOPHARM to its shareholders in June 2015. June 30, December 31, Current assets $ 70,182 $ 28,123 Non-current assets 11,059 1,539 Total assets 81,241 29,662 Current liabilities 7,633 6,274 Net assets $ 73,608 $ 23,388 Three Months Ended Six Months Ended 2016 2015 2016 2015 Revenues $ 47 $ 514 $ 329 $ 1,150 Operating expenses 14,383 25,424 32,043 109,493 Operating loss (14,336 ) (24,910 ) (31,714 ) (108,343 ) Other 1,424 4 1,427 3 Net loss $ (12,912 ) $ (24,906 ) $ (30,287 ) $ (108,340 ) Variable Interest Entities As of June 30, 2016 and December 31, 2015 , the Company determined that certain of its collaborators and joint ventures as well as 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 June 30, 2016 and December 31, 2015 was $137,920 and $3,598 , respectively, which represents the Company's maximum risk of loss related to the identified VIEs. Net Loss per Share 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 all periods presented. Segment Information While the Company generates revenues from multiple sources, including collaboration agreements, licensing, and products and services associated with bovine reproduction, management is organized around a singular research and development focus to further the development of the Company's underlying synthetic biology technologies. Accordingly, the Company has determined that it operates in one segment. As of June 30, 2016 and December 31, 2015 , the Company had $5,666 and $3,877 , respectively, of long-lived assets in foreign countries. The Company recognized revenues derived in foreign countries totaling $2,680 and $925 for the three months ended June 30, 2016 and 2015 , respectively, and $5,176 and $2,263 for the six months ended June 30, 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 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, April and May 2016, the FASB clarified the implementation guidance on principal versus agent, identifying performance obligations, licensing, narrow-scope improvements and practical expedients by issuing ASU 2016-08, Revenue from Contracts with Customers (Topic 606) - Principal versus Agent Considerations ("ASU 2016-08"), ASU 2016-10, Revenue from Contracts with Customers (Topic 606) - Identifying Performance Obligations and Licensing ("ASU 2016-10"), and ASU 2016-12, Revenue from Contracts with Customers (Topic 606) - Narrow-Scope Improvements and Practical Expedients ("ASU 2016-12"). 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	6 Months Ended
	Jun. 30, 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 June 30, 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 $104 and $267 are included in selling, general and administrative expenses in the accompanying consolidated statements of operations for the three and six months ended June 30, 2015 , respectively. 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 $381 is included in selling, general and administrative expenses in the accompanying consolidated statement of operations for the six months ended June 30, 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 and six months ended June 30, 2015 is presented as if the acquisitions had been consummated on January 1, 2014: Three Months Ended June 30, 2015 Six Months Ended June 30, 2015 Pro Forma Revenues $ 45,083 $ 79,310 Loss before income taxes (42,832 ) (22,584 ) Net loss (43,723 ) (23,176 ) Net loss attributable to the noncontrolling interests 831 2,124 Net loss attributable to Intrexon (42,892 ) (21,052 )

Investments in Joint Ventures

Investments in Joint Ventures	6 Months Ended
	Jun. 30, 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 included 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 June 30, 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 $4,973 as of June 30, 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 $1,777 and $2,000 as of June 30, 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 June 30, 2016 , the Company's remaining commitment was $14,378 . 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 $(483) and $(1,270) as of June 30, 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 $(201) and $(144) as of June 30, 2016 and December 31, 2015 , respectively, and is included in other accrued liabilities 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 June 30, 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 $4,794 and $6,379 as of June 30, 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	6 Months Ended
	Jun. 30, 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 and six months ended June 30, 2016 and 2015 . Three Months Ended June 30, 2016 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 922 $ 6,048 $ 6,970 Oragenics, Inc. 261 246 507 Fibrocell Science, Inc. 605 789 1,394 Genopaver, LLC 68 1,569 1,637 S & I Ophthalmic, LLC — 2,358 2,358 OvaXon, LLC — 808 808 Intrexon Energy Partners, LLC 625 3,587 4,212 Persea Bio, LLC 125 206 331 Ares Trading S.A. 1,597 621 2,218 Thrive Agrobiotics, Inc. 46 404 450 Intrexon Energy Partners II, LLC 500 394 894 Exotech Bio, Inc. 139 — 139 Relieve Genetics, Inc. 120 230 350 Intrexon T1D Partners, LLC 278 32 310 Other 2,769 2,134 4,903 Total $ 8,055 $ 19,426 $ 27,481 Three Months Ended June 30, 2015 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 644 $ 4,606 $ 5,250 Oragenics, Inc. 307 68 375 Fibrocell Science, Inc. 448 1,470 1,918 Genopaver, LLC 68 867 935 S & I Ophthalmic, LLC — 890 890 OvaXon, LLC — 662 662 Intrexon Energy Partners, LLC 625 2,731 3,356 Persea Bio, LLC 125 141 266 Ares Trading S.A. 739 — 739 Other 747 2,043 2,790 Total $ 3,703 $ 13,478 $ 17,181 Six Months Ended June 30, 2016 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 1,844 $ 12,107 $ 13,951 Oragenics, Inc. 524 789 1,313 Fibrocell Science, Inc. 1,210 2,041 3,251 Genopaver, LLC 137 3,078 3,215 S & I Ophthalmic, LLC — 3,544 3,544 OvaXon, LLC — 1,502 1,502 Intrexon Energy Partners, LLC 1,250 6,950 8,200 Persea Bio, LLC 250 405 655 Ares Trading S.A. 3,194 1,429 4,623 Thrive Agrobiotics, Inc. 92 792 884 Intrexon Energy Partners II, LLC 1,000 444 1,444 Exotech Bio, Inc. 139 — 139 Relieve Genetics, Inc. 120 230 350 Intrexon T1D Partners, LLC 278 32 310 Other 3,789 4,384 8,173 Total $ 13,827 $ 37,727 $ 51,554 Six Months Ended June 30, 2015 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 1,288 $ 7,763 $ 9,051 Oragenics, Inc. 569 76 645 Fibrocell Science, Inc. 896 3,183 4,079 Genopaver, LLC 137 1,467 1,604 S & I Ophthalmic, LLC — 1,645 1,645 OvaXon, LLC — 1,306 1,306 Intrexon Energy Partners, LLC 1,250 4,916 6,166 Persea Bio, LLC 250 256 506 Ares Trading S.A. 739 — 739 Other 1,605 4,618 6,223 Total $ 6,734 $ 25,230 $ 31,964 Except for the agreements discussed below, there have been no significant changes to arrangements with our collaborators and licensees in the six months ended June 30, 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, Inc. ("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, Inc. ("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. AD Skincare Collaboration In June 2016, the Company entered into an ECC with AD Skincare, Inc. ("AD Skincare"), an affiliate of Harvest and a related party. AD Skincare was formed for the purpose of entering into the ECC and developing an advanced topical delivery system to improve the efficacy of biologically active ingredients aimed at improving signs of aging human skin. Upon execution of the ECC, the Company received a technology access fee in the form of equity in AD Skincare valued at $4,333 as upfront consideration. The Company is also entitled to up to $2,000 of potential payments for substantive and non-substantive development milestones for each product developed under the ECC, as well as up to $17,000 in one-time commercial milestones. The Company receives reimbursement payments for research and development services provided pursuant to the ECC. AD Skincare will pay the Company royalties as a percentage in the low double-digits on the quarterly net sales of products developed under the ECC, as defined in the agreement. AD Skincare is responsible for the development and commercialization of the product candidates. The term of the ECC commenced in June 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 AD Skincare upon 90 days written notice to the Company. ZIOPHARM Collaborations In June 2016, the Company amended each of its two existing collaboration agreements with ZIOPHARM and as a result the rate of the royalty which the Company is entitled to receive on certain products commercialized pursuant to the agreements was reduced from 50% to 20% . As consideration for execution of the amendments, ZIOPHARM issued the Company 100,000 shares of ZIOPHARM's Series 1 Preferred Stock valued at $120,000 . The Company allocated the consideration received to each ECC based on the cumulative value of upfront and milestone payments previously received pursuant to that ECC. Because the Company has remaining performance obligations under each of the ZIOPHARM ECCs, the Company recorded the initial fair value received as deferred revenue and will recognize this amount straight-line over the remaining performance period for each ZIOPHARM ECC. No other financially significant terms of the ZIOPHARM ECCs were changed as a result of the amendments. See Note 7 for additional discussion of the terms of the preferred stock and the accounting treatment. 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: June 30, December 31, Upfront and milestone payments $ 310,937 $ 181,331 Prepaid research and development services 8,122 10,938 Prepaid product and service revenues 5,471 4,759 Other 709 701 Total $ 325,239 $ 197,729 Current portion of deferred revenue $ 53,863 $ 35,366 Long-term portion of deferred revenue 271,376 162,363 Total $ 325,239 $ 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: June 30, December 31, ZIOPHARM Oncology, Inc. $ 148,494 $ 30,338 Oragenics, Inc. 8,289 8,813 Fibrocell Science, Inc. 20,235 21,445 Genopaver, LLC 2,113 2,250 Intrexon Energy Partners, LLC 19,375 20,625 Persea Bio, LLC 4,250 4,500 Ares Trading S.A. 50,373 53,567 Thrive Agrobiotics, Inc. 1,529 1,621 Intrexon Energy Partners II, LLC 16,833 17,833 Exotech Bio, Inc. 4,861 — Relieve Genetics, Inc. 4,213 — Intrexon T1D Partners, LLC 9,564 — AD Skincare, Inc. 4,333 — Other 16,475 20,339 Total $ 310,937 $ 181,331

Short-term and Long-term Invest

Short-term and Long-term Investments	6 Months Ended
	Jun. 30, 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 June 30, 2016 : Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Aggregate Fair Value U.S. government debt securities $ 165,638 $ 220 $ — $ 165,858 Certificates of deposit 272 — — 272 Total $ 165,910 $ 220 $ — $ 166,130 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 June 30, 2016 was: Due within one year $ 115,667 After one year through two years 50,463 Total $ 166,130 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 June 30, 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.

Investment in Preferred Stock

Investment in Preferred Stock	6 Months Ended
	Jun. 30, 2016
Investment in Preferred Stock [Abstract]
Investment In Preferred Stock	Investment in Preferred Stock In June 2016, the Company received 100,000 shares of ZIOPHARM's Series 1 Preferred Stock (the "Preferred Shares"), with a per share stated value of $1,200 , as consideration for amending their two previously existing ECC agreements (Note 5 ). A summary of the terms of the Preferred Shares are as follows. Conversion. The Preferred Shares shall automatically convert into shares of ZIOPHARM common stock upon the date the first approval in the United States of (i) a ZIOPHARM product, as defined in and developed under one of the ECC agreements, or (ii) a product, as defined and developed under the License and Collaboration Agreement with Ares Trading S.A., a subsidiary of the biopharmaceutical business of Merck KGaA, and ZIOPHARM, is publicly announced (the "Conversion Event Date"). The Preferred Shares shall convert into a number of shares of ZIOPHARM common stock equal to the stated value of such Preferred Share, divided by the greater of: (i) the volume weighted average closing price of ZIOPHARM's common stock over the twenty trading days ending on the Conversion Event Date or (ii) $1.00 . The number of converted shares is subject to certain limitations defined in the amended and restated Certificate of Designation, Preferences, and Rights of Series 1 Preferred Stock (the "A&R Certificate of Designation"). Dividend Rights. The Company shall receive a monthly dividend, payable in additional Preferred Shares, equal to $12.00 per Preferred Share held per month divided by the stated value of the Preferred Shares, which is referred to as the PIK Dividend. For any Preferred Shares that are not converted on the Conversion Event Date, the rate of PIK Dividend on these unconverted Preferred Shares will automatically increase from $12.00 to $24.00 per Preferred Share per month. Voting Rights . The Preferred Shares do not have any voting rights except for certain protective voting rights defined in the A&R Certificate of Designation. Liquidation Rights. In the event of any voluntary or involuntary liquidation, dissolution or winding up of ZIOPHARM or a deemed liquidation event, as defined in the A&R Certificate of Designation, including a change of control or the sale, lease transfer or exclusive license of all or substantially all of ZIOPHARM's assets, the holders of the Preferred Shares shall be entitled to receive a portion of all funds to be distributed in proportion to the holders' proportionate share of ZIOPHARM's common stock on an as-converted to common stock basis (the "Series 1 Liquidation Amount"). For purposes of calculating the Series 1 Liquidation Amount, if such liquidation event occurs prior to the Conversion Event Date, each Preferred Share shall be deemed to be convertible into the number of shares of ZIOPHARM's common stock equal to (i) the stated value of each Preferred Share, divided by (ii) the volume weighted average price of ZIOPHARM's common stock for the twenty day period ending on the date of the public announcement of the liquidation event. In addition, ZIOPHARM may elect to redeem the Preferred Shares in connection with or following a deemed liquidation event at a price per share equal to the Series 1 Liquidation Amount. The Company elected the fair value option to account for its investment in ZIOPHARM preferred stock (the "investment in preferred stock"). The investment in preferred stock is categorized as Level 3 as there are significant unobservable inputs and the Preferred Shares are not traded on a public exchange. The fair value of the investment in preferred stock as of June 30, 2016 was estimated using a probability-weighted expected return ("PWERM") model. The key inputs used in the PWERM model were (i) estimating the future returns for conversion of the Preferred Shares for both product approval and a change in control of ZIOPHARM (the "conversion events") using market data of the change in value for guideline companies as a result of these conversion events; (ii) estimating the expected date and likelihood of each conversion event; and (iii) discounting these estimated future returns using a discount rate for the Preferred Shares considering industry debt issuances originated by public funds and venture capital rates of return. The fair value of the Company's investment in preferred stock is $120,000 as of June 30, 2016 . A significant change in unobservable inputs discussed above could result in a significant impact to the fair value of the Company's investment in preferred stock.

Fair Value Measurements

Fair Value Measurements	6 Months Ended
	Jun. 30, 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 June 30, 2016 : Quoted Prices in Active Markets (Level 1) Significant Other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) June 30, Assets U.S. government debt securities $ — $ 165,858 $ — $ 165,858 Equity securities 31,539 7,481 — 39,020 Preferred stock — — 120,000 120,000 Other — 308 — 308 Total $ 31,539 $ 173,647 $ 120,000 $ 325,186 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. The method used to estimate the fair value of the Level 3 asset is discussed in Note 7 . There were no transfers between levels of the fair value hierarchy in the six months ended June 30, 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 June 30, 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 June 30, 2016 . Financial liabilities measured on a recurring basis were not significant at December 31, 2015 .

Inventory

Inventory	6 Months Ended
	Jun. 30, 2016
Inventory Disclosure [Abstract]
Inventory	Inventory Inventory consists of the following: June 30, December 31, Supplies, semen and embryos $ 1,410 $ 1,402 Work in process 6,240 6,290 Livestock 16,062 16,907 Feed 780 1,964 Total inventory $ 24,492 $ 26,563

Property, Plant and Equipment,

Property, Plant and Equipment, Net	6 Months Ended
	Jun. 30, 2016
Property, Plant and Equipment [Abstract]
Property, Plant and Equipment, Net	Property, Plant and Equipment, Net Property, plant and equipment consist of the following: June 30, December 31, Land and land improvements $ 9,682 $ 9,119 Buildings and building improvements 7,526 7,520 Furniture and fixtures 2,352 1,283 Equipment 40,312 36,016 Leasehold improvements 7,630 6,888 Computer hardware and software 6,334 5,960 Construction and other assets in progress 2,440 2,193 76,276 68,979 Less: Accumulated depreciation and amortization (29,617 ) (26,240 ) Property, plant and equipment, net $ 46,659 $ 42,739 Depreciation expense was $2,304 and $1,828 for the three months ended June 30, 2016 and 2015 , respectively, and $4,437 and $3,781 for the six months ended June 30, 2016 and 2015 , respectively.

Goodwill and Intangible Assets,

Goodwill and Intangible Assets, Net	6 Months Ended
	Jun. 30, 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 six months ended June 30, 2016 are as follows: Balance at December 31, 2015 $ 165,169 Foreign currency translation adjustments (3,912 ) Balance at June 30, 2016 $ 161,257 No goodwill or accumulated impairment losses existed as of June 30, 2016 and December 31, 2015 . Intangible assets consist of the following at June 30, 2016 : Weighted Average Useful Life (Years) Gross Carrying Amount Accumulated Amortization Net Patents, related technologies and know-how 15.3 $ 170,046 $ (23,654 ) $ 146,392 Customer relationships 6.5 10,700 (3,706 ) 6,994 Trademarks 9.3 6,800 (1,405 ) 5,395 Covenant not to compete 2.0 390 (260 ) 130 In-process research and development 85,403 — 85,403 Total $ 273,339 $ (29,025 ) $ 244,314 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 The balance of in-process research and development as of June 30, 2016 primarily includes the in-process research and development acquired in the Company's Oxitec acquisition and amortization will begin once certain regulatory approvals have been obtained. Amortization expense was $3,722 and $1,981 for the three months ended June 30, 2016 and 2015 , respectively, and $7,237 and $3,577 for the six months ended June 30, 2016 and 2015 , respectively.

Lines of Credit and Long Term D

Lines of Credit and Long Term Debt	6 Months Ended
	Jun. 30, 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 May 1, 2017. 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 3.41% at June 30, 2016 . As of June 30, 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 June 30, 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 June 30, 2016 , there was an outstanding balance of $461 . Long Term Debt Long term debt consists of the following: June 30, December 31, Notes payable $ 5,884 $ 6,477 Royalty-based financing 1,985 1,807 Other 152 244 Long term debt 8,021 8,528 Less current portion 491 930 Long term debt, less current portion $ 7,530 $ 7,598 Trans Ova has a note payable to American State Bank which matures in April 2033 and has an outstanding principal balance of $5,428 as of June 30, 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. Exemplar has notes payable with outstanding principal balances totaling $456 as of June 30, 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 $2,216 , 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 $1,985 as of June 30, 2016 . Future maturities of long term debt are as follows: 2016 $ 298 2017 385 2018 529 2019 343 2020 313 2021 312 Thereafter 3,856 Total $ 6,036 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	6 Months Ended
	Jun. 30, 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 and six months ended June 30, 2016 , the Company had U.S. taxable loss of approximately $7,780 and $17,680 , respectively, for which no income tax benefit was recognized. For the three and six months ended June 30, 2016 , the Company recognized $120 and $213 of current foreign income tax benefit, respectively. For the three and six months ended June 30, 2015 , the Company had U.S. taxable income of approximately $65,400 and $38,800 , respectively, and $777 income tax expense was recognized. For the three and six months ended June 30, 2016 , the Company recorded deferred tax benefit of $471 and $2,659 , respectively. There was $157 and $952 of deferred tax expense for the three and six months ended June 30, 2015 , respectively. The Company's net deferred tax assets, excluding certain deferred tax liabilities totaling $18,680 , 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 June 30, 2016 , the Company has loss carryforwards for U.S. federal income tax purposes of approximately $266,400 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 $53,400 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 $117,900 , most of which do not expire.

Shareholders' Equity

Shareholders' Equity	6 Months Ended
	Jun. 30, 2016
Equity [Abstract]
Shareholders' Equity	Shareholders' Equity Dividend to Shareholders In June 2015, the Company distributed to its shareholders 17,830,305 shares of ZIOPHARM common stock, representing all of the equity interests of ZIOPHARM held by the Company at the time of the distribution and resulting in a realized gain of $81,401 . The distribution constituted a dividend to shareholders of record as of June 4, 2015. In connection with the distribution, pursuant to the terms of the Company's equity incentive plans, the conversion terms of all outstanding options for shares of the Company's common stock as of June 4, 2015 were adjusted to reflect the value of the distribution with respect to shares of the Company's common stock by decreasing the exercise prices and increasing the number of shares. This adjustment resulted in 312,795 additional shares at a weighted average exercise price of $25.40 . Components of Accumulated Other Comprehensive Loss The components of accumulated other comprehensive loss are as follows: June 30, December 31, Unrealized gain (loss) on investments $ 220 $ (519 ) Foreign currency translation adjustments (21,871 ) (12,233 ) Total accumulated other comprehensive loss $ (21,651 ) $ (12,752 )

Share-Based Payments

Share-Based Payments	6 Months Ended
	Jun. 30, 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 Six Months Ended 2016 2015 2016 2015 Cost of products $ 20 $ 21 $ 40 $ 55 Cost of services 70 105 138 203 Research and development 2,178 2,138 4,743 3,907 Selling, general and administrative 4,383 5,616 14,918 13,974 Total $ 6,651 $ 7,880 $ 19,839 $ 18,139 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 June 30, 2016 , there were 597,491 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 June 30, 2016 , there were 16,000,000 shares authorized for issuance under the 2013 Plan, of which 10,714,034 stock options were outstanding and 3,936,628 shares were available for grant. 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 3,137,860 30.66 Exercised (1,113,327 ) (15.87 ) Forfeited (1,752,627 ) (45.24 ) Expired (3,909 ) (30.35 ) Balances at June 30, 2016 11,311,525 31.81 8.56 Exercisable at June 30, 2016 2,754,250 25.36 7.15 Vested and Expected to Vest at June 30, 2016(1) 9,441,799 31.39 8.43 (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 June 30, 2016 and December 31, 2015 were $106,977 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 statements of operations and totaled $ 463 and $ 934 for the three and six months ended June 30, 2016 , respectively. Other Plans As of June 30, 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 2006 Plan") at a weighted average exercise price of $0.26 per share of which 5,231,040 were exercisable. As of December 31, 2015 , there were 5,382,000 options outstanding under the AquaBounty 2006 Plan at a weighted average exercise price of $0.26 per share of which 4,320,333 were exercisable. In March 2016, AquaBounty's Board of Directors adopted the AquaBounty 2016 Equity Incentive Plan ("AquaBounty 2016 Plan") to replace the AquaBounty 2006 Plan. The AquaBounty 2016 Plan provides for the issuance of incentive stock options, non-qualified stock options and awards of restricted and direct stock purchases to directors, officers, employees and consultants of AquaBounty. The AquaBounty 2016 Plan was approved by AquaBounty's shareholders at its annual meeting in April 2016. Upon the effectiveness of the AquaBounty 2016 Plan, no new awards may be granted under the AquaBounty 2006 Plan. As of June 30, 2016 , there were no options outstanding under the AquaBounty 2016 Plan.

License Agreement

License Agreement	6 Months Ended
	Jun. 30, 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 six months ended June 30, 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 provides 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	6 Months Ended
	Jun. 30, 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 June 30, 2016 , future minimum lease payments under operating leases having initial or remaining noncancelable lease terms in excess of one year are as follows: 2016 $ 1,966 2017 4,401 2018 2,834 2019 2,595 2020 2,647 2021 1,789 Total $ 16,232 Rent expense, including other facility expenses, was $2,302 and $2,247 for the three months ended June 30, 2016 and 2015 , respectively, and $4,334 and $4,381 for the six months ended June 30, 2016 and 2015 , respectively. The Company maintains subleases for certain of its facilities. Rental income under sublease agreements was $335 and $394 for the three months ended June 30, 2016 and 2015 , respectively, and $670 and $819 for the six months ended June 30, 2016 and 2015 , respectively. Future rental income is expected to be $17 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 the court's order, aggregate royalty and license payments were $3,170 , of which $2,759 had not yet been deposited by XY, LLC. For the six months ended June 30, 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. 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 Intrexon's common stock between May 12, 2015 and April 20, 2016 (the "Class Period"). The complaints name as defendants Intrexon and certain of its current 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 the Company's 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 derived from a report published in April 2016 on the Seeking Alpha financial blog. The plaintiffs seek compensatory damages, interest and an award of reasonable attorneys' fees and costs. In July 2016, the court hearing the matters entered an order consolidating the lawsuits and appointing a lead plaintiff. The Company intends to defend the lawsuit vigorously; however, there can be no assurance regarding the ultimate outcome of these lawsuits. 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 June 30, 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	6 Months Ended
	Jun. 30, 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 15 ). 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 and six months ended June 30, 2016 , the Company issued 85,300 shares and 165,170 shares, respectively, with values of $2,143 and $4,410 , respectively, 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 $99 and $111 for the three months ended June 30, 2016 and 2015 , respectively, and $145 and $152 for the six months ended June 30, 2016 and 2015 , respectively. See also Note 15 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. In June 2016, the Company purchased 2,261,419 shares of Oragenics common stock at $0.52 per share as part of a qualified financing. As of June 30, 2016 , the Company's maximum commitment remaining was $8,833 . The Company recognized $23,612 and $15,239 of collaboration revenues from related parties in the three months ended June 30, 2016 and 2015 , respectively, and $43,611 and $28,035 in the six months ended June 30, 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 are 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 provides Harvest with exclusive rights of first-look and first negotiation. For any opportunities it decides to pursue, Harvest establishes new collaboration entities which enter into an ECC with the Company in a designated field. The terms of such ECCs are 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 are 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 $613 and $1,258 for the three and six months ended June 30, 2016 , respectively.

Net Loss per Share

Net Loss per Share	6 Months Ended
	Jun. 30, 2016
Earnings Per Share [Abstract]
Net Loss per Share	Net Loss per Share The following table presents the computation of basic and diluted net loss per share for the three and six months ended June 30, 2016 and 2015 : Three Months Ended Six Months Ended 2016 2015 2016 2015 Historical net loss per share: Numerator: Net loss attributable to Intrexon $ (49,064 ) $ (40,663 ) $ (113,493 ) $ (13,566 ) Denominator: Weighted average shares outstanding, basic and diluted 118,141,377 109,318,471 117,501,264 107,720,040 Net loss attributable to Intrexon per share, basic and diluted $ (0.42 ) $ (0.37 ) $ (0.97 ) $ (0.13 ) The following potentially dilutive securities as of June 30, 2016 and 2015 , have been excluded from the above computations of diluted weighted average shares outstanding for the three and six months then ended, as they would have been anti-dilutive: June 30, 2016 2015 Options 11,311,525 9,503,729 Warrants 45,716 220,021 Total 11,357,241 9,723,750

Subsequent Events

Subsequent Events	6 Months Ended
	Jun. 30, 2016
Subsequent Events [Abstract]
Subsequent Events	Subsequent Events In August 2016, the Company and affiliates of Third Security committed to participate in a financing transaction of Fibrocell Science, Inc., which provides for the issuance of up to $25,000 in convertible promissory notes and warrants to purchase common stock. The Company and affiliates of Third Security will participate based on their respective current pro rata ownership interest and the initial closing of the financing is expected to occur during the third quarter of 2016. In July 2016, a purported shareholder derivative action captioned Basile v. Kirk et al. was filed in the Circuit Court of Fairfax County, Virginia, against certain of the Company's directors, the Company's Chief Executive Officer, and Third Security. The complaint alleges causes of action for breaches of fiduciary duty and unjust enrichment relating to the entry by the Company into the Services Agreement with Third Security. The plaintiff seeks, among other things, damages in an unspecified amount, disgorgement of improper benefits, appropriate equitable relief, and an award of attorney fees and other costs and expenses. The Board of Directors of the Company appointed a Special Litigation Committee consisting of independent directors to investigate the claims and allegations made in the derivative action and to decide on behalf of the Company whether the claims and allegations should be pursued. In July 2016, the Company entered into a land lease agreement to commence in January 2017 to be used for its Arctic ® apples. The initial term is through December 2037 and future minimum lease payments under this leasing arrangement total approximately $8,300 . The Company shall have the right to terminate the lease with six months ' advance written notice under certain circumstances as defined in the lease agreement.

Summary of Significant Accoun28

Summary of Significant Accounting Policies (Policies)	6 Months Ended
	Jun. 30, 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 June 30, 2016 and results of operations and cash flows for the interim periods ended June 30, 2016 and 2015 . The year-end consolidated balance sheet data was derived from the Company's audited financial statements but does not include all disclosures required by U.S. GAAP. 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.
Investment in Preferred Stock	Investment in Preferred Stock The Company holds preferred stock received from one of its collaborators, ZIOPHARM Oncology, Inc. ("ZIOPHARM"), which may be converted to common stock upon the occurrence of certain events in the future (Note 7 ). The Company elected the fair value option to account for its investment in preferred stock whereby the value of preferred stock is adjusted to fair value as of each reporting date and unrealized gains and losses are reported in the consolidated statement of operations. This investment is subject to fluctuation in the future due to, among other things, the likelihood and timing of conversion of the preferred stock into common stock, the volatility of ZIOPHARM's common stock, and changes in general economic and financial conditions of ZIOPHARM. The investment is classified as noncurrent in the consolidated balance sheet because the Company does not intend to sell the investment or expect it to be converted into shares of common stock within one year.
Equity Method Investments	Equity Method Investments The Company accounts for its investments in each of its joint ventures and for its investments in start-up entities backed by the Harvest Intrexon Enterprise Fund I, LP ("Harvest") (Note 18 ) using the equity method of accounting because 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 Loss per Share	Net Loss per Share 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 all periods presented.
Segment Information	Segment Information While the Company generates revenues from multiple sources, including collaboration agreements, licensing, and products and services associated with bovine reproduction, management is organized around a singular research and development focus to further the development of the Company's underlying synthetic biology technologies. Accordingly, the Company has determined that it operates in one segment.
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 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, April and May 2016, the FASB clarified the implementation guidance on principal versus agent, identifying performance obligations, licensing, narrow-scope improvements and practical expedients by issuing ASU 2016-08, Revenue from Contracts with Customers (Topic 606) - Principal versus Agent Considerations ("ASU 2016-08"), ASU 2016-10, Revenue from Contracts with Customers (Topic 606) - Identifying Performance Obligations and Licensing ("ASU 2016-10"), and ASU 2016-12, Revenue from Contracts with Customers (Topic 606) - Narrow-Scope Improvements and Practical Expedients ("ASU 2016-12"). 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 Accoun29

Summary of Significant Accounting Policies (Tables)	6 Months Ended
	Jun. 30, 2016
Accounting Policies [Abstract]
Summarized Unaudited Financial Information for the Equity Method Investments	Summarized unaudited financial data as of June 30, 2016 and December 31, 2015 and for the three and six months ended June 30, 2016 and 2015 , for the Company's equity method investments are shown in the following tables. Summarized unaudited financial data for ZIOPHARM has been included for the three and six months ended June 30, 2015 as the Company determined it had significant influence over ZIOPHARM until the Company distributed all of its common stock held in ZIOPHARM to its shareholders in June 2015. June 30, December 31, Current assets $ 70,182 $ 28,123 Non-current assets 11,059 1,539 Total assets 81,241 29,662 Current liabilities 7,633 6,274 Net assets $ 73,608 $ 23,388 Three Months Ended Six Months Ended 2016 2015 2016 2015 Revenues $ 47 $ 514 $ 329 $ 1,150 Operating expenses 14,383 25,424 32,043 109,493 Operating loss (14,336 ) (24,910 ) (31,714 ) (108,343 ) Other 1,424 4 1,427 3 Net loss $ (12,912 ) $ (24,906 ) $ (30,287 ) $ (108,340 )

Mergers and Acquisitions (Table

Mergers and Acquisitions (Tables)	6 Months Ended
	Jun. 30, 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 and six months ended June 30, 2015 is presented as if the acquisitions had been consummated on January 1, 2014: Three Months Ended June 30, 2015 Six Months Ended June 30, 2015 Pro Forma Revenues $ 45,083 $ 79,310 Loss before income taxes (42,832 ) (22,584 ) Net loss (43,723 ) (23,176 ) Net loss attributable to the noncontrolling interests 831 2,124 Net loss attributable to Intrexon (42,892 ) (21,052 )

Collaboration and Licensing R31

Collaboration and Licensing Revenue (Tables)	6 Months Ended
	Jun. 30, 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 and six months ended June 30, 2016 and 2015 . Three Months Ended June 30, 2016 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 922 $ 6,048 $ 6,970 Oragenics, Inc. 261 246 507 Fibrocell Science, Inc. 605 789 1,394 Genopaver, LLC 68 1,569 1,637 S & I Ophthalmic, LLC — 2,358 2,358 OvaXon, LLC — 808 808 Intrexon Energy Partners, LLC 625 3,587 4,212 Persea Bio, LLC 125 206 331 Ares Trading S.A. 1,597 621 2,218 Thrive Agrobiotics, Inc. 46 404 450 Intrexon Energy Partners II, LLC 500 394 894 Exotech Bio, Inc. 139 — 139 Relieve Genetics, Inc. 120 230 350 Intrexon T1D Partners, LLC 278 32 310 Other 2,769 2,134 4,903 Total $ 8,055 $ 19,426 $ 27,481 Three Months Ended June 30, 2015 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 644 $ 4,606 $ 5,250 Oragenics, Inc. 307 68 375 Fibrocell Science, Inc. 448 1,470 1,918 Genopaver, LLC 68 867 935 S & I Ophthalmic, LLC — 890 890 OvaXon, LLC — 662 662 Intrexon Energy Partners, LLC 625 2,731 3,356 Persea Bio, LLC 125 141 266 Ares Trading S.A. 739 — 739 Other 747 2,043 2,790 Total $ 3,703 $ 13,478 $ 17,181 Six Months Ended June 30, 2016 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 1,844 $ 12,107 $ 13,951 Oragenics, Inc. 524 789 1,313 Fibrocell Science, Inc. 1,210 2,041 3,251 Genopaver, LLC 137 3,078 3,215 S & I Ophthalmic, LLC — 3,544 3,544 OvaXon, LLC — 1,502 1,502 Intrexon Energy Partners, LLC 1,250 6,950 8,200 Persea Bio, LLC 250 405 655 Ares Trading S.A. 3,194 1,429 4,623 Thrive Agrobiotics, Inc. 92 792 884 Intrexon Energy Partners II, LLC 1,000 444 1,444 Exotech Bio, Inc. 139 — 139 Relieve Genetics, Inc. 120 230 350 Intrexon T1D Partners, LLC 278 32 310 Other 3,789 4,384 8,173 Total $ 13,827 $ 37,727 $ 51,554 Six Months Ended June 30, 2015 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 1,288 $ 7,763 $ 9,051 Oragenics, Inc. 569 76 645 Fibrocell Science, Inc. 896 3,183 4,079 Genopaver, LLC 137 1,467 1,604 S & I Ophthalmic, LLC — 1,645 1,645 OvaXon, LLC — 1,306 1,306 Intrexon Energy Partners, LLC 1,250 4,916 6,166 Persea Bio, LLC 250 256 506 Ares Trading S.A. 739 — 739 Other 1,605 4,618 6,223 Total $ 6,734 $ 25,230 $ 31,964
Summary of Deferred Revenue	Deferred revenue consists of the following: June 30, December 31, Upfront and milestone payments $ 310,937 $ 181,331 Prepaid research and development services 8,122 10,938 Prepaid product and service revenues 5,471 4,759 Other 709 701 Total $ 325,239 $ 197,729 Current portion of deferred revenue $ 53,863 $ 35,366 Long-term portion of deferred revenue 271,376 162,363 Total $ 325,239 $ 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: June 30, December 31, ZIOPHARM Oncology, Inc. $ 148,494 $ 30,338 Oragenics, Inc. 8,289 8,813 Fibrocell Science, Inc. 20,235 21,445 Genopaver, LLC 2,113 2,250 Intrexon Energy Partners, LLC 19,375 20,625 Persea Bio, LLC 4,250 4,500 Ares Trading S.A. 50,373 53,567 Thrive Agrobiotics, Inc. 1,529 1,621 Intrexon Energy Partners II, LLC 16,833 17,833 Exotech Bio, Inc. 4,861 — Relieve Genetics, Inc. 4,213 — Intrexon T1D Partners, LLC 9,564 — AD Skincare, Inc. 4,333 — Other 16,475 20,339 Total $ 310,937 $ 181,331

Short-term and Long-term Inve32

Short-term and Long-term Investments (Tables)	6 Months Ended
	Jun. 30, 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 June 30, 2016 : Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Aggregate Fair Value U.S. government debt securities $ 165,638 $ 220 $ — $ 165,858 Certificates of deposit 272 — — 272 Total $ 165,910 $ 220 $ — $ 166,130 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 June 30, 2016 was: Due within one year $ 115,667 After one year through two years 50,463 Total $ 166,130

Fair Value Measurements (Tables

Fair Value Measurements (Tables)	6 Months Ended
	Jun. 30, 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 June 30, 2016 : Quoted Prices in Active Markets (Level 1) Significant Other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) June 30, Assets U.S. government debt securities $ — $ 165,858 $ — $ 165,858 Equity securities 31,539 7,481 — 39,020 Preferred stock — — 120,000 120,000 Other — 308 — 308 Total $ 31,539 $ 173,647 $ 120,000 $ 325,186 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)	6 Months Ended
	Jun. 30, 2016
Inventory Disclosure [Abstract]
Schedule of Inventory	Inventory consists of the following: June 30, December 31, Supplies, semen and embryos $ 1,410 $ 1,402 Work in process 6,240 6,290 Livestock 16,062 16,907 Feed 780 1,964 Total inventory $ 24,492 $ 26,563

Property, Plant and Equipment35

Property, Plant and Equipment, Net (Tables)	6 Months Ended
	Jun. 30, 2016
Property, Plant and Equipment [Abstract]
Schedule of Property, Plant and Equipment	Property, plant and equipment consist of the following: June 30, December 31, Land and land improvements $ 9,682 $ 9,119 Buildings and building improvements 7,526 7,520 Furniture and fixtures 2,352 1,283 Equipment 40,312 36,016 Leasehold improvements 7,630 6,888 Computer hardware and software 6,334 5,960 Construction and other assets in progress 2,440 2,193 76,276 68,979 Less: Accumulated depreciation and amortization (29,617 ) (26,240 ) Property, plant and equipment, net $ 46,659 $ 42,739

Goodwill and Intangible Asset36

Goodwill and Intangible Assets, Net (Tables)	6 Months Ended
	Jun. 30, 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 six months ended June 30, 2016 are as follows: Balance at December 31, 2015 $ 165,169 Foreign currency translation adjustments (3,912 ) Balance at June 30, 2016 $ 161,257
Schedule of Intangible Assets	Intangible assets consist of the following at June 30, 2016 : Weighted Average Useful Life (Years) Gross Carrying Amount Accumulated Amortization Net Patents, related technologies and know-how 15.3 $ 170,046 $ (23,654 ) $ 146,392 Customer relationships 6.5 10,700 (3,706 ) 6,994 Trademarks 9.3 6,800 (1,405 ) 5,395 Covenant not to compete 2.0 390 (260 ) 130 In-process research and development 85,403 — 85,403 Total $ 273,339 $ (29,025 ) $ 244,314 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 Term37

Lines of Credit and Long Term Debt (Tables)	6 Months Ended
	Jun. 30, 2016
Debt Disclosure [Abstract]
Schedule of Long Term Debt Instruments	Long term debt consists of the following: June 30, December 31, Notes payable $ 5,884 $ 6,477 Royalty-based financing 1,985 1,807 Other 152 244 Long term debt 8,021 8,528 Less current portion 491 930 Long term debt, less current portion $ 7,530 $ 7,598
Schedule of Future Maturities of Long Term Debt	Future maturities of long term debt are as follows: 2016 $ 298 2017 385 2018 529 2019 343 2020 313 2021 312 Thereafter 3,856 Total $ 6,036

Shareholders' Equity (Tables)

Shareholders' Equity (Tables)	6 Months Ended
	Jun. 30, 2016
Equity [Abstract]
Components of Accumulated Other Comprehensive Loss	The components of accumulated other comprehensive loss are as follows: June 30, December 31, Unrealized gain (loss) on investments $ 220 $ (519 ) Foreign currency translation adjustments (21,871 ) (12,233 ) Total accumulated other comprehensive loss $ (21,651 ) $ (12,752 )

Share-Based Payments (Tables)

Share-Based Payments (Tables)	6 Months Ended
	Jun. 30, 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 Six Months Ended 2016 2015 2016 2015 Cost of products $ 20 $ 21 $ 40 $ 55 Cost of services 70 105 138 203 Research and development 2,178 2,138 4,743 3,907 Selling, general and administrative 4,383 5,616 14,918 13,974 Total $ 6,651 $ 7,880 $ 19,839 $ 18,139
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 3,137,860 30.66 Exercised (1,113,327 ) (15.87 ) Forfeited (1,752,627 ) (45.24 ) Expired (3,909 ) (30.35 ) Balances at June 30, 2016 11,311,525 31.81 8.56 Exercisable at June 30, 2016 2,754,250 25.36 7.15 Vested and Expected to Vest at June 30, 2016(1) 9,441,799 31.39 8.43 (1) The number of stock options expected to vest takes into account an estimate of expected forfeitures.

Commitments and Contingencies (

Commitments and Contingencies (Tables)	6 Months Ended
	Jun. 30, 2016
Commitments and Contingencies Disclosure [Abstract]
Future Minimum Lease Payments Under Noncancelable Operating Leases	At June 30, 2016 , future minimum lease payments under operating leases having initial or remaining noncancelable lease terms in excess of one year are as follows: 2016 $ 1,966 2017 4,401 2018 2,834 2019 2,595 2020 2,647 2021 1,789 Total $ 16,232

Net Loss per Share (Tables)

Net Loss per Share (Tables)	6 Months Ended
	Jun. 30, 2016
Earnings Per Share [Abstract]
Computation of Basic and Diluted Net Loss per Share	The following table presents the computation of basic and diluted net loss per share for the three and six months ended June 30, 2016 and 2015 : Three Months Ended Six Months Ended 2016 2015 2016 2015 Historical net loss per share: Numerator: Net loss attributable to Intrexon $ (49,064 ) $ (40,663 ) $ (113,493 ) $ (13,566 ) Denominator: Weighted average shares outstanding, basic and diluted 118,141,377 109,318,471 117,501,264 107,720,040 Net loss attributable to Intrexon per share, basic and diluted $ (0.42 ) $ (0.37 ) $ (0.97 ) $ (0.13 )
Schedule of Antidilutive Securities Excluded from Computation of Net Loss per Share	The following potentially dilutive securities as of June 30, 2016 and 2015 , have been excluded from the above computations of diluted weighted average shares outstanding for the three and six months then ended, as they would have been anti-dilutive: June 30, 2016 2015 Options 11,311,525 9,503,729 Warrants 45,716 220,021 Total 11,357,241 9,723,750

Organization (Details)

Organization (Details)	Jun. 30, 2016
AquaBounty Technologies, Inc.
Noncontrolling Interest [Line Items]
Parent ownership interest	63.00%
Biological & Popular Culture, Inc.
Noncontrolling Interest [Line Items]
Parent ownership interest	51.00%

Summary of Significant Accoun43

Summary of Significant Accounting Policies - Additional Information (Details) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2016USD ($)	Jun. 30, 2015USD ($)	Jun. 30, 2016USD ($)segment	Jun. 30, 2015USD ($)	Dec. 31, 2015USD ($)
Organization And Significant Accounting Policies [Line Items]
Fair value of financial assets measured at fair value on a recurring basis	$ 325,186		$ 325,186		$ 291,762
Maximum risk of loss related to the identified VIEs	137,920		$ 137,920		3,598
Number of segments | segment			1
Property, plant and equipment, net	46,659		$ 46,659		42,739
Revenues	52,501	$ 44,891	95,939	$ 78,740
Foreign Countries
Organization And Significant Accounting Policies [Line Items]
Property, plant and equipment, net	5,666		5,666		3,877
Revenues	2,680	925	5,176	2,263
Equity securities
Organization And Significant Accounting Policies [Line Items]
Fair value of financial assets measured at fair value on a recurring basis	$ 39,020		$ 39,020		$ 83,653
Oragenics, Inc.
Organization And Significant Accounting Policies [Line Items]
Company's ownership percentage	29.50%		29.50%		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	$ 6,626		$ 6,626		$ 16,601
Unrealized appreciation (depreciation) in fair value of equity securities	$ (4,797)	$ 2,943	$ (11,142)	$ 3,879

Summary of Significant Accoun44

Summary of Significant Accounting Policies - Summarized Unaudited Financial Information for the Equity Method Investments (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015	Dec. 31, 2015
Schedule of Equity Method Investments [Line Items]
Operating expenses	$ 75,723	$ 62,321	$ 159,694	$ 183,293
Operating loss	(23,222)	(17,430)	(63,755)	(104,553)
Other	(22,347)	(20,950)	(43,772)	94,728
Equity Method Investments
Schedule of Equity Method Investments [Line Items]
Current assets	70,182		70,182		$ 28,123
Non-current assets	11,059		11,059		1,539
Total assets	81,241		81,241		29,662
Current liabilities	7,633		7,633		6,274
Net assets	73,608		73,608		$ 23,388
Revenues	47	514	329	1,150
Operating expenses	14,383	25,424	32,043	109,493
Operating loss	(14,336)	(24,910)	(31,714)	(108,343)
Other	1,424	4	1,427	3
Net loss	$ (12,912)	$ (24,906)	$ (30,287)	$ (108,340)

Mergers and Acquisitions - Oxit

Mergers and Acquisitions - Oxitec - Additional Information (Details) - Oxitec Limited $ in Thousands	1 Months Ended
	Sep. 30, 2015USD ($)shares
Business Acquisition [Line Items]
Percentage of outstanding common stock acquired	100.00%
Consideration transferred, shares issued or issuable | shares	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 | shares	480,422
Cash consideration withheld as escrow	$ 1,991
Consideration withheld as escrow, transfer period after closing	18 months
Consideration transferred	$ 146,394
Selling, general and administrative
Business Acquisition [Line Items]
Acquisition related costs	$ 1,675

Mergers and Acquisitions - Ox46

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 - Ox47

Mergers and Acquisitions - Oxitec - Fair Value of Assets Acquired and Liabilities Assumed (Details) - USD ($) $ in Thousands	Jun. 30, 2016	Dec. 31, 2015	Sep. 30, 2015
Business Acquisition [Line Items]
Goodwill	$ 161,257	$ 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	6 Months Ended
	Apr. 30, 2015	Jun. 30, 2015	Jun. 30, 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		$ 104	$ 267

Mergers and Acquisitions - Ok49

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 - Ok50

Mergers and Acquisitions - Okanagan - Fair Value of Assets Acquired and Liabilities Assumed (Details) - USD ($) $ in Thousands	Jun. 30, 2016	Dec. 31, 2015	Apr. 30, 2015
Business Acquisition [Line Items]
Goodwill	$ 161,257	$ 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		6 Months Ended
	Aug. 31, 2015	Feb. 28, 2015	Jun. 30, 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			$ 381

Mergers and Acquisitions - Ac52

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 - Ac53

Mergers and Acquisitions - ActoGeniX - Fair Value of Assets Acquired and Liabilities Assumed (Details) - USD ($) $ in Thousands	Jun. 30, 2016	Dec. 31, 2015	Feb. 28, 2015
Business Acquisition [Line Items]
Goodwill	$ 161,257	$ 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		6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Business Acquisition, Pro Forma Information, Nonrecurring Adjustment [Line Items]
Loss before income taxes	$ (50,622)	$ (40,560)	$ (118,223)	$ (13,961)
Net loss	(50,031)	(41,494)	(115,351)	(15,690)
Net loss attributable to the noncontrolling interests	$ 967	831	$ 1,858	2,124
2015 Business Acquisitions | Pro Forma
Business Acquisition, Pro Forma Information, Nonrecurring Adjustment [Line Items]
Revenues		45,083		79,310
Loss before income taxes		(42,832)		(22,584)
Net loss		(43,723)		(23,176)
Net loss attributable to the noncontrolling interests		831		2,124
Net loss attributable to Intrexon		$ (42,892)		$ (21,052)

Investments in Joint Ventures -

Investments in Joint Ventures - Intrexon T1D Partners - Additional Information (Details) - Intrexon T1D Partners, LLC	1 Months Ended
	Mar. 31, 2016USD ($)	Jun. 30, 2016USD ($)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 Ventures56

Investments in Joint Ventures - EnviroFlight - Additional Information (Details) - USD ($)	1 Months Ended	6 Months Ended
	Feb. 29, 2016	Jun. 30, 2016	Jun. 30, 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		22,714,000		$ 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		4,973,000
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 Ventures57

Investments in Joint Ventures - Intrexon Energy Partners II - Additional Information (Details)	1 Months Ended
	Dec. 31, 2015USD ($)	Jun. 30, 2016USD ($)board_seat
Schedule Of Investments In Joint Venture [Line Items]
Investment	$ 9,977,000	$ 22,714,000
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	$ 1,777,000
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 Ventures58

Investments in Joint Ventures - Intrexon Energy Partners - Additional Information (Details)	1 Months Ended
	Mar. 31, 2014USD ($)	Jun. 30, 2016USD ($)board_seat	Dec. 31, 2015USD ($)
Schedule Of Investments In Joint Venture [Line Items]
Investment		$ 22,714,000	$ 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		$ 14,378,000
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		$ (483,000)	$ (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 Ventures59

Investments in Joint Ventures - OvaXon - Additional Information (Details)	1 Months Ended
	Jan. 31, 2014USD ($)	Jun. 30, 2016USD ($)board_seat	Dec. 31, 2015USD ($)
Schedule Of Investments In Joint Venture [Line Items]
Investment		$ 22,714,000	$ 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 | Other Accrued Liabilities
Schedule Of Investments In Joint Venture [Line Items]
Investment		$ (201,000)	$ (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 Ventures60

Investments in Joint Ventures - S & I Ophthalmic - Additional Information (Details)	1 Months Ended	33 Months Ended
	Oct. 31, 2013USD ($)	Jun. 30, 2016USD ($)board_seat	Dec. 31, 2015USD ($)
Schedule Of Investments In Joint Venture [Line Items]
Investment		$ 22,714,000	$ 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		$ 4,794,000	$ 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 R61

Collaboration and Licensing Revenue - Summarized Collaboration and Licensing Revenues (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	$ 27,481	$ 17,181	$ 51,554	$ 31,964
Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	8,055	3,703	13,827	6,734
Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	19,426	13,478	37,727	25,230
ZIOPHARM Oncology, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	6,970	5,250	13,951	9,051
ZIOPHARM Oncology, Inc. | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	922	644	1,844	1,288
ZIOPHARM Oncology, Inc. | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	6,048	4,606	12,107	7,763
Oragenics, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	507	375	1,313	645
Oragenics, Inc. | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	261	307	524	569
Oragenics, Inc. | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	246	68	789	76
Fibrocell Science, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,394	1,918	3,251	4,079
Fibrocell Science, Inc. | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	605	448	1,210	896
Fibrocell Science, Inc. | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	789	1,470	2,041	3,183
Genopaver, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,637	935	3,215	1,604
Genopaver, LLC | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	68	68	137	137
Genopaver, LLC | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,569	867	3,078	1,467
S & I Ophthalmic, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	2,358	890	3,544	1,645
S & I Ophthalmic, LLC | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	0	0	0	0
S & I Ophthalmic, LLC | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	2,358	890	3,544	1,645
OvaXon, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	808	662	1,502	1,306
OvaXon, LLC | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	0	0	0	0
OvaXon, LLC | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	808	662	1,502	1,306
Intrexon Energy Partners, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	4,212	3,356	8,200	6,166
Intrexon Energy Partners, LLC | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	625	625	1,250	1,250
Intrexon Energy Partners, LLC | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	3,587	2,731	6,950	4,916
Persea Bio, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	331	266	655	506
Persea Bio, LLC | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	125	125	250	250
Persea Bio, LLC | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	206	141	405	256
Ares Trading S.A.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	2,218	739	4,623	739
Ares Trading S.A. | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,597	739	3,194	739
Ares Trading S.A. | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	621	0	1,429	0
Thrive Agrobiotics, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	450		884
Thrive Agrobiotics, Inc. | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	46		92
Thrive Agrobiotics, Inc. | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	404		792
Intrexon Energy Partners II, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	894		1,444
Intrexon Energy Partners II, LLC | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	500		1,000
Intrexon Energy Partners II, LLC | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	394		444
Exotech Bio, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	139		139
Exotech Bio, Inc. | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	139		139
Exotech Bio, Inc. | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	0		0
Relieve Genetics, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	350		350
Relieve Genetics, Inc. | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	120		120
Relieve Genetics, Inc. | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	230		230
Intrexon T1D Partners, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	310		310
Intrexon T1D Partners, LLC | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	278		278
Intrexon T1D Partners, LLC | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	32		32
Other
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	4,903	2,790	8,173	6,223
Other | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	2,769	747	3,789	1,605
Other | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	$ 2,134	$ 2,043	$ 4,384	$ 4,618

Collaboration and Licensing R62

Collaboration and Licensing Revenue - Additional Information (Details) - USD ($)	1 Months Ended		5 Months Ended
	Jun. 30, 2016	Mar. 31, 2016	May 31, 2016
Exotech Bio, Inc.
Collaboration and Licensing Agreements [Line Items]
Required notice period for voluntary termination of collaborative agreement		90 days
Exotech Bio, Inc. | Maximum
Collaboration and Licensing Agreements [Line Items]
Milestone payments required upon successful achievement, per product		$ 52,500,000
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]
Required notice period for voluntary termination of collaborative agreement		90 days
Relieve Genetics, Inc. | Maximum
Collaboration and Licensing Agreements [Line Items]
Milestone payments required upon successful achievement, per product		$ 52,500,000
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
AD Skincare, Inc.
Collaboration and Licensing Agreements [Line Items]
Required notice period for voluntary termination of collaborative agreement	90 days
AD Skincare, Inc. | Maximum
Collaboration and Licensing Agreements [Line Items]
Milestone payments required upon successful achievement, per product	$ 2,000,000
Maximum milestone payments required upon successful achievement, one-time	17,000,000
AD Skincare, Inc. | Upfront | Upfront and Milestone Payments
Collaboration and Licensing Agreements [Line Items]
Collaborative arrangement consideration received, value	$ 4,333,000
ZIOPHARM Oncology, Inc.
Collaboration and Licensing Agreements [Line Items]
Royalty rate as a percentage of net profit	20.00%		50.00%
ZIOPHARM Oncology, Inc. | Other Contractual Payments | Upfront and Milestone Payments
Collaboration and Licensing Agreements [Line Items]
Collaborative arrangement consideration received, value	$ 120,000,000
Collaborative arrangement consideration received, number of preferred shares	100,000

Collaboration and Licensing R63

Collaboration and Licensing Revenue - Summary of Deferred Revenue (Details) - USD ($) $ in Thousands	Jun. 30, 2016	Dec. 31, 2015
Deferred Revenue Arrangement [Line Items]
Deferred revenue	$ 325,239	$ 197,729
Current portion of deferred revenue	53,863	35,366
Long-term portion of deferred revenue	271,376	162,363
Upfront and milestone payments
Deferred Revenue Arrangement [Line Items]
Deferred revenue	310,937	181,331
Prepaid research and development services
Deferred Revenue Arrangement [Line Items]
Deferred revenue	8,122	10,938
Prepaid product and service revenues
Deferred Revenue Arrangement [Line Items]
Deferred revenue	5,471	4,759
Other
Deferred Revenue Arrangement [Line Items]
Deferred revenue	$ 709	$ 701

Collaboration and Licensing R64

Collaboration and Licensing Revenue - Summary of Deferred Revenue by Collaborator (Details) - USD ($) $ in Thousands	Jun. 30, 2016	Dec. 31, 2015
Deferred Revenue Arrangement [Line Items]
Deferred revenue	$ 325,239	$ 197,729
Upfront and Milestone Payments
Deferred Revenue Arrangement [Line Items]
Deferred revenue	310,937	181,331
Upfront and Milestone Payments | ZIOPHARM Oncology, Inc.
Deferred Revenue Arrangement [Line Items]
Deferred revenue	148,494	30,338
Upfront and Milestone Payments | Oragenics, Inc.
Deferred Revenue Arrangement [Line Items]
Deferred revenue	8,289	8,813
Upfront and Milestone Payments | Fibrocell Science, Inc.
Deferred Revenue Arrangement [Line Items]
Deferred revenue	20,235	21,445
Upfront and Milestone Payments | Genopaver, LLC
Deferred Revenue Arrangement [Line Items]
Deferred revenue	2,113	2,250
Upfront and Milestone Payments | Intrexon Energy Partners, LLC
Deferred Revenue Arrangement [Line Items]
Deferred revenue	19,375	20,625
Upfront and Milestone Payments | Persea Bio, LLC
Deferred Revenue Arrangement [Line Items]
Deferred revenue	4,250	4,500
Upfront and Milestone Payments | Ares Trading S.A.
Deferred Revenue Arrangement [Line Items]
Deferred revenue	50,373	53,567
Upfront and Milestone Payments | Thrive Agrobiotics, Inc.
Deferred Revenue Arrangement [Line Items]
Deferred revenue	1,529	1,621
Upfront and Milestone Payments | Intrexon Energy Partners II, LLC
Deferred Revenue Arrangement [Line Items]
Deferred revenue	16,833	17,833
Upfront and Milestone Payments | Exotech Bio, Inc.
Deferred Revenue Arrangement [Line Items]
Deferred revenue	4,861	0
Upfront and Milestone Payments | Relieve Genetics, Inc.
Deferred Revenue Arrangement [Line Items]
Deferred revenue	4,213	0
Upfront and Milestone Payments | Intrexon T1D Partners, LLC
Deferred Revenue Arrangement [Line Items]
Deferred revenue	9,564	0
Upfront and Milestone Payments | AD Skincare, Inc.
Deferred Revenue Arrangement [Line Items]
Deferred revenue	4,333	0
Upfront and Milestone Payments | Other
Deferred Revenue Arrangement [Line Items]
Deferred revenue	$ 16,475	$ 20,339

Short-term and Long-term Inve65

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	Jun. 30, 2016	Dec. 31, 2015
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	$ 165,910	$ 208,494
Gross Unrealized Gains	220	21
Gross Unrealized Losses	0	(540)
Aggregate Fair Value	166,130	207,975
U.S. government debt securities
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	165,638	208,223
Gross Unrealized Gains	220	21
Gross Unrealized Losses	0	(540)
Aggregate Fair Value	165,858	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 Inve66

Short-term and Long-term Investments - Summary of Estimated Fair Value of Available-for-Sale Investments Classified by Contractual Maturities (Details) - USD ($) $ in Thousands	Jun. 30, 2016	Dec. 31, 2015
Investments, Debt and Equity Securities [Abstract]
Due within one year	$ 115,667
After one year through two years	50,463
Total	$ 166,130	$ 207,975

Investment in Preferred Stock (

Investment in Preferred Stock (Details) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended	6 Months Ended
	Jun. 30, 2016	Jun. 30, 2016	Dec. 31, 2015
Schedule of Investments [Line Items]
Fair value of financial assets measured at fair value on a recurring basis	$ 325,186	$ 325,186	$ 291,762
Preferred stock
Schedule of Investments [Line Items]
Fair value of financial assets measured at fair value on a recurring basis	$ 120,000	$ 120,000
ZIOPHARM Oncology, Inc.
Schedule of Investments [Line Items]
Preferred shares, stated value (in usd per share)	$ 1,200	$ 1,200
Threshold consecutive trading days, conversion of shares		20 days
Preferred shares, dividend rate (in usd per share)		$ 12
Preferred shares, dividend rate, for unconverted shares after conversion event (in usd per share)		24
ZIOPHARM Oncology, Inc. | Minimum
Schedule of Investments [Line Items]
Preferred shares, conversion calculation, divisor (in usd per share)		$ 1
Other Contractual Payments | Upfront and Milestone Payments | ZIOPHARM Oncology, Inc.
Schedule of Investments [Line Items]
Collaborative arrangement consideration received, number of preferred shares	100,000

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	Jun. 30, 2016	Dec. 31, 2015
Assets
Fair value of financial assets measured at fair value on a recurring basis	$ 325,186	$ 291,762
U.S. government debt securities
Assets
Fair value of financial assets measured at fair value on a recurring basis	165,858	207,704
Equity securities
Assets
Fair value of financial assets measured at fair value on a recurring basis	39,020	83,653
Preferred stock
Assets
Fair value of financial assets measured at fair value on a recurring basis	120,000
Other
Assets
Fair value of financial assets measured at fair value on a recurring basis	308	405
Quoted Prices in Active Markets (Level 1)
Assets
Fair value of financial assets measured at fair value on a recurring basis	31,539	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	31,539	65,850
Quoted Prices in Active Markets (Level 1) | Preferred stock
Assets
Fair value of financial assets measured at fair value on a recurring basis	0
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	173,647	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	165,858	207,704
Significant Other Observable Inputs (Level 2) | Equity securities
Assets
Fair value of financial assets measured at fair value on a recurring basis	7,481	17,803
Significant Other Observable Inputs (Level 2) | Preferred stock
Assets
Fair value of financial assets measured at fair value on a recurring basis	0
Significant Other Observable Inputs (Level 2) | Other
Assets
Fair value of financial assets measured at fair value on a recurring basis	308	405
Significant Unobservable Inputs (Level 3)
Assets
Fair value of financial assets measured at fair value on a recurring basis	120,000	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) | Preferred stock
Assets
Fair value of financial assets measured at fair value on a recurring basis	120,000
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) $ in Thousands	Jun. 30, 2016USD ($)
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

Inventory (Details)

Inventory (Details) - USD ($) $ in Thousands	Jun. 30, 2016	Dec. 31, 2015
Inventory [Line Items]
Inventory	$ 24,492	$ 26,563
Supplies, semen and embryos
Inventory [Line Items]
Inventory	1,410	1,402
Work in process
Inventory [Line Items]
Inventory	6,240	6,290
Livestock
Inventory [Line Items]
Inventory	16,062	16,907
Feed
Inventory [Line Items]
Inventory	$ 780	$ 1,964

Property, Plant and Equipment71

Property, Plant and Equipment, Net - Schedule of Property, Plant and Equipment (Details) - USD ($) $ in Thousands	Jun. 30, 2016	Dec. 31, 2015
Property, Plant and Equipment [Abstract]
Land and land improvements	$ 9,682	$ 9,119
Buildings and building improvements	7,526	7,520
Furniture and fixtures	2,352	1,283
Equipment	40,312	36,016
Leasehold improvements	7,630	6,888
Computer hardware and software	6,334	5,960
Construction and other assets in progress	2,440	2,193
Property, plant and equipment, gross	76,276	68,979
Less: Accumulated depreciation and amortization	(29,617)	(26,240)
Property, plant and equipment, net	$ 46,659	$ 42,739

Property, Plant and Equipment72

Property, Plant and Equipment, Net - Additional Information (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Property, Plant and Equipment [Abstract]
Depreciation expense	$ 2,304	$ 1,828	$ 4,437	$ 3,781

Goodwill and Intangible Asset73

Goodwill and Intangible Assets, Net - Schedule of Changes in Carrying Amount of Goodwill (Details) $ in Thousands	6 Months Ended
	Jun. 30, 2016USD ($)
Goodwill
Beginning balance	$ 165,169
Foreign currency translation adjustments	(3,912)
Ending balance	$ 161,257

Goodwill and Intangible Asset74

Goodwill and Intangible Assets, Net - Additional Information (Details) - USD ($)	3 Months Ended		6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015	Dec. 31, 2015
Goodwill and Intangible Assets Disclosure [Abstract]
Goodwill accumulated impairment losses	$ 0		$ 0		$ 0
Amortization expense	$ 3,722,000	$ 1,981,000	$ 7,237,000	$ 3,577,000

Goodwill and Intangible Asset75

Goodwill and Intangible Assets, Net - Schedule of Intangible Assets (Details) - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2016	Dec. 31, 2015
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	$ 273,339	$ 269,227
Accumulated Amortization	(29,025)	(21,692)
Net	244,314	247,535
Patents, related technologies and know-how
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	170,046	157,411
Accumulated Amortization	(23,654)	(17,775)
Net	146,392	139,636
Customer relationships
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	10,700	10,700
Accumulated Amortization	(3,706)	(2,739)
Net	6,994	7,961
Trademarks
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	6,800	6,800
Accumulated Amortization	(1,405)	(1,018)
Net	5,395	5,782
Covenant not to compete
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	390	384
Accumulated Amortization	(260)	(160)
Net	130	224
In-process research and development
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	85,403	93,932
Accumulated Amortization	0	0
Net	$ 85,403	$ 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 Term76

Lines of Credit and Long Term Debt - Lines of Credit - Additional Information (Details) - Revolving Line of Credit	6 Months Ended
	Jun. 30, 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	3.41%
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	$ 461,000

Lines of Credit and Long Term77

Lines of Credit and Long Term Debt - Schedule of Long Term Debt Instruments (Details) - USD ($) $ in Thousands	Jun. 30, 2016	Dec. 31, 2015
Debt Instrument [Line Items]
Long term debt	$ 8,021	$ 8,528
Less current portion	491	930
Long term debt, net of current portion	7,530	7,598
Notes payable
Debt Instrument [Line Items]
Long term debt	5,884	6,477
Royalty-based financing
Debt Instrument [Line Items]
Long term debt	1,985	1,807
Other
Debt Instrument [Line Items]
Long term debt	$ 152	$ 244

Lines of Credit and Long Term78

Lines of Credit and Long Term Debt - Long Term Debt - Additional Information (Details) - USD ($)	6 Months Ended
	Jun. 30, 2016	Dec. 31, 2015	Mar. 31, 2013
Debt Instrument [Line Items]
Long term debt	$ 8,021,000	$ 8,528,000
Notes payable to banks | Trans Ova Genetics, LC | American State Bank
Debt Instrument [Line Items]
Long term debt	5,428,000
Debt instrument, periodic payment	$ 39,000
Debt instrument, interest rate, stated percentage	3.95%
Notes payable
Debt Instrument [Line Items]
Long term debt	$ 5,884,000	6,477,000
Notes payable | Exemplar Genetics, LLC
Debt Instrument [Line Items]
Long term debt	456,000
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	$ 1,985,000	$ 1,807,000
Royalty-based financing | AquaBounty Technologies, Inc. | Atlantic Canada Opportunities Agency
Debt Instrument [Line Items]
Long term debt	1,985,000
Amount available under the grant for research and development	$ 2,216,000
Claims period	5 years
Royalty on products, percentage	10.00%
Amount claimed			$ 1,952,000
Long term debt, fair value at date of business combination			1,107,000
Accreted difference between face value of amount drawn and acquisition date fair value			$ 845,000

Lines of Credit and Long Term79

Lines of Credit and Long Term Debt - Schedule of Future Maturities of Long Term Debt (Details) $ in Thousands	Jun. 30, 2016USD ($)
Debt Disclosure [Abstract]
2,016	$ 298
2,017	385
2,018	529
2,019	343
2,020	313
2,021	312
Thereafter	3,856
Total	$ 6,036

Income Taxes (Details)

Income Taxes (Details) - USD ($)	3 Months Ended		6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Operating Loss Carryforwards [Line Items]
Deferred income tax expense (benefit)	$ (471,000)	$ 157,000	$ (2,659,000)	$ 952,000
Deferred tax liabilities	18,680,000		18,680,000
Domestic Tax Authority
Operating Loss Carryforwards [Line Items]
Taxable income (loss)	(7,780,000)	65,400,000	(17,680,000)	38,800,000
Current income tax expense (benefit)	0	$ 777,000	0	$ 777,000
Operating loss carryforwards	266,400,000		266,400,000
Federal and state research and development tax credits	6,770,000		$ 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	53,400,000		$ 53,400,000
Foreign Tax Authority
Operating Loss Carryforwards [Line Items]
Current income tax expense (benefit)	(120,000)		(213,000)
Operating loss carryforwards	$ 117,900,000		$ 117,900,000

Shareholders' Equity - Dividend

Shareholders' Equity - Dividend to Shareholders (Details) $ / shares in Units, $ in Thousands	1 Months Ended
	Jun. 30, 2015USD ($)$ / sharesshares
Intrexon Stock Option Plans
Class of Stock [Line Items]
Adjustment due to dividend (in shares)	312,795
Adjustment due to dividend (in usd per share) | $ / shares	$ 25.40
ZIOPHARM Oncology, Inc.
Class of Stock [Line Items]
Noncash dividend, shares	17,830,305
Realized investment gains | $	$ 81,401

Shareholders' Equity - Componen

Shareholders' Equity - Components of Accumulated Other Comprehensive Loss (Details) - USD ($) $ in Thousands	Jun. 30, 2016	Dec. 31, 2015
Accumulated Other Comprehensive Income (Loss) [Line Items]
Total accumulated other comprehensive loss	$ (21,651)	$ (12,752)
Unrealized gain (loss) on investments
Accumulated Other Comprehensive Income (Loss) [Line Items]
Total accumulated other comprehensive loss	220	(519)
Foreign currency translation adjustments
Accumulated Other Comprehensive Income (Loss) [Line Items]
Total accumulated other comprehensive loss	$ (21,871)	$ (12,233)

Share-Based Payments - Schedule

Share-Based Payments - Schedule of Stock-Based Compensation Expense (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation costs	$ 6,651	$ 7,880	$ 19,839	$ 18,139
Cost of products
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation costs	20	21	40	55
Cost of services
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation costs	70	105	138	203
Research and development
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation costs	2,178	2,138	4,743	3,907
Selling, general and administrative
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation costs	$ 4,383	$ 5,616	$ 14,918	$ 13,974

Share-Based Payments - Addition

Share-Based Payments - Additional Information (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended	6 Months Ended
	Jun. 30, 2016	Jun. 30, 2016	Apr. 30, 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	$ 463	$ 934
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)	597,491	597,491
Intrexon Stock Option Plan - 2013 Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Remaining shares available to grant	3,936,628	3,936,628
Options outstanding (in shares)	10,714,034	10,714,034
Number of shares authorized for issuance	16,000,000	16,000,000
Intrexon Stock Option Plans
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Options outstanding (in shares)	11,311,525	11,311,525		11,043,528
Unrecognized compensation costs related to nonvested awards	$ 106,977	$ 106,977		$ 113,655
Recognized over weighted-average period		3 years
Weighted average exercise price of option (in usd per share)	$ 31.81	$ 31.81		$ 32.66
Shares exercisable at end of period	2,754,250	2,754,250
AquaBounty Stock Option Plan - 2006 Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Remaining shares available to grant			0
Options outstanding (in shares)	5,607,000	5,607,000		5,382,000
Weighted average exercise price of option (in usd per share)	$ 0.26	$ 0.26		$ 0.26
Shares exercisable at end of period	5,231,040	5,231,040		4,320,333
AquaBounty Stock Option Plan - 2016 Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Options outstanding (in shares)	0	0

Share-Based Payments - Schedu85

Share-Based Payments - Schedule of Stock Option Activity (Details) - Intrexon Stock Option Plans - $ / shares	6 Months Ended	12 Months Ended
	Jun. 30, 2016	Dec. 31, 2015
Number of Shares
Balances at beginning of period (in shares)	11,043,528
Granted (in shares)	3,137,860
Exercised (in shares)	(1,113,327)
Forfeited (in shares)	(1,752,627)
Expired (in shares)	(3,909)
Balances at end of period (in shares)	11,311,525	11,043,528
Exercisable at end of period (in shares)	2,754,250
Vested and Expected to Vest at end of period (in shares)	9,441,799
Weighted Average Exercise Price
Balances at beginning of period (in usd per share)	$ 32.66
Granted (in usd per share)	30.66
Exercised (in usd per share)	(15.87)
Forfeited (in usd per share)	(45.24)
Expired (in usd per share)	(30.35)
Balances at period end (in usd per share)	31.81	$ 32.66
Exercisable, weighted average exercise price, at end of period (in usd per share)	25.36
Vested and Expected to Vest, weighted average exercise price at end of period (in usd per share)	$ 31.39
Weighted Average Remaining Contractual Term (Years)
Balances, weighted average remaining contractual period	8 years 6 months 22 days	8 years 5 months 27 days
Exercisable at period end, weighted average remaining contractual period	7 years 1 month 24 days
Vested and Expected to Vest at period end, weighted average remaining contractual period	8 years 5 months 5 days

License Agreement (Details)

License Agreement (Details)	1 Months Ended
	Jan. 31, 2015USD ($)shares
Other Commitments [Line Items]
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	Jun. 30, 2016USD ($)
Commitments and Contingencies Disclosure [Abstract]
2,016	$ 1,966
2,017	4,401
2,018	2,834
2,019	2,595
2,020	2,647
2,021	1,789
Total	$ 16,232

Commitments and Contingencies88

Commitments and Contingencies - Operating Leases - Additional Information (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Commitments and Contingencies Disclosure [Abstract]
Rent expense	$ 2,302	$ 2,247	$ 4,334	$ 4,381
Rental income under sublease agreement	335	$ 394	670	$ 819
Future rental income under sublease agreements, 2016	17		17
Future rental income under sublease agreements, 2017	$ 36		$ 36

Commitments and Contingencies89

Commitments and Contingencies - Contingencies - Additional Information (Details) $ in Thousands	1 Months Ended		6 Months Ended	50 Months Ended
	May 31, 2016claim	Apr. 30, 2016USD ($)	Jun. 30, 2016USD ($)	Apr. 30, 2016USD ($)
Licensing and patent infringement suit
Loss Contingencies [Line Items]
Damages awarded to (against) Trans Ova		$ 528
Cumulative payments for royalties and licenses				$ 3,170
Royalties payments not yet deposited			$ 2,759
Licensing and patent infringement suit | Selling, general and administrative
Loss Contingencies [Line Items]
Litigation settlement expense			$ 4,228
Licensing and patent infringement suit | XY, LLC
Loss Contingencies [Line Items]
Damages awarded to (against) Trans Ova		$ (6,066)
Hoffman v. Intrexon Corporation et al. and Gibrall v. Intrexon Corporation et al.
Loss Contingencies [Line Items]
Number of lawsuits | claim	2

Related Party Transactions (Det

Related Party Transactions (Details) - USD ($)	1 Months Ended			3 Months Ended		6 Months Ended
	Jun. 30, 2016	Nov. 30, 2015	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Related Party Transaction [Line Items]
Shares issued as payment for services						$ 5,689,000
Collaboration and licensing revenues				$ 27,481,000	$ 17,181,000	51,554,000	$ 31,964,000
Third Security, LLC
Related Party Transaction [Line Items]
Expense for services				$ 99,000	111,000	$ 145,000	152,000
Initial term of services agreement		1 year
Shares issued as payment for services (in shares)				85,300		165,170
Shares issued as payment for services				$ 2,143,000		$ 4,410,000
Third Security, LLC | Common Stock
Related Party Transaction [Line Items]
Expense for services		$ 800,000
Oragenics, Inc.
Related Party Transaction [Line Items]
Common stock purchased from collaborative partners, shares	2,261,419
Price per share of common shares (usd per share)	$ 0.52			$ 0.52		$ 0.52
Oragenics, Inc. | Maximum
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%			30.00%		30.00%
Common stock purchase commitment	$ 8,833,000		$ 10,000,000	$ 8,833,000	10,000,000	$ 8,833,000	10,000,000
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				23,612,000	$ 15,239,000	43,611,000	$ 28,035,000
Harvest Intrexon Enterprise Fund I, LP | Other nonoperating income
Related Party Transaction [Line Items]
Management fees revenue				$ 613,000		$ 1,258,000

Net Loss per Share - Computatio

Net Loss per Share - Computation of Basic and Diluted Net Loss Per Share (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Numerator:
Net loss attributable to Intrexon	$ (49,064)	$ (40,663)	$ (113,493)	$ (13,566)
Denominator:
Weighted average shares outstanding, basic and diluted	118,141,377	109,318,471	117,501,264	107,720,040
Net loss attributable to Intrexon per share, basic and diluted (in usd per share)	$ (0.42)	$ (0.37)	$ (0.97)	$ (0.13)

Net Loss per Share - Schedule o

Net Loss per Share - Schedule of Antidilutive Securities Excluded from Calculation of Net Loss per Share (Details) - shares	3 Months Ended		6 Months Ended
	Jun. 30, 2016	Jun. 30, 2015	Jun. 30, 2016	Jun. 30, 2015
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of net loss per share (in shares)	11,357,241	9,723,750	11,357,241	9,723,750
Options
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of net loss per share (in shares)	11,311,525	9,503,729	11,311,525	9,503,729
Warrants
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of net loss per share (in shares)	45,716	220,021	45,716	220,021

Subsequent Events (Details)

Subsequent Events (Details) - USD ($)	1 Months Ended
	Jul. 31, 2016	Jan. 01, 2017	Sep. 30, 2016	Jun. 30, 2016
Subsequent Event [Line Items]
Total future minimum lease payments under operating leases				$ 16,232,000
Subsequent Event | Scenario, Forecast | Land Lease
Subsequent Event [Line Items]
Total future minimum lease payments under operating leases		$ 8,300,000
Notice period to terminate lease	6 months
Subsequent Event | Scenario, Forecast | Maximum | Convertible Debt | Fibrocell Science, Inc.
Subsequent Event [Line Items]
Total approved future financing, convertible debt			$ 25,000,000