Precigen (PGEN) 10-Q 9 Nov 16 2016 Q3 Quarterly report Financial data

Document and Entity Information

Document and Entity Information - shares	9 Months Ended
	Sep. 30, 2016	Oct. 31, 2016
Document And Entity Information [Abstract]
Document Type	10-Q
Amendment Flag	false
Document Period End Date	Sep. 30, 2016
Document Fiscal Year Focus	2,016
Document Fiscal Period Focus	Q3
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		118,575,964

Consolidated Balance Sheets

Consolidated Balance Sheets - USD ($) $ in Thousands	Sep. 30, 2016	Dec. 31, 2015
Current assets
Cash and cash equivalents	$ 69,707	$ 135,782
Restricted cash	6,987	0
Short-term investments	166,839	102,528
Receivables
Trade, net	22,034	25,101
Related parties	16,159	23,597
Notes, net	1,505	601
Other	2,521	2,995
Inventory	21,880	26,563
Prepaid expenses and other	8,591	6,634
Total current assets	316,223	323,801
Long-term investments	44,122	105,447
Equity securities	39,432	83,653
Investment in preferred stock	123,676	0
Property, plant and equipment, net	54,429	42,739
Intangible assets, net	238,581	247,535
Goodwill	159,793	165,169
Investments in affiliates	25,847	9,977
Other assets	3,485	3,725
Total assets	1,005,588	982,046
Current liabilities
Accounts payable	7,866	4,967
Accrued compensation and benefits	11,011	19,050
Other accrued liabilities	16,353	7,949
Deferred revenue	54,937	35,366
Lines of credit	549	561
Current portion of long term debt	471	930
Current portion of deferred consideration	8,723	6,931
Related party payables	611	150
Total current liabilities	100,521	75,904
Long term debt, net of current portion	7,950	7,598
Deferred consideration, net of current portion	0	8,698
Deferred revenue, net of current portion	267,460	162,363
Deferred tax liabilities	18,060	21,802
Other long term liabilities	3,177	795
Total liabilities	397,168	277,160
Commitments and contingencies (Note 17)
Total equity
Common stock, no par value, 200,000,000 shares authorized as of September 30, 2016 and December 31, 2015; 118,446,717 and 116,658,886 shares issued and outstanding as of September 30, 2016 and December 31, 2015, respectively	0	0
Additional paid-in capital	1,310,979	1,249,559
Accumulated deficit	(685,204)	(542,729)
Accumulated other comprehensive loss	(25,302)	(12,752)
Total Intrexon shareholders' equity	600,473	694,078
Noncontrolling interests	7,947	10,808
Total equity	608,420	704,886
Total liabilities and total equity	$ 1,005,588	$ 982,046

Consolidated Balance Sheets (Pa

Consolidated Balance Sheets (Parenthetical) - shares	Sep. 30, 2016	Dec. 31, 2015
Statement of Financial Position [Abstract]
Common stock, shares authorized	200,000,000	200,000,000
Common stock, shares issued	118,446,717	116,658,886
Common stock, shares outstanding	118,446,717	116,658,886

Consolidated Statements of Oper

Consolidated Statements of Operations - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Revenues
Collaboration and licensing revenues	$ 30,590	$ 34,726	$ 82,144	$ 66,690
Product revenues	9,260	9,446	28,699	32,645
Service revenues	8,706	8,945	33,298	32,157
Other revenues	429	250	783	615
Total revenues	48,985	53,367	144,924	132,107
Operating Expenses
Cost of products	9,156	11,215	29,471	31,654
Cost of services	5,803	5,451	17,807	17,316
Research and development	29,035	21,598	83,266	121,286
Selling, general and administrative	33,812	23,019	106,956	74,320
Total operating expenses	77,806	61,283	237,500	244,576
Operating loss	(28,821)	(7,916)	(92,576)	(112,469)
Other Income (Expense), Net
Unrealized and realized appreciation (depreciation) in fair value of equity securities	412	(30,453)	(45,388)	64,392
Interest expense	(227)	(310)	(759)	(1,012)
Interest and dividend income	4,494	567	5,817	1,211
Other income (expense), net	(32)	589	1,205	530
Total other income (expense), net	4,647	(29,607)	(39,125)	65,121
Equity in net loss of affiliates	(6,255)	(2,429)	(16,951)	(6,565)
Loss before income taxes	(30,429)	(39,952)	(148,652)	(53,913)
Income tax benefit (expense)	418	923	3,290	(806)
Net loss	(30,011)	(39,029)	(145,362)	(54,719)
Net loss attributable to the noncontrolling interests	1,029	816	2,887	2,940
Net loss attributable to Intrexon	$ (28,982)	$ (38,213)	$ (142,475)	$ (51,779)
Net loss attributable to Intrexon per share, basic and diluted (in usd per share)	$ (0.24)	$ (0.34)	$ (1.21)	$ (0.47)
Weighted average shares outstanding, basic and diluted	118,346,782	112,244,129	117,785,160	109,244,641

Consolidated Statements of Comp

Consolidated Statements of Comprehensive Loss - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Statement of Comprehensive Income [Abstract]
Net loss	$ (30,011)	$ (39,029)	$ (145,362)	$ (54,719)
Other comprehensive income (loss):
Unrealized gain (loss) on investments	(151)	230	588	249
Foreign currency translation adjustments	(3,495)	(3,102)	(13,167)	(5,374)
Comprehensive loss	(33,657)	(41,901)	(157,941)	(59,844)
Comprehensive loss attributable to the noncontrolling interests	1,024	778	2,916	2,874
Comprehensive loss attributable to Intrexon	$ (32,633)	$ (41,123)	$ (155,025)	$ (56,970)

Consolidated Statements of Shar

Consolidated Statements of Shareholders' and Total Equity - 9 months ended Sep. 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	$ 0	$ 1,249,559	$ (12,752)	$ (542,729)	$ 694,078	$ 10,808
Increase (Decrease) in Stockholders' Equity
Stock-based compensation expense	30,610		30,555			30,555	55
Exercises of stock options and warrants (in shares)		1,322,843
Exercises of stock options and warrants	18,180		18,180			18,180
Shares issued as payment for services (in shares)		328,648
Shares issued as payment for services	8,284		8,284			8,284
Shares issued in asset acquisition (in shares)		136,340
Shares issued in asset acquisition	4,401		4,401			4,401
Net loss	(145,362)				(142,475)	(142,475)	(2,887)
Other comprehensive loss	$ (12,579)			(12,550)		(12,550)	(29)
Balances (in shares) at Sep. 30, 2016	118,446,717	118,446,717
Balances at Sep. 30, 2016	$ 608,420	$ 0	$ 1,310,979	$ (25,302)	$ (685,204)	$ 600,473	$ 7,947

Consolidated Statements of Cash

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015
Cash flows from operating activities
Net loss	$ (145,362)	$ (54,719)
Adjustments to reconcile net loss to net cash provided by (used in) operating activities:
Depreciation and amortization	17,657	12,202
Loss on disposal of property, plant and equipment	297	519
Unrealized and realized (appreciation) depreciation on equity securities	45,388	(64,392)
Noncash dividend income	(3,676)	0
Amortization of discount/premium on investments	862	298
Equity in net loss of affiliates	16,951	6,565
Stock-based compensation expense	30,631	26,524
Shares issued as payment for services	8,284	480
Shares issued as consideration for license agreement	0	59,579
Provision for bad debts	1,609	1,562
Deferred income taxes	(2,967)	374
Other noncash items	1,259	305
Changes in operating assets and liabilities:
Restricted cash	(6,987)	0
Receivables:
Trade	2,118	(12,014)
Related parties	7,438	(11,182)
Notes	(42)	1
Other	381	6,390
Inventory	4,683	3,451
Prepaid expenses and other	(985)	(4,005)
Other assets	2,134	(3,817)
Accounts payable	2,901	(3,560)
Accrued compensation and benefits	(8,001)	5,895
Other accrued liabilities	7,771	1,323
Deferred revenue	(14,099)	52,400
Deferred consideration	(630)	(943)
Related party payables	479	(67)
Other long term liabilities	126	168
Net cash provided by (used in) operating activities	(31,780)	23,337
Cash flows from investing activities
Purchases of investments	(75,246)	(181,572)
Maturities of investments	71,987	70,000
Purchases of equity securities and warrants	(2,308)	(17,080)
Acquisitions of businesses, net of cash received	0	(114,480)
Acquisition of noncontrolling interest	0	(1,566)
Investments in affiliates	(9,415)	(4,699)
Cash paid in asset acquisition	(7,244)	0
Purchases of property, plant and equipment	(20,197)	(9,841)
Proceeds from sale of property, plant and equipment	243	420
Issuances of notes receivable	(2,964)	0
Proceeds from notes receivable	0	1,500
Net cash used in investing activities	(45,144)	(257,318)
Cash flows from financing activities
Proceeds from issuance of shares in public offerings, net of issuance costs	0	328,234
Advances from lines of credit	2,308	13,719
Repayments of advances from lines of credit	(2,320)	(15,517)
Proceeds from long term debt	547	81
Payments of long term debt	(848)	(1,032)
Payments of deferred consideration	(6,705)	(6,252)
Proceeds from stock option exercises	18,180	12,208
Net cash provided by financing activities	11,162	331,441
Effect of exchange rate changes on cash and cash equivalents	(313)	507
Net increase (decrease) in cash and cash equivalents	(66,075)	97,967
Cash and cash equivalents
Beginning of period	135,782	27,466
End of period	69,707	125,433
Supplemental disclosure of cash flow information
Cash paid during the period for interest	875	1,119
Cash paid during the period for income taxes	0	1,165
Significant noncash financing and investing activities
Note receivable as consideration for collaboration agreement	0	5,000
Stock received as consideration for collaboration agreements	18,766	4,667
Preferred stock received as consideration for collaboration amendments	120,000	0
Stock issued in business combinations	0	126,863
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
Deferred consideration payable related to acquisition	0	11,440
Purchases of equipment included in accounts payable and other accrued liabilities	$ 926	$ 533

Organization

Organization	9 Months Ended
	Sep. 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. 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. 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. 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. As of September 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	9 Months Ended
	Sep. 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 September 30, 2016 and results of operations and cash flows for the interim periods ended September 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. Restricted Cash Restricted cash represents funds deposited with the U.S. Treasury, as required by a court decision resulting from litigation against Trans Ova (Note 17 ). 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 since the Company does not intend to sell the investment nor expect it to be converted into shares of common stock within one year. Until such time as the Company converts the instrument into common stock, the Company is entitled to a monthly dividend payable in additional shares of preferred stock and records dividend income based on the fair value of the preferred shares. 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"), one of its collaborators, as of September 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 $6,171 and $16,601 as of September 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 September 30, 2016 and December 31, 2015 , respectively. Unrealized appreciation (depreciation) in the fair value of these securities was $(455) and $2,404 for the three months ended September 30, 2016 and 2015 , respectively, and $(11,597) and $6,283 for the nine months ended September 30, 2016 and 2015 , respectively. Summarized unaudited financial data as of September 30, 2016 and December 31, 2015 and for the three and nine months ended September 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 through June 30, 2015 for the nine months ended September 30, 2015 as the Company determined it had significant influence over ZIOPHARM until the Company distributed its investment in ZIOPHARM to shareholders in June 2015. September 30, December 31, Current assets $ 81,049 $ 28,123 Non-current assets 10,992 1,539 Total assets 92,041 29,662 Current liabilities 8,325 6,274 Net assets $ 83,716 $ 23,388 Three Months Ended Nine Months Ended 2016 2015 2016 2015 Revenues $ 65 $ 330 $ 394 $ 1,480 Operating expenses 18,363 8,687 50,406 118,180 Operating loss (18,298 ) (8,357 ) (50,012 ) (116,700 ) Other 75 (34 ) 1,502 (31 ) Net loss $ (18,223 ) $ (8,391 ) $ (48,510 ) $ (116,731 ) Variable Interest Entities As of September 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 September 30, 2016 and December 31, 2015 was $145,786 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 September 30, 2016 and December 31, 2015 , the Company had $11,331 and $3,877 , respectively, of long-lived assets in foreign countries. The Company recognized revenues derived in foreign countries totaling $3,502 and $1,183 for the three months ended September 30, 2016 and 2015 , respectively, and $8,678 and $3,446 for the nine months ended September 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 August 2016, the Financial Accounting Standards Board ("FASB") issued Accounting Standards Update ("ASU") 2016-15, Statement of Cash Flows (Topic 230) - Classification of Certain Cash Receipts and Cash Payments ("ASU 2016-15"). The provisions of ASU 2016-15 address eight specific cash flow issues and how those certain cash receipts and cash payments are presented and classified in the statement of cash flows under Topic 230, Statement of Cash Flows, and other Topics. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2017, with early adoption permitted, 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 March 2016, the FASB issued 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.

Mergers and Acquisitions

Mergers and Acquisitions	9 Months Ended
	Sep. 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 September 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, of which $1,644 are included in selling, general and administrative expenses in the accompanying consolidated statements of operations for three and nine months ended September 30, 2015 . 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 $267 are included in selling, general and administrative expenses in the accompanying consolidated statement of operations for the nine months ended September 30, 2015. ActoGeniX Acquisition In February 2015, the Company acquired 100% of the membership interests of ActoGeniX NV ("ActoGeniX"), a European biopharmaceutical company, pursuant to a Stock Purchase Agreement (the "ActoGeniX Purchase Agreement"). ActoGeniX's platform technology complements the Company's suite of proprietary technologies available for current and future collaborators. Pursuant to the ActoGeniX Purchase Agreement, the former members of ActoGeniX received an aggregate of 965,377 shares of the Company's common stock and $32,739 in cash in exchange for all membership interests of ActoGeniX. The results of ActoGeniX's operations subsequent to the acquisition date have been included in the consolidated financial statements. The fair value of the total consideration transferred was $72,474 . The acquisition date fair value of each class of consideration transferred is presented below: Cash $ 32,739 Common shares 39,735 $ 72,474 The fair value of the shares of the Company's common stock issued was based on the quoted closing price of the Company's common stock as of the closing date of the acquisition. The estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown below: Cash $ 3,180 Other receivables 305 Prepaid expenses and other 31 Property, plant and equipment 209 Intangible assets 68,100 Other non-current assets 23 Total assets acquired 71,848 Accounts payable 230 Accrued compensation and benefits 196 Other accrued liabilities 253 Deferred revenue 732 Deferred tax liabilities 612 Total liabilities assumed 2,023 Net assets acquired 69,825 Goodwill 2,649 Total consideration $ 72,474 The acquired intangible assets primarily include in-process research and development, the fair value of which was determined using the multi-period excess earnings and with-and-without methods, which are both variations of the income approach that convert future cash flows to single discounted present value amounts. In August 2015, the Company re-evaluated the acquired in-process research and development and determined that it was placed in service as developed technology and began amortizing the original amount capitalized using a useful life of eighteen years . Goodwill, which is not expected to be deductible for tax purposes, represents the assembled workforce and anticipated buyer-specific synergies arising from the combination of the Company's and ActoGeniX's technologies. The Company incurred $418 of acquisition-related costs, of which $381 is included in selling, general and administrative expenses in the accompanying consolidated statement of operations for the nine months ended September 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 nine months ended September 30, 2015 is presented as if the acquisitions had been consummated on January 1, 2014: Three Months Ended September 30, 2015 Nine Months Ended September 30, 2015 Pro Forma Revenues $ 53,754 $ 133,060 Loss before income taxes (43,979 ) (66,686 ) Net loss (43,057 ) (66,319 ) Net loss attributable to the noncontrolling interests 816 2,940 Net loss attributable to Intrexon (42,241 ) (63,379 )

Investments in Joint Ventures

Investments in Joint Ventures	9 Months Ended
	Sep. 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. As of September 30, 2016 , the Company's remaining commitment was $3,650 . 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. The Company's investment in Intrexon T1D Partners was $1,078 as of September 30, 2016 and is included in investments in affiliates in the accompanying consolidated balance sheet. 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 $3,839 as of September 30, 2016 . New EnviroFlight met a regulatory milestone, as defined in the asset purchase agreement, and the members of Old EnviroFlight received a portion of the contingent consideration consisting of 59,337 shares of the Company's common stock valued at $1,583 in October 2016. The members of Old EnviroFlight may receive up to $4,000 of additional shares of the Company's common stock if certain commercial milestones are met prior to February 2019. The Company's investment in New EnviroFlight was $4,611 as of September 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 $1,591 and $2,000 as of September 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 September 30, 2016 , the Company's remaining commitment was $12,367 . 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 $(627) and $(1,270) as of September 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 $435 and $(144) as of September 30, 2016 and December 31, 2015 , respectively, and is included in investments in affiliates and other accrued liabilities, respectively, in the accompanying consolidated balance sheets. S & I Ophthalmic In September 2013, the Company entered into a Limited Liability Company Agreement ("Sun LLC Agreement") with Caraco Pharmaceutical Laboratories, Ltd. ("Sun Pharmaceutical Subsidiary"), an indirect subsidiary of Sun Pharmaceutical Industries Ltd. ("Sun Pharmaceutical"), an international specialty pharmaceutical company focused on chronic diseases, to form S & I Ophthalmic, LLC ("S & I Ophthalmic"). The Sun LLC Agreement governs the affairs and the conduct of business of S & I Ophthalmic. S & I Ophthalmic leverages experience and technology from both the Company and Sun Pharmaceutical. Both the Company and Sun Pharmaceutical Subsidiary made an initial capital contribution of $5,000 in October 2013 for a 50% membership interest in S & I Ophthalmic. S & I Ophthalmic is governed by a board of managers ("S & I Ophthalmic Board") which has four members, two each from the Company and Sun Pharmaceutical Subsidiary. In cases in which the S & I Ophthalmic Board determines that additional capital contributions are necessary in order for S & I Ophthalmic to conduct business and comply with its obligations, each of the Company and Sun Pharmaceutical Subsidiary has committed to making additional capital contributions to S & I Ophthalmic subject to certain limits defined in the agreement. Each has the right, but not the obligation, to make additional capital contributions above the defined limits when and if solicited by the S & I Ophthalmic Board. In 2015, both the Company and Sun Pharmaceutical Subsidiary 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 $3,737 and $6,379 as of September 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	9 Months Ended
	Sep. 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 nine months ended September 30, 2016 and 2015 . Three Months Ended September 30, 2016 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 4,843 $ 5,586 $ 10,429 Oragenics, Inc. 262 294 556 Fibrocell Science, Inc. 604 563 1,167 Genopaver, LLC 68 1,625 1,693 S & I Ophthalmic, LLC — 2,782 2,782 OvaXon, LLC — 709 709 Intrexon Energy Partners, LLC 625 4,230 4,855 Persea Bio, LLC 125 208 333 Ares Trading S.A. 1,597 719 2,316 Thrive Agrobiotics, Inc. 46 379 425 Intrexon Energy Partners II, LLC 500 372 872 Exotech Bio, Inc. 139 82 221 Relieve Genetics, Inc. 120 342 462 Intrexon T1D Partners, LLC 276 511 787 AD Skincare, Inc. 120 65 185 Other 895 1,903 2,798 Total $ 10,220 $ 20,370 $ 30,590 Three Months Ended September 30, 2015 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 645 $ 4,006 $ 4,651 Oragenics, Inc. 4,868 332 5,200 Fibrocell Science, Inc. 4,823 1,317 6,140 Genopaver, LLC 68 993 1,061 S & I Ophthalmic, LLC — 1,193 1,193 OvaXon, LLC — 549 549 Intrexon Energy Partners, LLC 625 3,185 3,810 Persea Bio, LLC 125 297 422 Ares Trading S.A. 1,597 260 1,857 Other 7,841 2,002 9,843 Total $ 20,592 $ 14,134 $ 34,726 Nine Months Ended September 30, 2016 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 6,687 $ 17,693 $ 24,380 Oragenics, Inc. 786 1,083 1,869 Fibrocell Science, Inc. 1,814 2,604 4,418 Genopaver, LLC 205 4,703 4,908 S & I Ophthalmic, LLC — 6,326 6,326 OvaXon, LLC — 2,211 2,211 Intrexon Energy Partners, LLC 1,875 11,180 13,055 Persea Bio, LLC 375 613 988 Ares Trading S.A. 4,791 2,148 6,939 Thrive Agrobiotics, Inc. 138 1,171 1,309 Intrexon Energy Partners II, LLC 1,500 816 2,316 Exotech Bio, Inc. 278 82 360 Relieve Genetics, Inc. 240 572 812 Intrexon T1D Partners, LLC 554 543 1,097 AD Skincare, Inc. 120 65 185 Other 4,684 6,287 10,971 Total $ 24,047 $ 58,097 $ 82,144 Nine Months Ended September 30, 2015 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 1,933 $ 11,769 $ 13,702 Oragenics, Inc. 5,437 408 5,845 Fibrocell Science, Inc. 5,719 4,500 10,219 Genopaver, LLC 205 2,460 2,665 S & I Ophthalmic, LLC — 2,838 2,838 OvaXon, LLC — 1,855 1,855 Intrexon Energy Partners, LLC 1,875 8,101 9,976 Persea Bio, LLC 375 553 928 Ares Trading S.A. 2,336 260 2,596 Other 9,446 6,620 16,066 Total $ 27,326 $ 39,364 $ 66,690 Except for the agreements discussed below, there have been no significant changes to arrangements with our collaborators and licensees in the nine months ended September 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. Genten Therapeutics Collaboration In September 2016, the Company entered into an ECC with Genten Therapeutics, Inc. ("Genten Therapeutics"), an affiliate of Harvest and a related party. Genten Therapeutics was formed for the purpose of entering into the ECC and developing and commercializing products using the Company's technology for expression of gluten peptides, alone or in combination with immunomodulatory cytokines, to reestablish immune tolerance for patients with celiac disease. Upon execution of the ECC, the Company received a technology access fee in the form of a $1,500 cash payment and equity in Genten Therapeutics valued at $3,000 as upfront consideration. The Company is entitled to receive additional equity interests in Genten Therapeutics upon the first instance of the achievement of a certain non-substantive development milestone. The Company is also entitled to up to $82,000 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. Genten Therapeutics 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. Genten Therapeutics is responsible for the development and commercialization of the product candidates. The term of the ECC commenced in September 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 Genten Therapeutics upon 90 days written notice to the Company. CRS Bio Collaboration In September 2016, the Company entered into an ECC with CRS Bio, Inc. ("CRS Bio"), an affiliate of Harvest and a related party. CRS Bio was formed for the purpose of entering into the ECC and developing and commercializing products through targeted delivery of antibodies for treatment of chronic rhinosinusitis with and without nasal polyps, by utilizing the Company's technology to block inflammatory mediators in the nasal passage, leading to improved breathing and, importantly, patients' quality of life. Upon execution of the ECC, the Company received a technology access fee in the form of equity in CRS Bio valued at $2,100 . The Company is entitled to receive additional equity interests in CRS Bio upon the first instance of the achievement of a certain non-substantive development milestone. The Company is also entitled to up to $75,000 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. CRS 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. CRS Bio is responsible for the development and commercialization of the product candidates. The term of the ECC commenced in September 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 CRS Bio upon 90 days written notice to the Company. Deferred Revenue Deferred revenue primarily consists of consideration received for upfront and milestone payments in connection with the Company's collaborations and licensing agreements, prepayments for research and development services performed for collaborators and licensees, and prepayments for product and service revenues. Deferred revenue consists of the following: September 30, December 31, Upfront and milestone payments $ 309,126 $ 181,331 Prepaid research and development services 7,057 10,938 Prepaid product and service revenues 5,594 4,759 Other 620 701 Total $ 322,397 $ 197,729 Current portion of deferred revenue $ 54,937 $ 35,366 Long-term portion of deferred revenue 267,460 162,363 Total $ 322,397 $ 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: September 30, December 31, ZIOPHARM Oncology, Inc. $ 143,651 $ 30,338 Oragenics, Inc. 8,027 8,813 Fibrocell Science, Inc. 19,631 21,445 Genopaver, LLC 2,045 2,250 Intrexon Energy Partners, LLC 18,750 20,625 Persea Bio, LLC 4,125 4,500 Ares Trading S.A. 48,776 53,567 Thrive Agrobiotics, Inc. 1,483 1,621 Intrexon Energy Partners II, LLC 16,333 17,833 Exotech Bio, Inc. 4,722 — Relieve Genetics, Inc. 4,093 — Intrexon T1D Partners, LLC 9,383 — AD Skincare, Inc. 4,213 — Genten Therapeutics, Inc. 4,523 — CRS Bio, Inc. 2,111 — Other 17,260 20,339 Total $ 309,126 $ 181,331

Short-term and Long-term Invest

Short-term and Long-term Investments	9 Months Ended
	Sep. 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 September 30, 2016 : Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Aggregate Fair Value U.S. government debt securities $ 210,620 $ 79 $ (10 ) $ 210,689 Certificates of deposit 272 — — 272 Total $ 210,892 $ 79 $ (10 ) $ 210,961 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 September 30, 2016 was: Due within one year $ 166,839 After one year through two years 44,122 Total $ 210,961 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 September 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	9 Months Ended
	Sep. 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 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. There have been no significant changes in the fair value of the Preferred Shares during the three months ended September 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. The fair value of the Company's investment in preferred stock, including additional Preferred Shares received as dividends, is $123,676 as of September 30, 2016 . During the three and nine months ended September 30, 2016 , the Company received 3,063 shares of additional Preferred Shares and recognized $3,676 of dividend income in the accompanying consolidated statements of operations. The only change in the Level 3 investment during the three months ended September 30, 2016 was this receipt of additional Preferred Shares arising from the dividend.

Fair Value Measurements

Fair Value Measurements	9 Months Ended
	Sep. 30, 2016
Fair Value Disclosures [Abstract]
Fair Value Measurements	Fair Value Measurements The carrying amount of cash and cash equivalents, restricted cash, 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 September 30, 2016 : Quoted Prices in Active Markets (Level 1) Significant Other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) September 30, Assets U.S. government debt securities $ — $ 210,689 $ — $ 210,689 Equity securities 31,245 8,187 — 39,432 Preferred stock — — 123,676 123,676 Other — 2,296 — 2,296 Total $ 31,245 $ 221,172 $ 123,676 $ 376,093 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 nine months ended September 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 $3,839 at September 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 ) whereby 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. The fair value of this liability increased $179 during the three months ended September 30, 2016 (Note 4 ). Financial liabilities measured on a recurring basis were not significant at December 31, 2015 .

Inventory

Inventory	9 Months Ended
	Sep. 30, 2016
Inventory Disclosure [Abstract]
Inventory	Inventory Inventory consists of the following: September 30, December 31, Supplies, semen and embryos $ 1,278 $ 1,402 Work in process 5,831 6,290 Livestock 12,588 16,907 Feed 2,183 1,964 Total inventory $ 21,880 $ 26,563

Property, Plant and Equipment,

Property, Plant and Equipment, Net	9 Months Ended
	Sep. 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: September 30, December 31, Land and land improvements $ 11,276 $ 9,119 Buildings and building improvements 7,965 7,520 Furniture and fixtures 1,234 1,283 Equipment 41,343 36,016 Leasehold improvements 10,479 6,888 Computer hardware and software 6,912 5,960 Construction and other assets in progress 7,523 2,193 86,732 68,979 Less: Accumulated depreciation and amortization (32,303 ) (26,240 ) Property, plant and equipment, net $ 54,429 $ 42,739 Depreciation expense was $2,332 and $1,987 for the three months ended September 30, 2016 and 2015 , respectively, and $6,769 and $5,768 for the nine months ended September 30, 2016 and 2015 , respectively.

Goodwill and Intangible Assets,

Goodwill and Intangible Assets, Net	9 Months Ended
	Sep. 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 nine months ended September 30, 2016 are as follows: Balance at December 31, 2015 $ 165,169 Foreign currency translation adjustments (5,376 ) Balance at September 30, 2016 $ 159,793 No goodwill or accumulated impairment losses existed as of September 30, 2016 and December 31, 2015 . Intangible assets consist of the following at September 30, 2016 : Weighted Average Useful Life (Years) Gross Carrying Amount Accumulated Amortization Net Patents, related technologies and know-how 15.3 $ 170,520 $ (26,596 ) $ 143,924 Customer relationships 6.5 10,700 (4,189 ) 6,511 Trademarks 9.3 6,800 (1,598 ) 5,202 Covenant not to compete 2.0 395 (312 ) 83 In-process research and development 82,861 — 82,861 Total $ 271,276 $ (32,695 ) $ 238,581 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 September 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 $3,651 and $2,857 for the three months ended September 30, 2016 and 2015 , respectively, and $10,888 and $6,434 for the nine months ended September 30, 2016 and 2015 , respectively.

Lines of Credit and Long Term D

Lines of Credit and Long Term Debt	9 Months Ended
	Sep. 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 3.48% at September 30, 2016 . As of September 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 September 30, 2016 . Exemplar has a $700 revolving line of credit with American State Bank which matures on October 30, 2017. The line of credit bears interest at 4.50% per annum. As of September 30, 2016 , there was an outstanding balance of $549 . Long Term Debt Long term debt consists of the following: September 30, December 31, Notes payable $ 5,769 $ 6,477 Royalty-based financing 2,003 1,807 Other 649 244 Long term debt 8,421 8,528 Less current portion 471 930 Long term debt, less current portion $ 7,950 $ 7,598 Trans Ova has a note payable to American State Bank which matures in April 2033 and has an outstanding principal balance of $5,338 as of September 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 $431 as of September 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. In August 2016, AquaBounty obtained a loan from Finance PEI ("FPEI"), a Canadian government-owned corporation. As of September 30, 2016 there was an outstanding balance of $543 . AquaBounty pays monthly installments of $4 , which includes interest of 4.00% , with a balloon payment due in July 2021. The loan is collateralized by certain of AquaBounty's assets. 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 $2,185 , 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 $2,003 as of September 30, 2016 . Future maturities of long term debt are as follows: 2016 $ 168 2017 404 2018 549 2019 364 2020 335 2021 774 Thereafter 3,824 Total $ 6,418 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	9 Months Ended
	Sep. 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 nine months ended September 30, 2016 , the Company had U.S. taxable income of approximately $8,334 and U.S. taxable loss of approximately $9,346 , respectively, for which no income tax benefit was recognized. For the three and nine months ended September 30, 2016 , the Company recognized $110 and $323 of current foreign income tax benefit, respectively. For the three months ended September 30, 2015 , the Company had U.S. taxable loss of approximately $15,865 , which resulted in an income tax benefit of $318 . For the nine months ended September 30, 2015 , the Company had U.S. taxable income of approximately $22,935 , which resulted in $459 of current income tax expense due to the corporate alternative minimum tax. For the three and nine months ended September 30, 2015 , the Company recognized $27 of current foreign income tax benefit. For the three and nine months ended September 30, 2016 , the Company recorded deferred tax benefit of $308 and $2,967 , respectively. For the three and nine months ended September 30, 2015 , the Company recorded deferred tax benefit of $578 and deferred tax expense of $374 , respectively. The Company's net deferred tax assets, excluding certain deferred tax liabilities totaling $18,060 , 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 September 30, 2016 , the Company has loss carryforwards for U.S. federal income tax purposes of approximately $257,700 available to offset future taxable income and federal and state research and development tax credits of approximately $7,060 , 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 $54,400 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 $120,600 , most of which do not expire.

Shareholders' Equity

Shareholders' Equity	9 Months Ended
	Sep. 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: September 30, December 31, Unrealized gain (loss) on investments $ 69 $ (519 ) Foreign currency translation adjustments (25,371 ) (12,233 ) Total accumulated other comprehensive loss $ (25,302 ) $ (12,752 )

Share-Based Payments

Share-Based Payments	9 Months Ended
	Sep. 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 Nine Months Ended 2016 2015 2016 2015 Cost of products $ 21 $ 21 $ 61 $ 76 Cost of services 68 98 206 301 Research and development 2,236 2,234 6,979 6,141 Selling, general and administrative 8,467 6,032 23,385 20,006 Total $ 10,792 $ 8,385 $ 30,631 $ 26,524 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 September 30, 2016 , there were 570,977 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 September 30, 2016 , there were 16,000,000 shares authorized for issuance under the 2013 Plan, of which 10,532,430 stock options were outstanding and 3,982,064 shares were available for grant. As of September 30, 2016 , an additional 1,000,000 options were issued and outstanding outside the 2008 Plan and 2013 Plan. These options were awarded as an inducement grant to an executive officer in accordance with New York Stock Exchange Rule 303A.08 and are generally subject to the same terms and conditions as awards granted under the 2013 Plan. Stock option activity 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 4,384,860 29.42 Exercised (1,162,843 ) (15.63 ) Forfeited (2,127,334 ) (43.29 ) Expired (34,804 ) (35.76 ) Balances at September 30, 2016 12,103,407 31.24 8.50 Exercisable at September 30, 2016 3,369,252 27.99 7.25 Vested and Expected to Vest at September 30, 2016(1) 10,177,058 30.99 8.37 (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 September 30, 2016 and December 31, 2015 were $106,649 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. In October 2016, the independent members of Intrexon's Board of Directors, with the recommendation of the Compensation Committee of the Board of Directors, approved a new Restricted Stock Unit Agreement for the CEO providing for a term of two months . The new RSU Agreement, which will expire on December 31, 2016, provides for the same monthly salary payable in fully vested shares of common stock pursuant to the same terms as the original RSU Agreement. 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 $ 1,397 for the three and nine months ended September 30, 2016 , respectively. Other Plans As of September 30, 2016 , there were 5,567,000 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 5,321,598 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 September 30, 2016 , there were no options outstanding under the AquaBounty 2016 Plan.

License Agreement

License Agreement	9 Months Ended
	Sep. 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 nine months ended September 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	9 Months Ended
	Sep. 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 September 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 $ 705 2017 6,362 2018 5,695 2019 5,434 2020 5,487 2021 4,888 Thereafter 20,179 Total $ 48,750 Rent expense, including other facility expenses, was $2,075 and $2,167 for the three months ended September 30, 2016 and 2015 , respectively, and $6,410 and $6,548 for the nine months ended September 30, 2016 and 2015 , respectively. The Company maintains subleases for certain of its facilities. Rental income under sublease agreements was $184 and $334 for the three months ended September 30, 2016 and 2015 , respectively, and $854 and $1,153 for the nine months ended September 30, 2016 and 2015 , respectively. Future rental income is expected to be $9 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 ("XY") alleging that certain of Trans Ova's activities breach a licensing agreement and infringe on patents that XY 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 and Trans Ova had each breached the licensing agreement and that Trans Ova had infringed the intellectual property of XY. 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 in the amount of $6,066 , each with prejudgment interest. The order provides for the continuation of Trans Ova's license to XY's technology, subject to an ongoing royalty for Trans Ova which is subject to a post-judgment motion, including XY's motion for enhanced damages, and potential appeals therefrom. Since the inception of the license, Trans Ova has remitted payments to XY 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. For the nine months ended September 30, 2016, the Company recorded litigation 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, including prejudgment interest, over the liability previously recorded by Trans Ova for uncashed checks previously remitted to XY. In August 2016, Trans Ova deposited the net damages amount, including prejudgment interest, into the court's treasury, to be held until the appeals process is complete and final judgment amounts are determined. As of September 30, 2016 , this amount is included in restricted cash on the accompanying consolidated balance sheet. 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 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'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"). In July 2016, the court consolidated the lawsuits and appointed a lead plaintiff. The consolidated amended complaint names as defendants Intrexon and certain of Intrexon's current and former officers (the "Defendants"). It alleges, among other things, that the Defendants made materially false and/or misleading statements during the Class Period with respect to the Company's business, operations, and prospects in violation of Section 10(b) of the Securities Exchange Act of 1934, as amended. The plaintiffs' claims are based upon allegations in 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. The Company intends to defend the lawsuit vigorously; however, there can be no assurance regarding the ultimate outcome of this case. 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 CEO, and Third Security, and naming the Company as a nominal defendant. 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. The action has been stayed pending the report of the Special Litigation Committee. 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 September 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	9 Months Ended
	Sep. 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, the independent members of Intrexon's Board of Directors, with the recommendation of the Audit Committee of the 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 had 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. In October 2016, the independent members of Intrexon's Board of Directors, with the recommendation of the Audit Committee of the Board of Directors, approved the extension of the Services Agreement through December 2016. For the three and nine months ended September 30, 2016 , the Company issued 89,326 shares and 254,496 shares, respectively, with values of $2,132 and $6,542 , 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 $156 and $142 for the three months ended September 30, 2016 and 2015 , respectively, and $301 and $294 for the nine months ended September 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 September 2016, Fibrocell Science, Inc. ("Fibrocell"), one of the Company's collaborators, sold promissory notes convertible into shares of Fibrocell common stock ("convertible note") and warrants to purchase shares of Fibrocell common stock to certain institutional and accredited investors, including the Company and affiliates of Third Security. The Company paid $2,604 for a convertible note and warrants. As of September 30, 2016 , the value of the convertible note and warrants totaled $1,990 and is included in other assets on the accompanying consolidated balance sheet. 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 June 2016, the Company purchased 2,261,419 shares of Oragenics common stock at $0.52 per share. The Company recognized $26,688 and $31,740 of collaboration revenues from related parties in the three months ended September 30, 2016 and 2015 , respectively, and $70,299 and $59,775 in the nine months ended September 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 $1,871 for the three and nine months ended September 30, 2016 , respectively, and totaled $697 for the three and nine months ended September 30, 2015 .

Net Loss per Share

Net Loss per Share	9 Months Ended
	Sep. 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 nine months ended September 30, 2016 and 2015 : Three Months Ended Nine Months Ended 2016 2015 2016 2015 Historical net loss per share: Numerator: Net loss attributable to Intrexon $ (28,982 ) $ (38,213 ) $ (142,475 ) $ (51,779 ) Denominator: Weighted average shares outstanding, basic and diluted 118,346,782 112,244,129 117,785,160 109,244,641 Net loss attributable to Intrexon per share, basic and diluted $ (0.24 ) $ (0.34 ) $ (1.21 ) $ (0.47 ) The following potentially dilutive securities as of September 30, 2016 and 2015 , have been excluded from the above computations of diluted weighted average shares outstanding for the three and nine months then ended, as they would have been anti-dilutive: September 30, 2016 2015 Options 12,103,407 10,660,040 Warrants 30,191 194,719 Total 12,133,598 10,854,759

Subsequent Events Subsequent Ev

Subsequent Events Subsequent Events	9 Months Ended
	Sep. 30, 2016
Subsequent Events [Abstract]
Subsequent Events	Subsequent Events In November 2016, the Company entered into a stock purchase agreement with AquaBounty pursuant to which the Company will purchase 72,632,190 shares of AquaBounty's common stock for $25,000 subject to AquaBounty's common stock being approved for listing on the NASDAQ Capital Market ("NASDAQ") and other closing conditions as defined in the agreement. In November 2016, AquaBounty filed a Form 10 registration statement with the Securities and Exchange Commission as an initial step towards the listing of its common stock. The Company anticipates converting up to $10,000 of convertible promissory notes, plus accrued interest thereon, into shares of AquaBounty common stock in conjunction with these transactions. The Company also announced its intent to distribute a portion of its previously held shares of AquaBounty common stock to shareholders of Intrexon as a special stock dividend once AquaBounty shares are available to trade on NASDAQ. The number of shares to be distributed by the Company is subject to final determination and approval by the Board of Directors of the Company. After consideration of all transactions contemplated herein, the Company expects to continue to be the majority owner of AquaBounty.

Summary of Significant Accoun28

Summary of Significant Accounting Policies (Policies)	9 Months Ended
	Sep. 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 September 30, 2016 and results of operations and cash flows for the interim periods ended September 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.
Restricted Cash	Restricted Cash Restricted cash represents funds deposited with the U.S. Treasury, as required by a court decision resulting from litigation against Trans Ova (Note 17 ).
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 since the Company does not intend to sell the investment nor expect it to be converted into shares of common stock within one year. Until such time as the Company converts the instrument into common stock, the Company is entitled to a monthly dividend payable in additional shares of preferred stock and records dividend income based on the fair value of the preferred shares.
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 August 2016, the Financial Accounting Standards Board ("FASB") issued Accounting Standards Update ("ASU") 2016-15, Statement of Cash Flows (Topic 230) - Classification of Certain Cash Receipts and Cash Payments ("ASU 2016-15"). The provisions of ASU 2016-15 address eight specific cash flow issues and how those certain cash receipts and cash payments are presented and classified in the statement of cash flows under Topic 230, Statement of Cash Flows, and other Topics. The guidance is effective for annual periods and interim periods within those annual periods beginning after December 15, 2017, with early adoption permitted, 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 March 2016, the FASB issued 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.

Summary of Significant Accoun29

Summary of Significant Accounting Policies (Tables)	9 Months Ended
	Sep. 30, 2016
Accounting Policies [Abstract]
Summarized Unaudited Financial Information for the Equity Method Investments	Summarized unaudited financial data as of September 30, 2016 and December 31, 2015 and for the three and nine months ended September 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 through June 30, 2015 for the nine months ended September 30, 2015 as the Company determined it had significant influence over ZIOPHARM until the Company distributed its investment in ZIOPHARM to shareholders in June 2015. September 30, December 31, Current assets $ 81,049 $ 28,123 Non-current assets 10,992 1,539 Total assets 92,041 29,662 Current liabilities 8,325 6,274 Net assets $ 83,716 $ 23,388 Three Months Ended Nine Months Ended 2016 2015 2016 2015 Revenues $ 65 $ 330 $ 394 $ 1,480 Operating expenses 18,363 8,687 50,406 118,180 Operating loss (18,298 ) (8,357 ) (50,012 ) (116,700 ) Other 75 (34 ) 1,502 (31 ) Net loss $ (18,223 ) $ (8,391 ) $ (48,510 ) $ (116,731 )

Mergers and Acquisitions (Table

Mergers and Acquisitions (Tables)	9 Months Ended
	Sep. 30, 2016
Oxitec
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
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 nine months ended September 30, 2015 is presented as if the acquisitions had been consummated on January 1, 2014: Three Months Ended September 30, 2015 Nine Months Ended September 30, 2015 Pro Forma Revenues $ 53,754 $ 133,060 Loss before income taxes (43,979 ) (66,686 ) Net loss (43,057 ) (66,319 ) Net loss attributable to the noncontrolling interests 816 2,940 Net loss attributable to Intrexon (42,241 ) (63,379 )

Collaboration and Licensing R31

Collaboration and Licensing Revenue (Tables)	9 Months Ended
	Sep. 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 nine months ended September 30, 2016 and 2015 . Three Months Ended September 30, 2016 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 4,843 $ 5,586 $ 10,429 Oragenics, Inc. 262 294 556 Fibrocell Science, Inc. 604 563 1,167 Genopaver, LLC 68 1,625 1,693 S & I Ophthalmic, LLC — 2,782 2,782 OvaXon, LLC — 709 709 Intrexon Energy Partners, LLC 625 4,230 4,855 Persea Bio, LLC 125 208 333 Ares Trading S.A. 1,597 719 2,316 Thrive Agrobiotics, Inc. 46 379 425 Intrexon Energy Partners II, LLC 500 372 872 Exotech Bio, Inc. 139 82 221 Relieve Genetics, Inc. 120 342 462 Intrexon T1D Partners, LLC 276 511 787 AD Skincare, Inc. 120 65 185 Other 895 1,903 2,798 Total $ 10,220 $ 20,370 $ 30,590 Three Months Ended September 30, 2015 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 645 $ 4,006 $ 4,651 Oragenics, Inc. 4,868 332 5,200 Fibrocell Science, Inc. 4,823 1,317 6,140 Genopaver, LLC 68 993 1,061 S & I Ophthalmic, LLC — 1,193 1,193 OvaXon, LLC — 549 549 Intrexon Energy Partners, LLC 625 3,185 3,810 Persea Bio, LLC 125 297 422 Ares Trading S.A. 1,597 260 1,857 Other 7,841 2,002 9,843 Total $ 20,592 $ 14,134 $ 34,726 Nine Months Ended September 30, 2016 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 6,687 $ 17,693 $ 24,380 Oragenics, Inc. 786 1,083 1,869 Fibrocell Science, Inc. 1,814 2,604 4,418 Genopaver, LLC 205 4,703 4,908 S & I Ophthalmic, LLC — 6,326 6,326 OvaXon, LLC — 2,211 2,211 Intrexon Energy Partners, LLC 1,875 11,180 13,055 Persea Bio, LLC 375 613 988 Ares Trading S.A. 4,791 2,148 6,939 Thrive Agrobiotics, Inc. 138 1,171 1,309 Intrexon Energy Partners II, LLC 1,500 816 2,316 Exotech Bio, Inc. 278 82 360 Relieve Genetics, Inc. 240 572 812 Intrexon T1D Partners, LLC 554 543 1,097 AD Skincare, Inc. 120 65 185 Other 4,684 6,287 10,971 Total $ 24,047 $ 58,097 $ 82,144 Nine Months Ended September 30, 2015 Revenue Recognized From Total Upfront and Milestone Payments Research and Development Services ZIOPHARM Oncology, Inc. $ 1,933 $ 11,769 $ 13,702 Oragenics, Inc. 5,437 408 5,845 Fibrocell Science, Inc. 5,719 4,500 10,219 Genopaver, LLC 205 2,460 2,665 S & I Ophthalmic, LLC — 2,838 2,838 OvaXon, LLC — 1,855 1,855 Intrexon Energy Partners, LLC 1,875 8,101 9,976 Persea Bio, LLC 375 553 928 Ares Trading S.A. 2,336 260 2,596 Other 9,446 6,620 16,066 Total $ 27,326 $ 39,364 $ 66,690
Summary of Deferred Revenue	Deferred revenue consists of the following: September 30, December 31, Upfront and milestone payments $ 309,126 $ 181,331 Prepaid research and development services 7,057 10,938 Prepaid product and service revenues 5,594 4,759 Other 620 701 Total $ 322,397 $ 197,729 Current portion of deferred revenue $ 54,937 $ 35,366 Long-term portion of deferred revenue 267,460 162,363 Total $ 322,397 $ 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: September 30, December 31, ZIOPHARM Oncology, Inc. $ 143,651 $ 30,338 Oragenics, Inc. 8,027 8,813 Fibrocell Science, Inc. 19,631 21,445 Genopaver, LLC 2,045 2,250 Intrexon Energy Partners, LLC 18,750 20,625 Persea Bio, LLC 4,125 4,500 Ares Trading S.A. 48,776 53,567 Thrive Agrobiotics, Inc. 1,483 1,621 Intrexon Energy Partners II, LLC 16,333 17,833 Exotech Bio, Inc. 4,722 — Relieve Genetics, Inc. 4,093 — Intrexon T1D Partners, LLC 9,383 — AD Skincare, Inc. 4,213 — Genten Therapeutics, Inc. 4,523 — CRS Bio, Inc. 2,111 — Other 17,260 20,339 Total $ 309,126 $ 181,331

Short-term and Long-term Inve32

Short-term and Long-term Investments (Tables)	9 Months Ended
	Sep. 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 September 30, 2016 : Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Aggregate Fair Value U.S. government debt securities $ 210,620 $ 79 $ (10 ) $ 210,689 Certificates of deposit 272 — — 272 Total $ 210,892 $ 79 $ (10 ) $ 210,961 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 September 30, 2016 was: Due within one year $ 166,839 After one year through two years 44,122 Total $ 210,961

Fair Value Measurements (Tables

Fair Value Measurements (Tables)	9 Months Ended
	Sep. 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 September 30, 2016 : Quoted Prices in Active Markets (Level 1) Significant Other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) September 30, Assets U.S. government debt securities $ — $ 210,689 $ — $ 210,689 Equity securities 31,245 8,187 — 39,432 Preferred stock — — 123,676 123,676 Other — 2,296 — 2,296 Total $ 31,245 $ 221,172 $ 123,676 $ 376,093 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)	9 Months Ended
	Sep. 30, 2016
Inventory Disclosure [Abstract]
Schedule of Inventory	Inventory consists of the following: September 30, December 31, Supplies, semen and embryos $ 1,278 $ 1,402 Work in process 5,831 6,290 Livestock 12,588 16,907 Feed 2,183 1,964 Total inventory $ 21,880 $ 26,563

Property, Plant and Equipment35

Property, Plant and Equipment, Net (Tables)	9 Months Ended
	Sep. 30, 2016
Property, Plant and Equipment [Abstract]
Schedule of Property, Plant and Equipment	Property, plant and equipment consist of the following: September 30, December 31, Land and land improvements $ 11,276 $ 9,119 Buildings and building improvements 7,965 7,520 Furniture and fixtures 1,234 1,283 Equipment 41,343 36,016 Leasehold improvements 10,479 6,888 Computer hardware and software 6,912 5,960 Construction and other assets in progress 7,523 2,193 86,732 68,979 Less: Accumulated depreciation and amortization (32,303 ) (26,240 ) Property, plant and equipment, net $ 54,429 $ 42,739

Goodwill and Intangible Asset36

Goodwill and Intangible Assets, Net (Tables)	9 Months Ended
	Sep. 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 nine months ended September 30, 2016 are as follows: Balance at December 31, 2015 $ 165,169 Foreign currency translation adjustments (5,376 ) Balance at September 30, 2016 $ 159,793
Schedule of Intangible Assets	Intangible assets consist of the following at September 30, 2016 : Weighted Average Useful Life (Years) Gross Carrying Amount Accumulated Amortization Net Patents, related technologies and know-how 15.3 $ 170,520 $ (26,596 ) $ 143,924 Customer relationships 6.5 10,700 (4,189 ) 6,511 Trademarks 9.3 6,800 (1,598 ) 5,202 Covenant not to compete 2.0 395 (312 ) 83 In-process research and development 82,861 — 82,861 Total $ 271,276 $ (32,695 ) $ 238,581 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)	9 Months Ended
	Sep. 30, 2016
Debt Disclosure [Abstract]
Schedule of Long Term Debt Instruments	Long term debt consists of the following: September 30, December 31, Notes payable $ 5,769 $ 6,477 Royalty-based financing 2,003 1,807 Other 649 244 Long term debt 8,421 8,528 Less current portion 471 930 Long term debt, less current portion $ 7,950 $ 7,598
Schedule of Future Maturities of Long Term Debt	Future maturities of long term debt are as follows: 2016 $ 168 2017 404 2018 549 2019 364 2020 335 2021 774 Thereafter 3,824 Total $ 6,418

Shareholders' Equity (Tables)

Shareholders' Equity (Tables)	9 Months Ended
	Sep. 30, 2016
Equity [Abstract]
Components of Accumulated Other Comprehensive Loss	The components of accumulated other comprehensive loss are as follows: September 30, December 31, Unrealized gain (loss) on investments $ 69 $ (519 ) Foreign currency translation adjustments (25,371 ) (12,233 ) Total accumulated other comprehensive loss $ (25,302 ) $ (12,752 )

Share-Based Payments (Tables)

Share-Based Payments (Tables)	9 Months Ended
	Sep. 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 Nine Months Ended 2016 2015 2016 2015 Cost of products $ 21 $ 21 $ 61 $ 76 Cost of services 68 98 206 301 Research and development 2,236 2,234 6,979 6,141 Selling, general and administrative 8,467 6,032 23,385 20,006 Total $ 10,792 $ 8,385 $ 30,631 $ 26,524
Schedule of Stock Option Activity	Stock option activity 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 4,384,860 29.42 Exercised (1,162,843 ) (15.63 ) Forfeited (2,127,334 ) (43.29 ) Expired (34,804 ) (35.76 ) Balances at September 30, 2016 12,103,407 31.24 8.50 Exercisable at September 30, 2016 3,369,252 27.99 7.25 Vested and Expected to Vest at September 30, 2016(1) 10,177,058 30.99 8.37 (1) The number of stock options expected to vest takes into account an estimate of expected forfeitures.

Commitments and Contingencies (

Commitments and Contingencies (Tables)	9 Months Ended
	Sep. 30, 2016
Commitments and Contingencies Disclosure [Abstract]
Future Minimum Lease Payments Under Noncancelable Operating Leases	At September 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 $ 705 2017 6,362 2018 5,695 2019 5,434 2020 5,487 2021 4,888 Thereafter 20,179 Total $ 48,750

Net Loss per Share (Tables)

Net Loss per Share (Tables)	9 Months Ended
	Sep. 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 nine months ended September 30, 2016 and 2015 : Three Months Ended Nine Months Ended 2016 2015 2016 2015 Historical net loss per share: Numerator: Net loss attributable to Intrexon $ (28,982 ) $ (38,213 ) $ (142,475 ) $ (51,779 ) Denominator: Weighted average shares outstanding, basic and diluted 118,346,782 112,244,129 117,785,160 109,244,641 Net loss attributable to Intrexon per share, basic and diluted $ (0.24 ) $ (0.34 ) $ (1.21 ) $ (0.47 )
Schedule of Antidilutive Securities Excluded from Computation of Net Loss per Share	The following potentially dilutive securities as of September 30, 2016 and 2015 , have been excluded from the above computations of diluted weighted average shares outstanding for the three and nine months then ended, as they would have been anti-dilutive: September 30, 2016 2015 Options 12,103,407 10,660,040 Warrants 30,191 194,719 Total 12,133,598 10,854,759

Organization (Details)

Organization (Details)	Sep. 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 - Equity Method Investments - Additional Information (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015	Dec. 31, 2015
Schedule of Equity Method Investments [Line Items]
Fair value of financial assets measured at fair value on a recurring basis	$ 376,093		$ 376,093		$ 291,762
Oragenics
Schedule of Equity Method Investments [Line Items]
Company's ownership percentage	29.50%		29.50%		30.70%
Equity securities
Schedule of Equity Method Investments [Line Items]
Fair value of financial assets measured at fair value on a recurring basis	$ 39,432		$ 39,432		$ 83,653
Equity securities | Oragenics
Schedule of Equity Method Investments [Line Items]
Fair value of financial assets measured at fair value on a recurring basis	6,171		6,171		$ 16,601
Unrealized appreciation (depreciation) in fair value of equity securities	$ (455)	$ 2,404	$ (11,597)	$ 6,283

Summary of Significant Accoun44

Summary of Significant Accounting Policies - Variable Interest Entities - Additional Information (Details) - USD ($) $ in Thousands	Sep. 30, 2016	Dec. 31, 2015
Accounting Policies [Abstract]
Maximum risk of loss related to the identified VIEs	$ 145,786	$ 3,598

Summary of Significant Accoun45

Summary of Significant Accounting Policies - Segment Information - Additional Information (Details) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016USD ($)	Sep. 30, 2015USD ($)	Sep. 30, 2016USD ($)segment	Sep. 30, 2015USD ($)	Dec. 31, 2015USD ($)
Segment Reporting Information [Line Items]
Number of segments | segment			1
Property, plant and equipment, net	$ 54,429		$ 54,429		$ 42,739
Revenues	48,985	$ 53,367	144,924	$ 132,107
Foreign Countries
Segment Reporting Information [Line Items]
Property, plant and equipment, net	11,331		11,331		$ 3,877
Revenues	$ 3,502	$ 1,183	$ 8,678	$ 3,446

Summary of Significant Accoun46

Summary of Significant Accounting Policies - Summarized Unaudited Financial Information for the Equity Method Investments (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015	Dec. 31, 2015
Schedule of Equity Method Investments [Line Items]
Operating expenses	$ 77,806	$ 61,283	$ 237,500	$ 244,576
Operating loss	(28,821)	(7,916)	(92,576)	(112,469)
Other	4,647	(29,607)	(39,125)	65,121
Equity Method Investments
Schedule of Equity Method Investments [Line Items]
Current assets	81,049		81,049		$ 28,123
Non-current assets	10,992		10,992		1,539
Total assets	92,041		92,041		29,662
Current liabilities	8,325		8,325		6,274
Net assets	83,716		83,716		$ 23,388
Revenues	65	330	394	1,480
Operating expenses	18,363	8,687	50,406	118,180
Operating loss	(18,298)	(8,357)	(50,012)	(116,700)
Other	75	(34)	1,502	(31)
Net loss	$ (18,223)	$ (8,391)	$ (48,510)	$ (116,731)

Mergers and Acquisitions - Oxit

Mergers and Acquisitions - Oxitec - Additional Information (Details) - Oxitec $ in Thousands	1 Months Ended	3 Months Ended	9 Months Ended
	Sep. 30, 2015USD ($)shares	Sep. 30, 2015USD ($)	Sep. 30, 2015USD ($)
Business Acquisition [Line Items]
Percentage of outstanding common stock acquired	100.00%	100.00%	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
Acquisition related costs	$ 1,675
Selling, general and administrative
Business Acquisition [Line Items]
Acquisition related costs		$ 1,644	$ 1,644

Mergers and Acquisitions - Fair

Mergers and Acquisitions - Fair Value of Consideration Transferred (Details) - USD ($) $ in Thousands	1 Months Ended
	Sep. 30, 2015	Apr. 30, 2015	Feb. 28, 2015
Oxitec
Business Acquisition [Line Items]
Cash	$ 90,199
Common shares	56,195
Total consideration transferred	$ 146,394
ActoGeniX NV
Business Acquisition [Line Items]
Cash			$ 32,739
Common shares			39,735
Total consideration transferred			$ 72,474
Okanagan
Business Acquisition [Line Items]
Cash		$ 10,000
Common shares		30,933
Total consideration transferred		$ 40,933

Mergers and Acquisitions - Fa49

Mergers and Acquisitions - Fair Value of Assets Acquired and Liabilities Assumed (Details) - USD ($) $ in Thousands	Sep. 30, 2016	Dec. 31, 2015	Sep. 30, 2015	Apr. 30, 2015	Feb. 28, 2015
Business Acquisition [Line Items]
Goodwill	$ 159,793	$ 165,169
Oxitec
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
Okanagan
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
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 - Okan

Mergers and Acquisitions - Okanagan - Additional Information (Details) - Okanagan - USD ($) $ in Thousands	1 Months Ended	9 Months Ended
	Apr. 30, 2015	Sep. 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		$ 267

Mergers and Acquisitions - Acto

Mergers and Acquisitions - ActoGeniX - Additional Information (Details) - ActoGeniX NV - USD ($) $ in Thousands	1 Months Ended		9 Months Ended
	Aug. 31, 2015	Feb. 28, 2015	Sep. 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 - 2015

Mergers and Acquisitions - 2015 Acquisitions - Pro Forma Financial Information (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Business Acquisition, Pro Forma Information, Nonrecurring Adjustment [Line Items]
Loss before income taxes	$ (30,429)	$ (39,952)	$ (148,652)	$ (53,913)
Net loss	(30,011)	(39,029)	(145,362)	(54,719)
Net loss attributable to the noncontrolling interests	$ 1,029	816	$ 2,887	2,940
2015 Business Acquisitions | Pro Forma
Business Acquisition, Pro Forma Information, Nonrecurring Adjustment [Line Items]
Revenues		53,754		133,060
Loss before income taxes		(43,979)		(66,686)
Net loss		(43,057)		(66,319)
Net loss attributable to the noncontrolling interests		816		2,940
Net loss attributable to Intrexon		$ (42,241)		$ (63,379)

Investments in Joint Ventures -

Investments in Joint Ventures - Intrexon T1D Partners - Additional Information (Details)	1 Months Ended
	Mar. 31, 2016USD ($)	Sep. 30, 2016USD ($)board_seat	Dec. 31, 2015USD ($)
Schedule of Equity Method Investments [Line Items]
Investment		$ 25,847,000	$ 9,977,000
Intrexon T1D Partners
Schedule of Equity Method Investments [Line Items]
Membership interest	50.00%
Maximum additional capital contribution committed	$ 5,000,000
Additional capital contributions committed, remaining commitment		$ 3,650,000
Total number of seats on the joint venture's governing board | board_seat		5
Intrexon T1D Partners | Investors
Schedule of Equity Method Investments [Line Items]
Membership interest	50.00%
Capital contributions	$ 10,000,000
Maximum additional capital contribution committed	5,000,000
Intrexon T1D Partners | Upfront | Upfront and Milestone Payments
Schedule of Equity Method Investments [Line Items]
Collaborative arrangement consideration received, value	$ 10,000,000
Intrexon T1D Partners | Investments In Affiliates
Schedule of Equity Method Investments [Line Items]
Investment		$ 1,078,000

Investments in Joint Ventures54

Investments in Joint Ventures - EnviroFlight - Additional Information (Details) - USD ($)	1 Months Ended		9 Months Ended
	Oct. 31, 2016	Feb. 29, 2016	Sep. 30, 2016	Sep. 30, 2015	Dec. 31, 2015
Schedule of Equity Method Investments [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			25,847,000		$ 9,977,000
Significant Unobservable Inputs (Level 3)
Schedule of Equity Method Investments [Line Items]
Fair value of financial liabilities measured at fair value on a recurring basis			3,839,000
EnviroFlight
Schedule of Equity Method Investments [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
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
Contingent consideration for commercial milestones payable in common stock, maximum		4,000,000
EnviroFlight | Investments In Affiliates
Schedule of Equity Method Investments [Line Items]
Investment			4,611,000
EnviroFlight | Significant Unobservable Inputs (Level 3)
Schedule of Equity Method Investments [Line Items]
Fair value of financial liabilities measured at fair value on a recurring basis			$ 3,839,000
EnviroFlight | Patents, related technologies and know-how
Schedule of Equity Method Investments [Line Items]
Estimated fair value of developed technology acquired		$ 9,880,000
Expected useful life of intangible asset		21 years
EnviroFlight | Investors
Schedule of Equity Method Investments [Line Items]
Membership interest		50.00%
Maximum additional capital contribution committed		$ 5,000,000
EnviroFlight | Subsequent Event
Schedule of Equity Method Investments [Line Items]
Shares issued for contingent consideration (in shares)	59,337
Shares issued for contingent consideration	$ 1,583,000

Investments in Joint Ventures55

Investments in Joint Ventures - Intrexon Energy Partners II - Additional Information (Details)	1 Months Ended
	Dec. 31, 2015USD ($)	Sep. 30, 2016USD ($)board_seat
Schedule of Equity Method Investments [Line Items]
Investment	$ 9,977,000	$ 25,847,000
Intrexon Energy Partners II
Schedule of Equity Method Investments [Line Items]
Membership interest	50.00%
Maximum additional capital contribution committed	$ 10,000,000
Total number of seats on the joint venture's governing board | board_seat		5
Intrexon Energy Partners II | Investments In Affiliates
Schedule of Equity Method Investments [Line Items]
Investment	$ 2,000,000	$ 1,591,000
Intrexon Energy Partners II | Investors
Schedule of Equity Method Investments [Line Items]
Membership interest	50.00%
Capital contributions	$ 18,000,000
Maximum additional capital contribution committed	10,000,000
Intrexon Energy Partners II | All Investors
Schedule of Equity Method Investments [Line Items]
Capital contributions	4,000,000
Intrexon Energy Partners II | Upfront and Milestone Payments | Upfront
Schedule of Equity Method Investments [Line Items]
Collaborative arrangement consideration received, value	$ 18,000,000

Investments in Joint Ventures56

Investments in Joint Ventures - Intrexon Energy Partners - Additional Information (Details)	1 Months Ended
	Mar. 31, 2014USD ($)	Sep. 30, 2016USD ($)board_seat	Dec. 31, 2015USD ($)
Schedule of Equity Method Investments [Line Items]
Investment		$ 25,847,000	$ 9,977,000
Intrexon Energy Partners
Schedule of Equity Method Investments [Line Items]
Membership interest	50.00%
Maximum additional capital contribution committed	$ 25,000,000
Additional capital contributions committed, remaining commitment		$ 12,367,000
Total number of seats on the joint venture's governing board | board_seat		5
Intrexon Energy Partners | Other Accrued Liabilities
Schedule of Equity Method Investments [Line Items]
Investment		$ (627,000)	$ (1,270,000)
Intrexon Energy Partners | Investors
Schedule of Equity Method Investments [Line Items]
Membership interest	50.00%
Capital contributions	$ 25,000,000
Maximum additional capital contribution committed	25,000,000
Upfront and Milestone Payments | Intrexon Energy Partners | Upfront
Schedule of Equity Method Investments [Line Items]
Collaborative arrangement consideration received, value	$ 25,000,000

Investments in Joint Ventures57

Investments in Joint Ventures - OvaXon - Additional Information (Details) $ in Thousands	1 Months Ended
	Jan. 31, 2014USD ($)	Sep. 30, 2016USD ($)board_seat	Dec. 31, 2015USD ($)
Schedule of Equity Method Investments [Line Items]
Investment		$ 25,847	$ 9,977
OvaXon, LLC
Schedule of Equity Method Investments [Line Items]
Capital contributions	$ 1,500
Membership interest	50.00%
Total number of seats on the joint venture's governing board | board_seat		4
OvaXon, LLC | Other Accrued Liabilities
Schedule of Equity Method Investments [Line Items]
Investment			$ (144)
OvaXon, LLC | Investments In Affiliates
Schedule of Equity Method Investments [Line Items]
Investment		$ 435
OvaXon, LLC | Investors
Schedule of Equity Method Investments [Line Items]
Capital contributions	$ 1,500
Membership interest	50.00%

Investments in Joint Ventures58

Investments in Joint Ventures - S & I Ophthalmic - Additional Information (Details) $ in Thousands	1 Months Ended	12 Months Ended
	Oct. 31, 2013USD ($)	Dec. 31, 2015USD ($)	Sep. 30, 2016USD ($)board_seat
Schedule of Equity Method Investments [Line Items]
Investment		$ 9,977	$ 25,847
S & I Ophthalmic, LLC
Schedule of Equity Method Investments [Line Items]
Capital contributions	$ 5,000	5,000
Membership interest	50.00%
Total number of seats on the joint venture's governing board | board_seat			4
S & I Ophthalmic, LLC | Investors
Schedule of Equity Method Investments [Line Items]
Capital contributions	$ 5,000	5,000
Membership interest	50.00%
S & I Ophthalmic, LLC | Investments In Affiliates
Schedule of Equity Method Investments [Line Items]
Investment		$ 6,379	$ 3,737

Collaboration and Licensing R59

Collaboration and Licensing Revenue - Summarized Collaboration and Licensing Revenues (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	$ 30,590	$ 34,726	$ 82,144	$ 66,690
Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	10,220	20,592	24,047	27,326
Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	20,370	14,134	58,097	39,364
ZIOPHARM Oncology, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	10,429	4,651	24,380	13,702
ZIOPHARM Oncology, Inc. | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	4,843	645	6,687	1,933
ZIOPHARM Oncology, Inc. | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	5,586	4,006	17,693	11,769
Oragenics, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	556	5,200	1,869	5,845
Oragenics, Inc. | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	262	4,868	786	5,437
Oragenics, Inc. | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	294	332	1,083	408
Fibrocell Science, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,167	6,140	4,418	10,219
Fibrocell Science, Inc. | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	604	4,823	1,814	5,719
Fibrocell Science, Inc. | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	563	1,317	2,604	4,500
Genopaver, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,693	1,061	4,908	2,665
Genopaver, LLC | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	68	68	205	205
Genopaver, LLC | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,625	993	4,703	2,460
S & I Ophthalmic, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	2,782	1,193	6,326	2,838
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	2,782	1,193	6,326	2,838
OvaXon, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	709	549	2,211	1,855
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	709	549	2,211	1,855
Intrexon Energy Partners, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	4,855	3,810	13,055	9,976
Intrexon Energy Partners, LLC | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	625	625	1,875	1,875
Intrexon Energy Partners, LLC | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	4,230	3,185	11,180	8,101
Persea Bio, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	333	422	988	928
Persea Bio, LLC | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	125	125	375	375
Persea Bio, LLC | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	208	297	613	553
Ares Trading S.A.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	2,316	1,857	6,939	2,596
Ares Trading S.A. | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	1,597	1,597	4,791	2,336
Ares Trading S.A. | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	719	260	2,148	260
Thrive Agrobiotics, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	425		1,309
Thrive Agrobiotics, Inc. | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	46		138
Thrive Agrobiotics, Inc. | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	379		1,171
Intrexon Energy Partners II, LLC
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	872		2,316
Intrexon Energy Partners II, LLC | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	500		1,500
Intrexon Energy Partners II, LLC | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	372		816
Exotech Bio, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	221		360
Exotech Bio, Inc. | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	139		278
Exotech Bio, Inc. | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	82		82
Relieve Genetics, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	462		812
Relieve Genetics, Inc. | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	120		240
Relieve Genetics, Inc. | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	342		572
Intrexon T1D Partners
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	787		1,097
Intrexon T1D Partners | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	276		554
Intrexon T1D Partners | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	511		543
AD Skincare, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	185		185
AD Skincare, Inc. | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	120		120
AD Skincare, Inc. | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	65		65
Other
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	2,798	9,843	10,971	16,066
Other | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	895	7,841	4,684	9,446
Other | Research and Development Services
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaboration and licensing revenues	$ 1,903	$ 2,002	$ 6,287	$ 6,620

Collaboration and Licensing R60

Collaboration and Licensing Revenue - Additional Information (Details) - USD ($)	1 Months Ended			5 Months Ended
	Sep. 30, 2016	Jun. 30, 2016	Mar. 31, 2016	May 31, 2016
Exotech Bio, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Required notice period for voluntary termination of collaborative agreement			90 days
Exotech Bio, Inc. | Maximum
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Milestone payments to be received upon successful achievement, per product			$ 52,500,000
Exotech Bio, Inc. | Upfront | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaborative arrangement consideration received, value			$ 5,000,000
Relieve Genetics, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Required notice period for voluntary termination of collaborative agreement			90 days
Relieve Genetics, Inc. | Maximum
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Milestone payments to be received upon successful achievement, per product			$ 52,500,000
Relieve Genetics, Inc. | Upfront | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaborative arrangement consideration received, value			$ 4,333,000
Intrexon T1D Partners
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Required notice period for voluntary termination of collaborative agreement			90 days
Intrexon T1D Partners | Upfront | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaborative arrangement consideration received, value			$ 10,000,000
AD Skincare, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Required notice period for voluntary termination of collaborative agreement		90 days
AD Skincare, Inc. | Maximum
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Milestone payments to be received upon successful achievement, per product		$ 2,000,000
Milestone payments to be received upon successful achievement, one-time		17,000,000
AD Skincare, Inc. | Upfront | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaborative arrangement consideration received, value		$ 4,333,000
ZIOPHARM Oncology, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Royalty rate as a percentage of net profit		20.00%		50.00%
ZIOPHARM Oncology, Inc. | Other Contractual Payments | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaborative arrangement consideration received, value		$ 120,000,000
Collaborative arrangement consideration received, number of preferred shares (in shares)		100,000
Genten Therapeutics, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Required notice period for voluntary termination of collaborative agreement	90 days
Genten Therapeutics, Inc. | Maximum
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Milestone payments to be received upon successful achievement, per product	$ 82,000,000
Genten Therapeutics, Inc. | Upfront | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaborative arrangement consideration received, value	3,000,000
Collaborative arrangement consideration received in the form of cash	$ 1,500,000
CRS Bio, Inc.
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Required notice period for voluntary termination of collaborative agreement	90 days
CRS Bio, Inc. | Maximum
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Milestone payments to be received upon successful achievement, per product	$ 75,000,000
CRS Bio, Inc. | Upfront | Upfront and Milestone Payments
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Collaborative arrangement consideration received, value	$ 2,100,000

Collaboration and Licensing R61

Collaboration and Licensing Revenue - Summary of Deferred Revenue (Details) - USD ($) $ in Thousands	Sep. 30, 2016	Dec. 31, 2015
Deferred Revenue Arrangement [Line Items]
Deferred revenue	$ 322,397	$ 197,729
Current portion of deferred revenue	54,937	35,366
Long-term portion of deferred revenue	267,460	162,363
Deferred revenue	322,397	197,729
Upfront and milestone payments
Deferred Revenue Arrangement [Line Items]
Deferred revenue	309,126	181,331
Deferred revenue	309,126	181,331
Prepaid research and development services
Deferred Revenue Arrangement [Line Items]
Deferred revenue	7,057	10,938
Deferred revenue	7,057	10,938
Prepaid product and service revenues
Deferred Revenue Arrangement [Line Items]
Deferred revenue	5,594	4,759
Deferred revenue	5,594	4,759
Other
Deferred Revenue Arrangement [Line Items]
Deferred revenue	620	701
Deferred revenue	$ 620	$ 701

Collaboration and Licensing R62

Collaboration and Licensing Revenue - Summary of Deferred Revenue by Collaborator (Details) - USD ($) $ in Thousands	Sep. 30, 2016	Dec. 31, 2015
Deferred Revenue Arrangement [Line Items]
Deferred revenue	$ 322,397	$ 197,729
Upfront and Milestone Payments
Deferred Revenue Arrangement [Line Items]
Deferred revenue	309,126	181,331
Upfront and Milestone Payments | ZIOPHARM Oncology, Inc.
Deferred Revenue Arrangement [Line Items]
Deferred revenue	143,651	30,338
Upfront and Milestone Payments | Oragenics, Inc.
Deferred Revenue Arrangement [Line Items]
Deferred revenue	8,027	8,813
Upfront and Milestone Payments | Fibrocell Science, Inc.
Deferred Revenue Arrangement [Line Items]
Deferred revenue	19,631	21,445
Upfront and Milestone Payments | Genopaver, LLC
Deferred Revenue Arrangement [Line Items]
Deferred revenue	2,045	2,250
Upfront and Milestone Payments | Intrexon Energy Partners, LLC
Deferred Revenue Arrangement [Line Items]
Deferred revenue	18,750	20,625
Upfront and Milestone Payments | Persea Bio, LLC
Deferred Revenue Arrangement [Line Items]
Deferred revenue	4,125	4,500
Upfront and Milestone Payments | Ares Trading S.A.
Deferred Revenue Arrangement [Line Items]
Deferred revenue	48,776	53,567
Upfront and Milestone Payments | Thrive Agrobiotics, Inc.
Deferred Revenue Arrangement [Line Items]
Deferred revenue	1,483	1,621
Upfront and Milestone Payments | Intrexon Energy Partners II
Deferred Revenue Arrangement [Line Items]
Deferred revenue	16,333	17,833
Upfront and Milestone Payments | Exotech Bio, Inc.
Deferred Revenue Arrangement [Line Items]
Deferred revenue	4,722	0
Upfront and Milestone Payments | Relieve Genetics, Inc.
Deferred Revenue Arrangement [Line Items]
Deferred revenue	4,093	0
Upfront and Milestone Payments | Intrexon T1D Partners, LLC
Deferred Revenue Arrangement [Line Items]
Deferred revenue	9,383	0
Upfront and Milestone Payments | AD Skincare, Inc.
Deferred Revenue Arrangement [Line Items]
Deferred revenue	4,213	0
Upfront and Milestone Payments | Genten Therapeutics, Inc.
Deferred Revenue Arrangement [Line Items]
Deferred revenue	4,523	0
Upfront and Milestone Payments | CRS Bio, Inc.
Deferred Revenue Arrangement [Line Items]
Deferred revenue	2,111	0
Upfront and Milestone Payments | Other
Deferred Revenue Arrangement [Line Items]
Deferred revenue	$ 17,260	$ 20,339

Short-term and Long-term Inve63

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	Sep. 30, 2016	Dec. 31, 2015
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	$ 210,892	$ 208,494
Gross Unrealized Gains	79	21
Gross Unrealized Losses	(10)	(540)
Aggregate Fair Value	210,961	207,975
U.S. government debt securities
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	210,620	208,223
Gross Unrealized Gains	79	21
Gross Unrealized Losses	(10)	(540)
Aggregate Fair Value	210,689	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 Inve64

Short-term and Long-term Investments - Summary of Estimated Fair Value of Available-for-Sale Investments Classified by Contractual Maturities (Details) - USD ($) $ in Thousands	Sep. 30, 2016	Dec. 31, 2015
Investments, Debt and Equity Securities [Abstract]
Due within one year	$ 166,839
After one year through two years	44,122
Total	$ 210,961	$ 207,975

Investment in Preferred Stock (

Investment in Preferred Stock (Details) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended	3 Months Ended	9 Months Ended
	Jun. 30, 2016	Sep. 30, 2016	Sep. 30, 2016	Sep. 30, 2015	Dec. 31, 2015
Schedule of Investments [Line Items]
Fair value of financial assets measured at fair value on a recurring basis		$ 376,093	$ 376,093		$ 291,762
Noncash dividend income on preferred shares			3,676	$ 0
Preferred stock
Schedule of Investments [Line Items]
Fair value of financial assets measured at fair value on a recurring basis		$ 123,676	$ 123,676
ZIOPHARM Oncology, Inc.
Schedule of Investments [Line Items]
Preferred shares, stated value (in usd per share)	$ 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 (in shares)	100,000
ZIOPHARM Oncology, Inc.
Schedule of Investments [Line Items]
Dividend income, number of preferred shares received (in shares)		3,063	3,063
Noncash dividend income on preferred shares		$ 3,676	$ 3,676

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	Sep. 30, 2016	Dec. 31, 2015
Assets
Fair value of financial assets measured at fair value on a recurring basis	$ 376,093	$ 291,762
U.S. government debt securities
Assets
Fair value of financial assets measured at fair value on a recurring basis	210,689	207,704
Equity securities
Assets
Fair value of financial assets measured at fair value on a recurring basis	39,432	83,653
Preferred stock
Assets
Fair value of financial assets measured at fair value on a recurring basis	123,676
Other
Assets
Fair value of financial assets measured at fair value on a recurring basis	2,296	405
Quoted Prices in Active Markets (Level 1)
Assets
Fair value of financial assets measured at fair value on a recurring basis	31,245	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	31,245	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	221,172	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	210,689	207,704
Significant Other Observable Inputs (Level 2) | Equity securities
Assets
Fair value of financial assets measured at fair value on a recurring basis	8,187	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	2,296	405
Significant Unobservable Inputs (Level 3)
Assets
Fair value of financial assets measured at fair value on a recurring basis	123,676	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	123,676
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	3 Months Ended
	Sep. 30, 2016USD ($)
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Adjustments to fair value of financial liabilities measured at fair value on a recurring basis	$ 179
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	$ 3,839

Inventory (Details)

Inventory (Details) - USD ($) $ in Thousands	Sep. 30, 2016	Dec. 31, 2015
Inventory [Line Items]
Inventory	$ 21,880	$ 26,563
Supplies, semen and embryos
Inventory [Line Items]
Inventory	1,278	1,402
Work in process
Inventory [Line Items]
Inventory	5,831	6,290
Livestock
Inventory [Line Items]
Inventory	12,588	16,907
Feed
Inventory [Line Items]
Inventory	$ 2,183	$ 1,964

Property, Plant and Equipment69

Property, Plant and Equipment, Net - Schedule of Property, Plant and Equipment (Details) - USD ($) $ in Thousands	Sep. 30, 2016	Dec. 31, 2015
Property, Plant and Equipment [Abstract]
Land and land improvements	$ 11,276	$ 9,119
Buildings and building improvements	7,965	7,520
Furniture and fixtures	1,234	1,283
Equipment	41,343	36,016
Leasehold improvements	10,479	6,888
Computer hardware and software	6,912	5,960
Construction and other assets in progress	7,523	2,193
Property, plant and equipment, gross	86,732	68,979
Less: Accumulated depreciation and amortization	(32,303)	(26,240)
Property, plant and equipment, net	$ 54,429	$ 42,739

Property, Plant and Equipment70

Property, Plant and Equipment, Net - Additional Information (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Property, Plant and Equipment [Abstract]
Depreciation expense	$ 2,332	$ 1,987	$ 6,769	$ 5,768

Goodwill and Intangible Asset71

Goodwill and Intangible Assets, Net - Schedule of Changes in Carrying Amount of Goodwill (Details) $ in Thousands	9 Months Ended
	Sep. 30, 2016USD ($)
Goodwill
Beginning balance	$ 165,169
Foreign currency translation adjustments	(5,376)
Ending balance	$ 159,793

Goodwill and Intangible Asset72

Goodwill and Intangible Assets, Net - Additional Information (Details) - USD ($)	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015	Dec. 31, 2015
Goodwill and Intangible Assets Disclosure [Abstract]
Goodwill accumulated impairment losses	$ 0		$ 0		$ 0
Amortization expense	$ 3,651,000	$ 2,857,000	$ 10,888,000	$ 6,434,000

Goodwill and Intangible Asset73

Goodwill and Intangible Assets, Net - Schedule of Intangible Assets (Details) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2016	Dec. 31, 2015
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	$ 271,276	$ 269,227
Accumulated Amortization	(32,695)	(21,692)
Net	238,581	247,535
Patents, related technologies and know-how
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	170,520	157,411
Accumulated Amortization	(26,596)	(17,775)
Net	143,924	139,636
Customer relationships
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	10,700	10,700
Accumulated Amortization	(4,189)	(2,739)
Net	6,511	7,961
Trademarks
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	6,800	6,800
Accumulated Amortization	(1,598)	(1,018)
Net	5,202	5,782
Covenant not to compete
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	395	384
Accumulated Amortization	(312)	(160)
Net	83	224
In-process research and development
Finite-Lived Intangible Assets [Line Items]
Gross Carrying Amount	82,861	93,932
Accumulated Amortization	0	0
Net	$ 82,861	$ 93,932
Weighted Average | Patents, related technologies and know-how
Finite-Lived Intangible Assets [Line Items]
Weighted Average Useful Life	15 years 3 months 18 days
Weighted Average | Customer relationships
Finite-Lived Intangible Assets [Line Items]
Weighted Average Useful Life	6 years 6 months
Weighted Average | Trademarks
Finite-Lived Intangible Assets [Line Items]
Weighted Average Useful Life	9 years 3 months 18 days
Weighted Average | Covenant not to compete
Finite-Lived Intangible Assets [Line Items]
Weighted Average Useful Life	2 years

Lines of Credit and Long Term74

Lines of Credit and Long Term Debt - Lines of Credit - Additional Information (Details) - Revolving Line of Credit	9 Months Ended
	Sep. 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	3.48%
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	$ 549,000

Lines of Credit and Long Term75

Lines of Credit and Long Term Debt - Schedule of Long Term Debt Instruments (Details) - USD ($) $ in Thousands	Sep. 30, 2016	Dec. 31, 2015
Debt Instrument [Line Items]
Long term debt	$ 8,421	$ 8,528
Less current portion	471	930
Long term debt, net of current portion	7,950	7,598
Notes payable
Debt Instrument [Line Items]
Long term debt	5,769	6,477
Royalty-based financing
Debt Instrument [Line Items]
Long term debt	2,003	1,807
Other
Debt Instrument [Line Items]
Long term debt	$ 649	$ 244

Lines of Credit and Long Term76

Lines of Credit and Long Term Debt - Long Term Debt - Additional Information (Details) - USD ($)	9 Months Ended
	Sep. 30, 2016	Dec. 31, 2015	Mar. 31, 2013
Debt Instrument [Line Items]
Long term debt	$ 8,421,000	$ 8,528,000
Notes payable to banks | Trans Ova Genetics, LC | American State Bank
Debt Instrument [Line Items]
Long term debt	5,338,000
Debt instrument, periodic payment	$ 39,000
Debt instrument, interest rate, stated percentage	3.95%
Notes payable
Debt Instrument [Line Items]
Long term debt	$ 5,769,000	6,477,000
Notes payable | Exemplar Genetics, LLC
Debt Instrument [Line Items]
Long term debt	431,000
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%
Other
Debt Instrument [Line Items]
Long term debt	$ 649,000	244,000
Other | AquaBounty Technologies, Inc. | Finance PEI
Debt Instrument [Line Items]
Long term debt	543,000
Debt instrument, periodic payment	$ 4,000
Debt instrument, interest rate, stated percentage	4.00%
Royalty-based financing
Debt Instrument [Line Items]
Long term debt	$ 2,003,000	$ 1,807,000
Royalty-based financing | AquaBounty Technologies, Inc. | Atlantic Canada Opportunities Agency
Debt Instrument [Line Items]
Long term debt	2,003,000
Amount available under the grant for research and development	$ 2,185,000
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 Term77

Lines of Credit and Long Term Debt - Schedule of Future Maturities of Long Term Debt (Details) $ in Thousands	Sep. 30, 2016USD ($)
Debt Disclosure [Abstract]
2,016	$ 168
2,017	404
2,018	549
2,019	364
2,020	335
2,021	774
Thereafter	3,824
Total	$ 6,418

Income Taxes (Details)

Income Taxes (Details) - USD ($)	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Operating Loss Carryforwards [Line Items]
Deferred income tax expense (benefit)	$ (308,000)	$ (578,000)	$ (2,967,000)	$ 374,000
Deferred tax liabilities	18,060,000		18,060,000
Domestic Tax Authority
Operating Loss Carryforwards [Line Items]
Taxable income (loss)	8,334,000	(15,865,000)	(9,346,000)	22,935,000
Current income tax expense (benefit)	0	(318,000)	0	459,000
Operating loss carryforwards	257,700,000		257,700,000
Federal and state research and development tax credits	7,060,000		7,060,000
Operating loss carryforward benefits from stock compensation deductions	54,400,000		54,400,000
Foreign Tax Authority
Operating Loss Carryforwards [Line Items]
Current income tax expense (benefit)	(110,000)	$ (27,000)	(323,000)	$ (27,000)
Operating loss carryforwards	$ 120,600,000		$ 120,600,000

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	Sep. 30, 2016	Dec. 31, 2015
Accumulated Other Comprehensive Income (Loss) [Line Items]
Intrexon shareholders' equity	$ 600,473	$ 694,078
Unrealized gain (loss) on investments
Accumulated Other Comprehensive Income (Loss) [Line Items]
Intrexon shareholders' equity	69	(519)
Foreign currency translation adjustments
Accumulated Other Comprehensive Income (Loss) [Line Items]
Intrexon shareholders' equity	(25,371)	(12,233)
Total accumulated other comprehensive loss
Accumulated Other Comprehensive Income (Loss) [Line Items]
Intrexon shareholders' equity	$ (25,302)	$ (12,752)

Share-Based Payments - Schedule

Share-Based Payments - Schedule of Stock-Based Compensation Expense (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation costs	$ 10,792	$ 8,385	$ 30,631	$ 26,524
Cost of products
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation costs	21	21	61	76
Cost of services
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation costs	68	98	206	301
Research and development
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation costs	2,236	2,234	6,979	6,141
Selling, general and administrative
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Stock-based compensation costs	$ 8,467	$ 6,032	$ 23,385	$ 20,006

Share-Based Payments - Addition

Share-Based Payments - Additional Information (Details) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended		3 Months Ended	9 Months Ended
	Oct. 31, 2016	Nov. 30, 2015	Sep. 30, 2016	Sep. 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	$ 1,397
Intrexon Stock Option Plan - 2008 Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Remaining shares available to grant (in shares)							0
Options outstanding (in shares)			570,977	570,977
Intrexon Stock Option Plan - 2013 Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Remaining shares available to grant (in shares)			3,982,064	3,982,064
Options outstanding (in shares)			10,532,430	10,532,430
Number of shares authorized for issuance (in shares)			16,000,000	16,000,000
Intrexon Stock Option Plan - Other Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Options outstanding (in shares)			1,000,000	1,000,000
Intrexon Stock Option Plans
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Options outstanding (in shares)			12,103,407	12,103,407		11,043,528
Unrecognized compensation costs related to nonvested awards			$ 106,649	$ 106,649		$ 113,655
Recognized over weighted-average period				3 years
Weighted average exercise price of option (in usd per share)			$ 31.24	$ 31.24		$ 32.66
Shares exercisable at end of period (in shares)			3,369,252	3,369,252
AquaBounty Stock Option Plan - 2006 Plan
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Remaining shares available to grant (in shares)					0
Options outstanding (in shares)			5,567,000	5,567,000		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 (in shares)			5,321,598	5,321,598		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
Subsequent Event | Chief Executive Officer
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Initial term of compensation arrangement	2 months

Share-Based Payments - Schedu83

Share-Based Payments - Schedule of Stock Option Activity (Details) - Intrexon Stock Option Plans - $ / shares	9 Months Ended	12 Months Ended
	Sep. 30, 2016	Dec. 31, 2015
Number of Shares
Balances at beginning of period (in shares)	11,043,528
Granted (in shares)	4,384,860
Exercised (in shares)	(1,162,843)
Forfeited (in shares)	(2,127,334)
Expired (in shares)	(34,804)
Balances at end of period (in shares)	12,103,407	11,043,528
Exercisable at end of period (in shares)	3,369,252
Vested and Expected to Vest at end of period (in shares)	10,177,058
Weighted Average Exercise Price
Balances at beginning of period (in usd per share)	$ 32.66
Granted (in usd per share)	29.42
Exercised (in usd per share)	(15.63)
Forfeited (in usd per share)	(43.29)
Expired (in usd per share)	(35.76)
Balances at period end (in usd per share)	31.24	$ 32.66
Exercisable, weighted average exercise price, at end of period (in usd per share)	27.99
Vested and Expected to Vest, weighted average exercise price at end of period (in usd per share)	$ 30.99
Weighted Average Remaining Contractual Term (Years)
Balances, weighted average remaining contractual period	8 years 6 months	8 years 5 months 27 days
Exercisable at period end, weighted average remaining contractual period	7 years 2 months 30 days
Vested and Expected to Vest at period end, weighted average remaining contractual period	8 years 4 months 12 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 (in shares) | 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	Sep. 30, 2016USD ($)
Commitments and Contingencies Disclosure [Abstract]
2,016	$ 705
2,017	6,362
2,018	5,695
2,019	5,434
2,020	5,487
2,021	4,888
Thereafter	20,179
Total	$ 48,750

Commitments and Contingencies86

Commitments and Contingencies - Operating Leases - Additional Information (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Commitments and Contingencies Disclosure [Abstract]
Rent expense	$ 2,075	$ 2,167	$ 6,410	$ 6,548
Rental income under sublease agreement	184	$ 334	854	$ 1,153
Future rental income under sublease agreements, 2016	9		9
Future rental income under sublease agreements, 2017	$ 36		$ 36

Commitments and Contingencies87

Commitments and Contingencies - Contingencies - Additional Information (Details) $ in Thousands	1 Months Ended		9 Months Ended	50 Months Ended
	May 31, 2016claim	Apr. 30, 2016USD ($)	Sep. 30, 2016USD ($)	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
Royalty 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 ($) $ / shares in Units, $ in Thousands	1 Months Ended			3 Months Ended		9 Months Ended
	Sep. 30, 2016	Jun. 30, 2016	Nov. 30, 2015	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015	Dec. 31, 2015
Related Party Transaction [Line Items]
Shares issued as payment for services						$ 8,284
Fair value of financial assets measured at fair value on a recurring basis	$ 376,093			$ 376,093		376,093		$ 291,762
Collaboration and licensing revenues				30,590	$ 34,726	82,144	$ 66,690
Third Security, LLC
Related Party Transaction [Line Items]
Expense for services				$ 156	142	$ 301	294
Initial term of services agreement			1 year
Shares issued as payment for services (in shares)				89,326		254,496
Shares issued as payment for services				$ 2,132		$ 6,542
Third Security, LLC | Common Stock
Related Party Transaction [Line Items]
Expense for services			$ 800
Fibrocell Science, Inc.
Related Party Transaction [Line Items]
Payments to acquire convertible notes and warrants	$ 2,604
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
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%
Related Parties, Aggregated
Related Party Transaction [Line Items]
Collaboration and licensing revenues				$ 26,688	31,740	$ 70,299	59,775
Harvest Intrexon Enterprise Fund I, LP | Other nonoperating income
Related Party Transaction [Line Items]
Management fees revenue				613	$ 697	1,871	$ 697
Convertible Note and Warrants | Other Assets | Fibrocell Science, Inc.
Related Party Transaction [Line Items]
Fair value of financial assets measured at fair value on a recurring basis	$ 1,990			$ 1,990		$ 1,990

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		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 30, 2015
Numerator:
Net loss attributable to Intrexon	$ (28,982)	$ (38,213)	$ (142,475)	$ (51,779)
Denominator:
Weighted average shares outstanding, basic and diluted (in shares)	118,346,782	112,244,129	117,785,160	109,244,641
Net loss attributable to Intrexon per share, basic and diluted (in usd per share)	$ (0.24)	$ (0.34)	$ (1.21)	$ (0.47)

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		9 Months Ended
	Sep. 30, 2016	Sep. 30, 2015	Sep. 30, 2016	Sep. 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)	12,133,598	10,854,759	12,133,598	10,854,759
Options
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of net loss per share (in shares)	12,103,407	10,660,040	12,103,407	10,660,040
Warrants
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of net loss per share (in shares)	30,191	194,719	30,191	194,719

Subsequent Events (Details)

Subsequent Events (Details) - Subsequent Event $ in Thousands	Nov. 09, 2016USD ($)shares
AquaBounty Technologies, Inc.
Subsequent Event [Line Items]
Commitment to purchase additional shares of majority-owned subsidiary upon approval for NASDAQ listing, in shares | shares	72,632,190
Commitment to purchase additional shares of majority-owned subsidiary upon approval for NASDAQ listing	$ 25,000
Maximum | AquaBounty Technologies, Inc.
Subsequent Event [Line Items]
Principal balance of convertible promissory note receivable with a related party	$ 10,000