Precigen (PGEN) 10-Q 14 Aug 14 2014 Q2 Quarterly report Financial data

Document_and_Entity_Informatio

Document and Entity Information	6 Months Ended
	Jun. 30, 2014	Aug. 08, 2014
Document And Entity Information [Abstract]	'	'
Document Type	'10-Q	'
Amendment Flag	'false	'
Document Period End Date	30-Jun-14	'
Document Fiscal Year Focus	'2014	'
Document Fiscal Period Focus	'Q2	'
Trading Symbol	'XON	'
Entity Registrant Name	'INTREXON CORP	'
Entity Central Index Key	'0001356090	'
Current Fiscal Year End Date	'--12-31	'
Entity Filer Category	'Non-accelerated Filer	'
Entity Common Stock, Shares Outstanding	'	100,477,548

Consolidated_Balance_Sheets

Consolidated Balance Sheets (USD $)	Jun. 30, 2014	Dec. 31, 2013
In Thousands, unless otherwise specified
Current assets	'	'
Cash and cash equivalents	$74,505	$49,509
Short-term investments	101,046	127,980
Receivables	'	'
Trade	806	790
Related parties	8,304	5,285
Other	698	1,282
Prepaid expenses and other	2,944	2,710
Total current assets	188,303	187,556
Long-term investments	73,545	60,581
Property, plant and equipment, net	17,389	16,629
Intangible assets, net	45,406	41,956
Goodwill	34,865	13,823
Investments in affiliates	4,997	6,284
Other assets	1,137	1,118
Total assets	500,537	469,472
Current liabilities	'	'
Accounts payable	1,799	1,057
Accrued compensation and benefits	4,094	5,157
Other accrued liabilities	3,998	4,217
Deferred revenue	10,706	7,793
Related party payables	95	1,605
Total current liabilities	20,692	19,829
Long term debt	2,001	1,653
Deferred revenue	88,747	65,778
Other long term liabilities	731	869
Total liabilities	112,171	88,129
Commitments and contingencies (Note 14)	'	'
Total equity	'	'
Common stock, no par value, 200,000,000 shares authorized as of June 30, 2014 and December 31, 2013; 99,013,018 and 97,053,712 shares issued and outstanding as of June 30, 2014 and December 31, 2013, respectively	0	0
Additional paid-in capital	797,516	743,084
Accumulated deficit	-424,342	-376,414
Accumulated other comprehensive income	81	52
Total Intrexon shareholders' equity	373,255	366,722
Noncontrolling interests	15,111	14,621
Total equity	388,366	381,343
Total liabilities and total equity	500,537	469,472
Collaborative Partner Securities	'	'
Receivables	'	'
Equity securities	$134,895	$141,525

Consolidated_Balance_Sheets_Pa

Consolidated Balance Sheets (Parenthetical) (USD $)	Jun. 30, 2014	Dec. 31, 2013
Statement Of Financial Position [Abstract]	'	'
Common stock, no par value	'	'
Common stock, shares authorized	200,000,000	200,000,000
Common stock, shares issued	99,013,018	97,053,712
Common stock, shares outstanding	99,013,018	97,053,712

Consolidated_Statements_of_Ope

Consolidated Statements of Operations (USD $)	3 Months Ended		6 Months Ended
In Thousands, except Share data, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Revenues	'	'	'	'
Collaboration revenues	$11,764	$6,674	$19,601	$10,538
Other revenues	23	16	40	37
Total revenues	11,787	6,690	19,641	10,575
Operating Expenses	'	'	'	'
Research and development	14,479	13,510	26,570	24,921
General and administrative	15,390	7,434	29,025	13,914
Total operating expenses	29,869	20,944	55,595	38,835
Operating loss	-18,082	-14,254	-35,954	-28,260
Other Income (Expense)	'	'	'	'
Unrealized appreciation (depreciation) in fair value of equity securities	-33,777	7,734	-11,855	-21,635
Gain on previously held equity investment	0	0	0	7,415
Interest expense	-40	-11	-79	-25
Investment income	110	15	198	20
Other expense	-74	-3	-82	-6
Total other income (expense)	-33,781	7,735	-11,818	-14,231
Equity in net loss of affiliates	-1,355	'	-1,891	-390
Loss before income taxes	-53,218	-6,519	-49,663	-42,881
Income tax benefit (expense)	283	0	-23	0
Net loss	-52,935	-6,519	-49,686	-42,881
Net loss attributable to noncontrolling interests	892	556	1,758	607
Net loss attributable to Intrexon	-52,043	-5,963	-47,928	-42,274
Accretion of dividends on redeemable convertible preferred stock	'	-7,942	'	-14,347
Net loss attributable to common shareholders	($52,043)	($13,905)	($47,928)	($56,621)
Net loss attributable to common shareholders per share, basic and diluted	($0.53)	($2.45)	($0.49)	($10)
Weighted average shares outstanding, basic and diluted	98,892,601	5,667,557	98,113,493	5,664,665

Consolidated_Statements_of_Com

Consolidated Statements of Comprehensive Loss (USD $)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Statement Of Income And Comprehensive Income [Abstract]	'	'	'	'
Net loss	($52,935)	($6,519)	($49,686)	($42,881)
Other comprehensive income (loss):	'	'	'	'
Unrealized gain (loss) on investments	22	-15	91	-15
Foreign currency translation adjustments	-108	71	-67	54
Comprehensive loss	-53,021	-6,463	-49,662	-42,842
Comprehensive loss attributable to the noncontrolling interests	915	523	1,763	582
Comprehensive loss attributable to Intrexon	($52,106)	($5,940)	($47,899)	($42,260)

Consolidated_Statements_of_Sha

Consolidated Statements of Shareholders' and Total Equity (USD $)	Total	Common Stock	Additional Paid-in Capital	Accumulated Other Comprehensive Income	Accumulated Deficit	Total Intrexon Shareholders' Equity	Noncontrolling Interests
In Thousands, except Share data	USD ($)		USD ($)	USD ($)	USD ($)	USD ($)	USD ($)
Balances at Dec. 31, 2013	$381,343	'	$743,084	$52	($376,414)	$366,722	$14,621
Balances (in shares) at Dec. 31, 2013	97,053,712	97,053,712	'	'	'	'	'
Stock-based compensation expense	10,622	'	10,530	'	'	10,530	92
Exercises of stock options	976	'	970	'	'	970	6
Exercises of stock options, shares	'	273,945	'	'	'	'	'
Contribution of services by shareholder	977	'	977	'	'	977	'
Shares issued to nonemployee members of the Board of Directors	486	'	486	'	'	486	'
Shares issued to nonemployee members of the Board of Directors (in shares)	'	16,908	'	'	'	'	'
Shares issued in private placement	25,000	'	25,000	'	'	25,000	'
Shares issued in private placement (in shares)	'	972,004	'	'	'	'	'
Shares issued in Medistem, Inc. acquisition, net	18,880	'	18,880	'	'	18,880	'
Shares issued in Medistem, Inc. acquisition, net (in shares)	'	696,449	'	'	'	'	'
Adjustments for noncontrolling interest	-256	'	-2,411	'	'	-2,411	2,155
Net loss	-49,686	'	'	'	-47,928	-47,928	-1,758
Other comprehensive income (loss)	24	'	'	29	'	29	-5
Balances at Jun. 30, 2014	$388,366	'	$797,516	$81	($424,342)	$373,255	$15,111
Balances (in shares) at Jun. 30, 2014	99,013,018	99,013,018	'	'	'	'	'

Consolidated_Statements_of_Cas

Consolidated Statements of Cash Flows (USD $)	6 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013
Cash flows from operating activities	'	'
Net loss	($49,686)	($42,881)
Adjustments to reconcile net loss to net cash used in operating activities:	'	'
Depreciation and amortization	3,773	3,694
Loss on disposal of property and equipment	81	6
Unrealized depreciation on equity securities	11,855	21,635
Amortization of discount/premium on investments	792	51
Equity in net loss of affiliates	1,891	390
Gain on previously held equity investment	0	-7,415
Stock-based compensation expense	10,622	1,196
Contribution of services by shareholder	977	775
Shares issued to nonemployee members of the Board of Directors	486	85
Other noncash items	71	'
Receivables:	'	'
Trade	-18	-112
Related parties	-3,019	-489
Other	-121	-184
Prepaid expenses and other	-235	747
Other assets	71	-7,547
Accounts payable	339	722
Accrued compensation and benefits	-1,147	-537
Other accrued liabilities	-1,422	39
Deferred revenue	20,657	2,311
Related party payables	-10	-89
Other long term liabilities	-128	-10
Net cash used in operating activities	-4,171	-27,613
Cash flows from investing activities	'	'
Purchases of investments	-60,478	-95,246
Maturities of investments	73,747	'
Acquisition of business, net of cash received	-4,912	512
Investment in affiliate	-1,500	'
Purchases of property and equipment	-3,751	-776
Proceeds from sale of property and equipment	151	'
Issuance of related party note receivable	'	-300
Proceeds from related party notes receivable	'	500
Net cash provided by (used in) investing activities	3,257	-95,310
Cash flows from financing activities	'	'
Proceeds from issuance of Series F redeemable convertible preferred shares	'	150,000
Proceeds from issuance of shares in a private placement	25,000	'
Payments of capital lease obligations	-17	-34
Proceeds from long term debt	268	171
Payments of long term debt	'	-18
Proceeds from stock option exercises	976	9
Payment of stock issuance costs	-256	-3,148
Net cash provided by financing activities	25,971	146,980
Effect of exchange rate changes on cash and cash equivalents	-61	1
Net increase in cash and cash equivalents	24,996	24,058
Cash and cash equivalents	'	'
Beginning of period	49,509	10,403
End of period	74,505	34,461
Supplemental disclosure of cash flow information	'	'
Cash paid during the period for interest	14	48
Significant noncash financing and investing activities	'	'
Accretion of dividends on redeemable convertible preferred shares	'	14,347
Stock received as consideration for collaboration agreements	5,225	3,732
Stock issued in Medistem, Inc. acquisition, net	18,880	'
IPO fees included in accrued expenses	'	$1,526

Organization_and_Basis_of_Pres

Organization and Basis of Presentation	6 Months Ended
	Jun. 30, 2014
Accounting Policies [Abstract]	'
Organization and Basis of Presentation	'
	1. Organization and Basis of Presentation
	Intrexon Corporation (the “Company” or “Intrexon”) is a Virginia corporation focused on forming collaborations to create biologically based products and processes using synthetic biology. At June 30, 2014, the Company owned approximately 60% of AquaBounty Technologies, Inc. (“AquaBounty”), a biotechnology company focused on improving productivity in commercial aquaculture (Note 4), and 51% of Biological & Popular Culture, Inc. (“BioPop”) (Note 4). The Company has operations in California, Florida, Maryland, Virginia, and Budapest, Hungary. There have been no commercialized products derived from the Company’s collaborations to date.
	Effective July 26, 2013, the Company’s board of directors and shareholders approved a reverse stock split of 1-for-1.75 of the Company’s shares of common stock. Shareholders entitled to fractional shares as a result of the reverse stock split received a cash payment in lieu of receiving fractional shares. Shares of common stock underlying outstanding stock options and warrants were proportionately reduced and the respective exercise prices were proportionately increased in accordance with the terms of the agreements governing such securities. All share and per share data of the Company’s common stock, including shares of common stock underlying stock options and warrants, have been retroactively adjusted in the accompanying consolidated financial statements to reflect the reverse stock split.
	On August 13, 2013, the Company completed its initial public offering (“IPO”), whereby the Company sold 11,499,998 shares of common stock, inclusive of 1,499,999 shares of common stock sold by the Company pursuant to the full exercise of an overallotment option granted to the underwriters in connection with the IPO, at a price of $16.00 per share. The shares began trading on the New York Stock Exchange (“NYSE”) on August 8, 2013. The aggregate proceeds from the IPO were approximately $168,300, net of underwriting discounts and commissions of approximately $12,900 and offering expenses paid by the Company of approximately $2,800 (of which $2,300 were capitalized). Upon the closing of the IPO, all shares of the Company’s redeemable convertible preferred stock, including accrued but unpaid dividends thereon, converted into 79,705,130 shares of common stock. Additionally, in connection with the closing of the IPO, the Company amended and restated its articles of incorporation to increase the number of authorized shares of common stock to 200,000,000 and decrease the number of authorized shares of undesignated preferred stock to 25,000,000.
	These consolidated financial statements are presented in United States dollars and are prepared under accounting principles generally accepted in the United States of America (“U.S. GAAP”).

Summary_of_Significant_Account

Summary of Significant Accounting Policies	6 Months Ended
	Jun. 30, 2014
Accounting Policies [Abstract]	'
Summary of Significant Accounting Policies	'
	2. Summary of Significant Accounting Policies
	Principles of Consolidation
	The accompanying consolidated financial statements reflect the operations of the Company and its subsidiaries. All intercompany accounts and transactions have been eliminated.
	Unaudited Financial Information
	The accompanying interim consolidated financial statements are unaudited and have been prepared in accordance with U.S. GAAP. Certain information and footnote disclosures normally included in the Company’s annual financial statements have been condensed or omitted. These interim consolidated financial statements, in the opinion of management, reflect all normal recurring adjustments necessary for fair statement of the Company’s financial position as of June 30, 2014 and results of operations and cash flows for the interim periods ended June 30, 2014 and 2013. These interim financial results are not necessarily indicative of the results to be expected for the year ending December 31, 2014, 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, 2013.
	Revenue Recognition
	The Company generates revenue through contractual agreements with collaborators (known as exclusive channel collaborations, “ECC” or “ECCs”) whereby the collaborators 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. Generally, the terms of these collaborative agreements provide that the Company receives some or all of the following: (i) upfront payments upon consummation of the agreement, (ii) reimbursements for costs incurred by the Company for research and development and/or manufacturing efforts related to specific applications provided for in the agreement, (iii) milestone payments upon the achievement of specified development, regulatory and commercial activities, and (iv) royalties on sales of products arising from the collaboration.
	The Company’s collaboration agreements typically contain multiple elements, or deliverables, including technology licenses, research and development services, and in certain cases manufacturing services. The Company applies the provisions of Accounting Standards Update (“ASU”) No. 2009-13, Revenue Recognition (Topic 605): Multiple Deliverable Revenue Arrangements (“ASU 2009-13”). In accordance with the provisions of ASU 2009-13, the Company identifies the deliverables within the agreements and evaluates which deliverables represent separate units of accounting. Analyzing the agreements to identify deliverables requires the use of judgment. A deliverable is considered a separate unit of accounting when the deliverable has value to the collaborative partner on a standalone basis based on the consideration of the relevant facts and circumstances for each agreement.
	Consideration received is allocated at the inception of the agreement to all identified units of accounting based on their relative selling price. When available, the relative selling price for each deliverable is determined using vendor specific objective evidence (“VSOE”) of the selling price or third-party evidence of the selling price, if VSOE does not exist. If neither VSOE nor third-party evidence of the selling price exists, the Company uses its best estimate of the selling price (“BESP”) for the deliverable. The amount of allocable consideration is limited to amounts that are fixed or determinable. The consideration received is allocated among the separate units of accounting, and the applicable revenue recognition criteria are applied to each of the separate units. The Company recognizes the revenue allocated to each unit of accounting as the Company delivers the related goods or services. If the Company determines that certain deliverables should be treated as a single unit of accounting, then the revenue is recognized using either a proportional performance or straight-line method, depending on whether the Company can reasonably estimate the level of effort required to complete its performance obligations under an arrangement and whether such performance obligations are provided on a best-efforts basis. As the Company cannot reasonably estimate its performance obligations related to its collaborators, the Company recognizes revenue on a straight-line basis over the period it expects to complete its performance obligations.
	The terms of the Company’s agreements may provide for milestone payments upon achievement of certain defined events. The Company applies ASU No. 2010-17, Revenue Recognition — Milestone Method (“ASU 2010-17” or “Milestone Method”). Under the Milestone Method, the Company recognizes consideration that is contingent upon the achievement of a milestone in its entirety as revenue in the period in which the milestone is achieved only if the milestone is substantive in its entirety. A milestone is considered substantive when it meets all of the following criteria:
		-1	The consideration is commensurate with either the entity’s performance to achieve the milestone or the enhancement of the value of the delivered item or items as a result of a specific outcome resulting from the entity’s performance to achieve the milestone;
		-2	The consideration relates solely to past performance; and
		-3	The consideration is reasonable relative to all of the deliverables and payment terms within the arrangement.
	In the event that a milestone is not considered substantive, the Company recognizes the milestone consideration as revenue using the same method applied to upfront payments.
	Research and development services are a deliverable satisfied by the Company in accordance with the terms of the collaboration agreements and the Company considers these services to be inseparable from the license to the core technology; therefore, reimbursements of services performed are recognized as revenue. Because reimbursement (i) is contingent upon performance of the services by the Company, (ii) does not include a profit component, and (iii) does not relate to any future deliverable, the revenue is recognized during the period in which the related services are performed and collection of such amounts is reasonably assured. Payments received for manufacturing services will be recognized when the earnings process related to the manufactured materials has been completed. Royalties to be received under the agreements will be recognized as earned.
	Research and Development
	The Company considers that regulatory and other uncertainties inherent in the research and development of new products preclude it from capitalizing such costs. Research and development expenses include salaries and related costs of research and development personnel, and the costs of consultants, facilities, materials and supplies associated with research and development projects as well as various laboratory studies. Indirect research and development costs include depreciation, amortization and other indirect overhead expenses.
	The Company has research and development arrangements with third parties that include upfront and milestone payments. At June 30, 2014 and December 31, 2013, the Company had research and development commitments with third parties totaling $2,647 and $2,445, respectively, of which $1,049 and $957, respectively, had not yet been incurred. The commitments are generally cancellable by the Company at any time upon written notice.
	Cash and Cash Equivalents
	All highly liquid investments with an original maturity of three months or less at the date of purchase are considered to be cash equivalents. Cash balances at a limited number of banks may periodically exceed insurable amounts. The Company believes that it mitigates its risk by investing in or through major financial institutions with high quality credit ratings. Recoverability of investments is dependent upon the performance of the issuer. At June 30, 2014 and December 31, 2013, the Company had cash equivalent investments in highly liquid money market accounts at major financial institutions of $67,792 and $43,733, respectively.
	Short-term and Long-term Investments
	Short-term and long-term investments include U.S. government debt securities, commercial paper and certificates of deposit. The Company determines the appropriate classification as short-term or long-term at the time of purchase based on original maturities and management’s reasonable expectation of sales and redemption. The Company reevaluates such classification at each balance sheet date. The Company’s written investment policy requires investments to be explicitly rated by two of the three following rating services: Standard & Poor’s, Moody’s and/or Fitch and to have a minimum rating of A1, P1 and/or F-1, respectively, from those agencies. In addition, the investment policy limits the amount of credit exposure to any one issuer.
	Equity Securities
	The Company holds equity securities received and/or purchased from certain collaborators. Other than investments accounted for using the equity method, the Company elected the fair value option to account for its equity securities held in these collaborators. These equity securities are recorded at fair value at each reporting date and are subject to market price volatility. Unrealized gains and losses resulting from fair value adjustments are reported in the consolidated statement of operations. The fair value of these equity securities is subject to fluctuation in the future due to the volatility of the stock market, changes in general economic conditions and changes in the financial conditions of these collaborators. These equity securities are classified as noncurrent in the consolidated balance sheet since the Company does not intend to sell these equity securities within one year. The Company has not sold any of these equity securities to date.
	The Company records the fair value of securities received on the date the collaboration is consummated or the milestone is achieved using the closing, quoted price of the collaborator’s security on that date, assuming the transfer of consideration is considered perfunctory. If the transfer of the consideration is not considered perfunctory, the Company considers the specific facts and circumstances to determine the appropriate date on which to evaluate fair value. The Company also evaluates whether any discounts for trading restrictions or other basis for lack of marketability should be applied to the fair value of the securities at inception of the collaboration. In the event the Company concludes that a discount should be applied, the fair value of the securities is adjusted at inception of the collaboration and re-evaluated at each reporting period thereafter.
	Fair Value of Financial Instruments
	Fair value is the price that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date. As such, fair value is a market-based measurement that should be determined based on assumptions that market participants would use in pricing an asset and liability. As a basis for considering such assumptions, the Company uses a three-tier fair value hierarchy that prioritizes the inputs used in its fair value measurements. The hierarchy gives the highest priority to unadjusted quoted prices in active markets for identical assets or liabilities (Level 1 measurements) and the lowest priority to unobservable inputs (Level 3 measurements). The three levels of the fair value hierarchy are as follows:
			Level 1:		Quoted prices in active markets for identical assets and liabilities;
			Level 2:		Other than quoted prices included in Level 1 inputs that are observable for the asset or liability, either directly or indirectly; and
			Level 3:		Unobservable inputs for the asset or liability used to measure fair value to the extent that observable inputs are not available.
	Concentrations of Risk
	Due to the Company’s mix of fixed and variable rate securities holdings, the Company’s investment portfolio is susceptible to changes in interest rates. As of June 30, 2014, gross unrealized losses on the Company’s investments were not material. From time to time, the Company may liquidate some or all of its investments to fund operational needs or other activities, such as capital expenditures or business acquisitions. Depending on which investments the Company liquidates to fund these activities, the Company could recognize a portion, or all, of the gross unrealized losses.
	Equity Method Investments
	Through March 15, 2013, the Company accounted for its investment in AquaBounty using the equity method of accounting since the Company had the ability to exercise significant influence, but not control, over the operating activities of AquaBounty. The excess of the investment over the Company’s pro-rata share of AquaBounty’s net assets represented identifiable intangible assets and equity-method goodwill. On March 15, 2013, the Company acquired additional ownership interests in AquaBounty which resulted in the Company gaining control over AquaBounty, thereby requiring consolidation effective on that date (Note 4).
	The Company has entered into three strategic joint ventures (Note 5). The Company accounts for its investments in these joint ventures using the equity method of accounting since the Company has the ability to exercise significant influence, but not control, over the operating activities of these entities.
	The Company determined that it has significant influence over two of its collaborators, Ziopharm Oncology, Inc. (“Ziopharm”) and Oragenics, Inc. (“Oragenics”), as of June 30, 2014 and December 31, 2013, based on its ownership interests, representation on the board of directors of the collaborators and other qualitative factors. The Company accounts for its investments in Ziopharm and Oragenics using the fair value option. The fair value of the Company’s equity securities of Ziopharm was $66,053 and $71,134 as of June 30, 2014 and December 31, 2013, respectively, and is included as equity securities in the respective consolidated balance sheets. The Company’s ownership percentage of Ziopharm is 16.3% and 16.4% at June 30, 2014 and December 31, 2013, respectively. Unrealized appreciation (depreciation) in the fair value of the Company’s equity securities held in Ziopharm was $(9,015) and $3,789 for the three months ended June 30, 2014 and 2013, respectively, and $(5,081) and $(27,743) for the six months ended June 30, 2014 and 2013, respectively. Summarized unaudited financial information for Ziopharm for the three and six months ended June 30, 2014 and 2013 are as follows:
			Three months ended						Six months ended
			June 30,						June 30,
			2014			2013			2014			2013
	Revenues		$	200		$	200		$	400		$	400
	Operating expenses			11,377			18,496			21,361			42,279
	Loss from operations			(11,177	)		(18,296	)		(20,961	)		(41,879	)
	Other			5,601			(396	)		5,674			10,388
	Net loss		$	(5,576	)	$	(18,692	)	$	(15,287	)	$	(31,491	)
	In September 2013, the Company increased its investment in Oragenics, upon which the Company concluded it had significant influence over the operations of Oragenics. The fair value of the Company’s equity securities of Oragenics was $15,758 and $22,161 as of June 30, 2014 and December 31, 2013, respectively, and is included as equity securities in the respective consolidated balance sheets. The Company’s ownership interest in Oragenics was 24.4% and 24.6% at June 30, 2014 and December 31, 2013, respectively. Unrealized appreciation (depreciation) in the fair value of the Company’s equity securities held in Oragenics was $(7,113) and $(865) for the three months ended June 30, 2014 and 2013, respectively, and $(6,403) and $2,028 for the six months ended June 30, 2014 and 2013, respectively. Summarized unaudited financial information for Oragenics for the three and six months ended June 30, 2014 and 2013 are as follows:
			Three months ended						Six months ended
			June 30,						June 30,
			2014			2013			2014			2013
	Revenues, net		$	304		$	168		$	518		$	344
	Gross profit			178			81			313			194
	Operating expenses			2,081			2,156			3,864			4,005
	Loss from operations			(1,903	)		(2,075	)		(3,551	)		(3,811	)
	Other			7			1			15			147
	Net loss		$	(1,896	)	$	(2,074	)	$	(3,536	)	$	(3,664	)
	Variable Interest Entities
	The Company identifies entities that (1) do not have sufficient equity investment at risk to permit the entity to finance its activities without additional subordinated financial support or (2) in which the equity investors lack an essential characteristic of a controlling financial interest as variable interest entities (“VIE” or “VIEs”). The Company performs an initial and on-going evaluation of the entities with which the Company has variable interests to determine if any of these entities are a VIE. If an entity is identified as a VIE, the Company performs an assessment to determine whether the Company has both (1) the power to direct activities that most significantly impact the VIE’s economic performance and (2) have the obligation to absorb losses from or the right to receive benefits of the VIE that could potentially be significant to the VIE. If both of these criteria are satisfied, the Company is identified as the primary beneficiary of the VIE.
	As of June 30, 2014, the Company determined that Genopaver, LLC (“Genopaver”) and Intrexon Energy Partners, LLC (“Intrexon Energy Partners”) were 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. As of December 31, 2013, the Company determined that Genopaver was a VIE. The Company was not the primary beneficiary for this entity since it did not have the power to direct the activities that most significantly impact the economic performance of the VIE.
	Property, Plant and Equipment
	Property, plant and equipment are stated at cost, less accumulated depreciation and amortization. Major additions or betterments are capitalized and repairs and maintenance are generally expensed as incurred. Depreciation and amortization is calculated using the straight-line method over the estimated useful lives of the assets. The estimated useful lives of these assets are as follows:
			Years
	Building		13
	Furniture and fixtures		7
	Lab equipment		2–7
Computer hardware		5–7
Software		3–5
Leasehold improvements are amortized over the shorter of the useful life of the asset or the applicable lease term, generally one to four years.
Goodwill
Goodwill represents the future economic benefits arising from other assets acquired in a business combination that are not individually identified and separately recognized (Notes 3 and 10). Goodwill is reviewed for impairment at least annually. The Company performs a qualitative assessment to determine whether it is more-likely-than-not that the fair value of a reporting unit is less than its carrying amount prior to performing the two-step goodwill impairment test. If this is the case, the two-step goodwill impairment test is required. If it is more-likely-than-not that the fair value of a reporting unit is greater than the carrying amount, the two-step goodwill impairment test is not required.
If the two-step goodwill impairment test is required, first, the fair value of the reporting unit is compared with its carrying amount (including goodwill). If the fair value of the reporting unit is less than its carrying amount, an indication of goodwill impairment exists for the reporting unit and the entity must perform step two of the impairment test. Under step two, an impairment loss is recognized for any excess of the carrying amount of the reporting unit’s goodwill over the implied fair value of that goodwill. The implied fair value of goodwill is determined by allocating the fair value of the reporting unit in a manner similar to a purchase price allocation and the residual fair value after this allocation is the implied fair value of the reporting unit goodwill. Fair value of the reporting unit is determined using a discounted cash flow analysis. If the fair value of the reporting unit exceeds its carrying amount, step two does not need to be performed.
The Company performs its annual impairment review of goodwill in the fourth quarter, or sooner if a triggering event occurs prior to the annual impairment review.
Intangible Assets
Intangible assets subject to amortization consist of patents and related technologies acquired as a result of mergers and acquisitions (Note 3). These intangible assets are subject to amortization, were recorded at fair value at the date of acquisition and are stated net of accumulated amortization. Indefinite-lived intangible assets consist of in-process research and development acquired in mergers and acquisitions (Notes 3 and 4) and was recorded at fair value at the dates of the respective acquisitions.
The Company applies the provisions of ASC Topic 350, Intangibles, Goodwill and Other, which requires the amortization of long-lived intangible assets to reflect the pattern in which the economic benefits of the intangible asset are expected to be realized. The intangible assets are amortized over their remaining estimated useful lives, ranging from seven to fourteen years for the patents and related technologies.
Impairment of Long-Lived Assets
Long-lived assets to be held and used, including property, plant and equipment and intangible assets subject to amortization, are reviewed for impairment whenever events or changes in circumstances indicate that the carrying amount of the assets may not be recoverable. Conditions that would necessitate an impairment assessment include a significant decline in the observable market value of an asset, a significant change in the extent or manner in which an asset is used, or a significant adverse change that would indicate that the carrying amount of an asset or group of assets is not recoverable.
Indefinite-lived intangible assets, including in-process research and development, are tested for impairment annually, or more frequently if events or circumstances between annual tests indicate that the asset may be impaired. Impairment losses on indefinite-lived intangible assets are recognized based solely on a comparison of their fair value to carrying value, without consideration of any recoverability test. The Company monitors the progression of its in-process research and development, as the likelihood of success is contingent upon commercial development or regulatory approval.
Foreign Currency Translation
The assets and liabilities of foreign subsidiaries, where the local currency is the functional currency, are translated from their respective functional currencies into United States dollars at the exchange rates in effect at the balance sheet date, with resulting foreign currency translation adjustments recorded in the consolidated statement of comprehensive loss. Revenue and expense amounts are translated at average rates during the period.
Income Taxes
Income taxes are accounted for under the asset and liability method. Deferred tax assets and liabilities are recognized for the future tax consequences attributable to both differences between the financial statement carrying amounts of existing assets and liabilities and their respective tax bases as well as operating loss and tax credit carryforwards. Deferred tax assets and liabilities are measured using enacted tax rates expected to apply to taxable income in the years in which those temporary differences are expected to be recovered or settled. The effect on deferred tax assets and liabilities of a change in tax rates is recognized in income in the period that includes the enactment date of the change. Valuation allowances are established when necessary to reduce deferred tax assets to the amount expected to be realized.
The Company identifies any uncertain income tax positions and recognizes the effect of income tax positions only if those positions are more likely than not of being sustained. Recognized income tax positions are measured at the largest amount that is greater than 50% likely of being realized. Changes in recognition or measurement are reflected in the period in which the change in judgment occurs. The Company records interest, if any, related to unrecognized tax benefits as a component of interest expense. Penalties, if any, are recorded in general and administrative expenses.
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, preferred stock, 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
The Company has determined that it operates as one segment. The Company uses synthetic biology for the creation of distinct products developed in collaboration with third parties. For the three and six months ended June 30, 2014 and 2013, substantially all of the Company’s revenues are derived in the United States of America. As of June 30, 2014 and December 31, 2013, substantially all of the Company’s assets are located in the United States of America. As of June 30, 2014, the Company has $1,390 of property and equipment in Hungary.
Recently Issued Accounting Pronouncements
In May 2014, the Financial Accounting Standards Board (“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 is effective for fiscal years and interim periods within those years beginning after December 15, 2016, which 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 June 2014, the FASB issued ASU 2014-10, Development Stage Entities (Topic 915): Elimination of Certain Financial Reporting Requirements, Including an Amendment to Variable Interest Entities Guidance in Topic 810, Consolidation (“ASU 2014-10”). The provisions of ASU 2014-10 related to Topic 915 will not have a significant impact to the Company. ASU 2014-10 removes an exception provided to development-stage entities in Consolidation (Topic 810) for determining whether an entity is a variable interest entity. The revisions to Consolidation (Topic 810) are effective for interim and annual periods beginning after December 15, 2015, which are effective for the Company for the year ending December 31, 2016. The Company is currently evaluating the impact that the implementation of this standard will have on the Company’s consolidated financial statements.
Reclassifications
Certain insignificant reclassifications have been made to the prior interim period consolidated financial statements to conform to the current interim period presentation.
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.

Mergers_and_Acquisitions

Mergers and Acquisitions (Medistem, Inc.)	6 Months Ended
	Jun. 30, 2014
Medistem, Inc.	'
Mergers and Acquisitions	'
	3. Mergers and Acquisitions
	Medistem Acquisition
	On March 6, 2014, the Company acquired 100% of the outstanding common stock and securities convertible into common stock of California-based Medistem, Inc. (“Medistem”), a pioneer in the development of Endometrial Regenerative Cells (“ERCs”), for a combination of cash and Company common stock. The acquisition allows the Company to employ its synthetic biology platforms to engineer a diverse array of cell-based therapeutic candidates using Medistem’s multipotent ERCs. Pursuant to the terms of the merger agreement, Medistem equity holders received 714,144 shares of the Company’s common stock and $4,920 in cash in exchange for the outstanding Medistem common stock and securities convertible into common stock. Additionally, Medistem had issued the Company two promissory notes in the amount of $707, including accrued interest, which were settled upon closing of the merger. Certain members of Medistem’s management surrendered a total of 17,695 shares of their merger consideration to reimburse the Company for required payroll tax withholdings. The results of Medistem’s operations subsequent to March 6, 2014 have been included in the consolidated financial statements.
	The fair value of the total consideration transferred was $24,995. The acquisition date fair value of each class of consideration transferred was as follows:
	Cash	$	4,920
	Common shares		19,368
	Settlement of promissory notes		707
		$	24,995
	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 on March 6, 2014. The preliminary estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown below:
	Cash	$	8
	Intangible assets		4,824
	Total assets acquired		4,832
	Accounts payable		644
	Accrued compensation and benefits		85
	Other accrued expenses		150
	Total liabilities assumed		879
	Net assets acquired		3,953
	Goodwill		21,042
	Total consideration	$	24,995
	The fair value of assets acquired and liabilities assumed at the acquisition date are considered preliminary and is subject to revision when the valuation of intangible assets is finalized upon receipt of the final valuation report from a third party valuation expert. The preliminary fair value of acquired intangible assets was determined using the cost approach, which establishes value based on the cost of reproducing or replacing the asset. The acquired intangible assets consist of in-process research and development, which is an indefinite-lived intangible asset. The goodwill consists of buyer-specific synergies between the Company’s and Medistem’s technologies present. The goodwill is not expected to be deductible for tax purposes.
	As of June 30, 2014, the Company has incurred $680 of acquisition related costs, of which $20 and $310 is included in general and administrative expenses in the accompanying consolidated statement of operations for the three and six months ended June 30, 2014, respectively.
	The results of operations of Medistem are included in the consolidated statement of operations beginning on the day after the acquisition date. The following unaudited condensed pro forma financial information for the three months ended June 30, 2013 and the six months ended June 30, 2014 and 2013 is presented as if the acquisition had been consummated on January 1, 2013:
		Three Months Ended			Six Months Ended
		June 30,			June 30,
		2013			2014			2013
		Pro forma
	Revenues	$	6,690		$	19,641		$	10,575
	Loss before income taxes		(6,839	)		(50,245	)		(43,470	)
	Net loss		(6,839	)		(50,268	)		(43,470	)
	Net loss attributable to the noncontrolling interests		556			1,758			607
	Net loss attributable to Intrexon		(6,283	)		(48,510	)		(42,863	)
	Accretion of dividends on redeemable convertible preferred stock	$	(7,942	)	$	—		$	(14,347	)
	Net loss attributable to common shareholders	$	(14,225	)	$	(48,510	)	$	(57,210	)

Consolidated_MajorityOwned_Sub

Consolidated Majority-Owned Subsidiaries	6 Months Ended
	Jun. 30, 2014
Business Combinations [Abstract]	'
Consolidated Majority-Owned Subsidiaries	'
	4. Consolidated Majority-Owned Subsidiaries
	AquaBounty
	On November 16, 2012, the Company acquired 48,631,444 shares of AquaBounty common stock, representing 47.56% of the then outstanding shares of AquaBounty, for $6,000 through a definitive purchase agreement with an existing AquaBounty shareholder and its affiliate. On November 29, 2012, the Company executed a promissory note purchase agreement (“promissory note”) with AquaBounty. The promissory note allowed for the Company to loan up to $500 to AquaBounty. Draws on the promissory note by AquaBounty accrued annual interest of 3% and matured no later than May 28, 2013. Between December 2012 and February 2013, AquaBounty drew $500 on the promissory note. On March 15, 2013, AquaBounty repaid the $500 promissory note plus accrued interest.
	On March 15, 2013, the Company acquired 18,714,814 shares of AquaBounty for $4,907 in a private subscription offering, thereby increasing the Company’s ownership in AquaBounty to 53.82%, resulting in the Company consolidating AquaBounty pursuant to the step acquisition guidance in ASC 805. The Company recognized a gain of $7,415 to account for the difference between the carrying value and the fair value of the previously held 47.56% equity interest. The fair value of the consideration transferred included:
	Consideration paid	$	4,907
	Fair value of noncontrolling interest		15,153
	Fair value of the Company’s investment in affiliate held before the business combination		12,751
	Fair value of the consideration transferred	$	32,811
	The Company used the private subscription price to measure fair value of the Company’s previously held investment and noncontrolling interest. The estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown in the table below along with subsequent adjustments during the measurement period to the fair value of assets acquired and liabilities assumed. The adjustments were due to the completed valuation of intangible assets and long-term debt.
		Initial			Adjustments			Adjusted
		estimated						fair
		fair						value
		value
	Cash	$	5,419		$	—		$	5,419
	Short-term investments		14			—			14
	Trade receivables		4			—			4
	Other receivables		9			—			9
	Prepaid expenses and other		200			—			200
	Property, plant and equipment		1,241			—			1,241
	Intangible assets		14,900			—			14,900
	Other assets		22			—			22
	Total assets acquired		21,809			—			21,809
	Accounts payable		156			—			156
	Accrued compensation		94			—			94
	Other accrued liabilities		395			—			395
	Long term debt		2,199			(845	)		1,354
	Total liabilities assumed		2,844			(845	)		1,999
	Net assets acquired		18,965			845			19,810
	Goodwill		13,846			(845	)		13,001
	Total consideration	$	32,811		$	—		$	32,811
	The fair value of acquired intangible assets was determined using the multi-period excess earnings method, a variation of the income approach that estimates the value of an intangible asset equal to the present value of the incremental after-tax cash flows attributable to the intangible asset. The acquired intangible assets consist of in-process research and development until regulatory approval is obtained, at which point the intangible assets will be accounted for as definite lived intangible assets and amortized over the expected useful life of fifteen years. The goodwill represents future revenue opportunities and the potential for expansion of AquaBounty products and is not expected to be deductible for tax purposes.
	The results of operations of AquaBounty are included in the consolidated statement of operations beginning on the acquisition date. The following unaudited condensed pro forma financial information for the six months ended June 30, 2013 is presented as if the acquisition had been consummated on January 1, 2012:
		Six Months Ended
		June 30,
		2013
		Pro forma
	Revenues	$	10,575
	Net loss		(50,418	)
	Net loss attributable to noncontrolling interest		989
	Net loss attributable to Intrexon		(49,429	)
	Accretion of dividends on redeemable convertible preferred stock		(14,347	)
	Net loss attributable to Intrexon common shareholders	$	(63,776	)
	The pro forma net loss for the six months ended June 30, 2013 excludes the $7,415 non-recurring gain on remeasurement of the Company’s previously held investment in AquaBounty.
	On March 20, 2014, the Company acquired 19,040,366 additional shares of AquaBounty common stock for $10,000 in a private subscription offering, thereby increasing the Company’s aggregate ownership in AquaBounty to 59.85% upon closing.
	See Note 6 for a discussion of the Company’s ECC with AquaBounty.
	BioPop
	On October 1, 2013, the Company paid $1,300 to acquire 51% of the outstanding common stock of BioPop, and effective on that date, the Company began consolidating BioPop in its consolidated results of operations and financial position pursuant to ASC 805, Business Combinations (“ASC 805”). In connection with the transaction, the Company recorded goodwill of $822 and intangible assets of $430. The intangible assets consist of acquired technology and are being amortized over the expected useful life of four years.

Investments_in_Joint_Ventures

Investments in Joint Ventures	6 Months Ended
	Jun. 30, 2014
Equity Method Investments And Joint Ventures [Abstract]	'
Investments in Joint Ventures	'
	5. Investments in Joint Ventures
	Intrexon Energy Partners
	On March 26, 2014, the Company and certain investors (the “Investors”), including an affiliate of Third Security, LLC (“Third Security”), entered into a Limited Liability Company Agreement which governs the affairs and conduct of business of 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 contributed technology for a 50% membership interest in Intrexon Energy Partners. The 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 additional capital contributions of up to $25,000, and the 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 “IEP Board”) and subject to certain limitations. The Company and the Investors have the right, but not the obligation, to make additional capital contributions above these limits when and if solicited by the IEP Board.
	Intrexon Energy Partners is governed by the IEP Board which has five members. Two members of the IEP Board are designated by the Company and three members of the IEP Board are designated by a majority of the Investors.
	Intrexon Energy Partners incurred a net loss of $1,210 for the three months ended June 30, 2014 for research and development services provided by the Company. It is expected that the Company and the Investors will make additional capital contributions to Intrexon Energy Partners during the third quarter of 2014.
	See discussion of the Company’s ECC with Intrexon Energy Partners at Note 6. See discussion of a concurrent private placement securities purchase made by the Investors at Note 12.
	OvaXon
	On December 18, 2013, the Company and OvaScience, Inc. (“OvaScience”) entered into a Limited Liability Company Agreement (“OvaXon LLC Agreement”) which governs the affairs and conduct of business of OvaXon, LLC (“OvaXon”), a joint venture to create new applications for improving human and animal health. OvaXon leverages experience and technology from both the Company and OvaScience. Both the Company and OvaScience made an initial capital contribution of $1,500 in January 2014 for a 50% membership interest in OvaXon. In cases in which the board of managers of OvaXon (“OvaXon Board”) determines that additional capital contributions are necessary in order for OvaXon to conduct business and comply with its obligations under the ECC (Note 6), each of the Company and OvaScience have the right, but not the obligation, to make additional capital contributions to OvaXon subject to the OvaXon LLC Agreement.
	OvaXon is governed by the OvaXon Board which has four members. The Company, as well as OvaScience, has the initial right to appoint two members to the OvaXon Board. For so long as OvaScience and/or any of its affiliates is a member of OvaXon and holds at least 25% interest in OvaXon, OvaScience will have the sole authority to select and appoint on behalf of OvaXon each of the representatives of OvaXon on the ECC committees, and one such appointee will be an “Executive Officer” of OvaXon under the terms of the ECC with final authority to resolve certain ECC committee disputes.
	As of June 30, 2014 OvaXon had net assets of $2,216. OvaXon incurred a net loss of $590 and $784 for the three and six months ended June 30, 2014, respectively. The Company’s investment in OvaXon was $1,108 as of June 30, 2014.
	S & I Ophthalmic
	On September 30, 2013, the Company and an indirect subsidiary (“Sun Pharmaceutical Subsidiary”) of Sun Pharmaceutical Industries Ltd. (“Sun Pharmaceutical”) entered into a Limited Liability Company Agreement (“Sun LLC Agreement”) which governs the affairs and the conduct of business of S & I Ophthalmic, LLC (“S & I Ophthalmic”), a joint venture to develop therapies for the treatment of ocular diseases. 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. In cases in which the board of managers of S & I Ophthalmic (“S & I Board”) determines that additional capital contributions are necessary in order for S & I Ophthalmic to conduct business and comply with its obligations under the ECC (Note 6), each of the Company and Sun Pharmaceutical Subsidiary have 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 Board.
	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.
	S & I Ophthalmic is governed by the S & I Board which has four members. The Company, as well as Sun Pharmaceutical Subsidiary, has the initial right to appoint two members to the S & I Board. For so long as Sun Pharmaceutical Subsidiary and/or any of its affiliates is a member of S & I Ophthalmic and holds a percentage interest in S & I Ophthalmic that is at least equal to the percentage held by the Company and/or its affiliates, Sun Pharmaceutical Subsidiary will have the sole authority to select and appoint on behalf of S & I Ophthalmic each of the representatives of the S & I Ophthalmic on the ECC committees, and one such appointee will be an “Empowered Representative” of the S & I Ophthalmic under the terms of the ECC with final authority to resolve certain ECC committee disputes.
	As of June 30, 2014 and December 31, 2013, S & I Ophthalmic had net assets of $7,779 and $9,567, respectively. S & I Ophthalmic incurred a net loss of $910 and $1,788 for the three and six months ended June 30, 2014, respectively. The Company’s investment in S & I Ophthalmic was $3,889 and $4,784 as of June 30, 2014 and December 31, 2013, respectively.

Collaboration_Revenue

Collaboration Revenue	6 Months Ended
	Jun. 30, 2014
Organization Consolidation And Presentation Of Financial Statements [Abstract]	'
Collaboration Revenue	'
	6. Collaboration Revenue
	The Company’s collaborations provide for multiple deliverables to be delivered by the Company and typically include a license to the Company’s technology platforms, participation in collaboration committees, performance of certain research and development services and may include obligations for certain manufacturing services. The Company groups these deliverables into two units of accounting based on the nature of the deliverables and the separation criteria. The first deliverable (“Unit of Accounting 1”) includes the license to the Company’s technology platform, the Company’s participation on the collaboration committees and any research and development services associated with its technology platforms. The deliverables for Unit of Accounting 1 are combined because they cannot be individually separated. The second deliverable (“Unit of Accounting 2”) includes manufacturing services to be provided for any Company materials in an approved product. These services have standalone value and are contingent due to uncertainties on whether an approved product will ever be developed thereby requiring manufacture by the Company at that time. As VSOE and third party evidence of selling price is not available or practical, the BESP for each unit of accounting is determined using a historical cost approach due to the early stage of development of the Company’s technology. In establishing BESP for Unit of Accounting 1, the Company uses the accumulated costs incurred as of the collaboration by the Company on its technology platform licensed to the collaborator to approximate the cost to recreate the deliverables included in this unit of accounting. All upfront consideration is allocated to Unit of Accounting 1. Unit of Accounting 2 is determined to be a contingent deliverable at the inception of the collaboration due to the uncertainties surrounding whether an approved product will ever be developed and require manufacturing by the Company. The upfront consideration allocated to Unit of Accounting 1 is 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 when the services are performed and collection is reasonably assured. At the inception of each collaboration, the Company determines whether any milestone payments are substantive and can be recognized when earned in accordance with ASU 2010-17. The milestone payments are typically not considered substantive. Royalties related to product sales will be recognized when earned since payments relate directly to products that have been fully developed and for which the Company has satisfied all of its obligations.
	The Company determines whether collaborations are individually “significant” for disclosure based on a number of factors, including total revenue recorded by the Company pursuant to the collaboration, collaborators either consolidated or accounted for using the equity method, or other qualitative factors. The following table summarizes the amounts recorded in the consolidated statements of operations for each significant collaboration for the three and six months ended June 30, 2014 and 2013.
		Three months ended June 30, 2014
		Collaboration		Collaboration		Total
		revenue recognized		revenue recognized
		from upfront and		from research and
		milestone		development
		payments		services
	ZIOPHARM Oncology, Inc.	$	644	$	3,697	$	4,341
	Synthetic Biologics, Inc.		163		30		193
	Oragenics, Inc.		261		52		313
	Fibrocell Science, Inc.		448		883		1,331
	Genopaver, LLC		68		423		491
	S & I Ophthalmic, LLC		—		607		607
	OvaXon, LLC		—		579		579
	Intrexon Energy Partners, LLC		625		1,210		1,835
	Other		308		1,766		2,074
	Total	$	2,517	$	9,247	$	11,764
		Three months ended June 30, 2013
		Collaboration		Collaboration		Total
		revenue recognized		revenue recognized
		from upfront and		from research and
		milestone		development
		payments		services
	ZIOPHARM Oncology, Inc.	$	644	$	2,291	$	2,935
	Synthetic Biologics, Inc.		1,666		314		1,980
	Oragenics, Inc.		137		334		471
	Fibrocell Science, Inc.		158		615		773
	Genopaver, LLC		68		213		281
	Other		78		156		234
	Total	$	2,751	$	3,923	$	6,674
		Six months ended June 30, 2014
		Collaboration		Collaboration		Total
		revenue recognized		revenue recognized
		from upfront and		from research and
		milestone		development
		payments		services
	ZIOPHARM Oncology, Inc.	$	1,288	$	5,733	$	7,021
	Synthetic Biologics, Inc.		325		227		552
	Oragenics, Inc.		523		585		1,108
	Fibrocell Science, Inc.		896		1,745		2,641
	Genopaver, LLC		137		844		981
	S & I Ophthalmic, LLC		—		1,486		1,486
	OvaXon, LLC		—		748		748
	Intrexon Energy Partners, LLC		625		1,210		1,835
	Other		605		2,624		3,229
	Total	$	4,399	$	15,202	$	19,601
		Six months ended June 30, 2013
		Collaboration		Collaboration		Total
		revenue recognized		revenue recognized
		from upfront and		from research and
		milestone		development
		payments		services
	ZIOPHARM Oncology, Inc.	$	1,288	$	3,721	$	5,009
	Synthetic Biologics, Inc.		1,861		689		2,550
	Oragenics, Inc.		274		713		987
	Fibrocell Science, Inc.		316		1,045		1,361
	Genopaver, LLC		68		213		281
	Other		81		269		350
	Total	$	3,888	$	6,650	$	10,538
	The following is a summary of the terms of the Company’s significant collaborations.
Ziopharm Collaboration
Effective January 6, 2011, the Company entered into a worldwide ECC with Ziopharm. Pursuant to the ECC, Ziopharm received a license to the Company’s technology platform within the field of oncology as defined more specifically in the agreement. Upon execution of the ECC, the Company received 3,636,926 shares of Ziopharm’s common stock valued at $17,457 as upfront consideration. In addition to the deliverables discussed above, the Company transferred two clinical product candidates to Ziopharm that resulted in a separate unit of accounting for which $1,115 of the upfront consideration was allocated and recognized as collaboration revenue in 2011. The remaining $16,342 of upfront consideration was allocated to Unit of Accounting 1 discussed above. The Company is entitled to additional shares of common stock representing the lesser of (i) the original shares received or (ii) the number of shares representing 7.495% of Ziopharm’s outstanding shares at the date of the dosing of the first patient in a Phase II clinical trial of a product candidate created, produced or developed by Ziopharm using the Company’s technology (“Ziopharm Milestone”). On October 24, 2012, the Ziopharm Milestone was achieved and the Company received 3,636,926 shares of Ziopharm’s common stock valued at $18,330 as milestone consideration. Since the Ziopharm Milestone was not substantive, the Company allocated the Ziopharm Milestone to the applicable units of accounting and is being recognized in a manner similar to these units of accounting. The Company receives reimbursement payments for research and development services provided and manufacturing services for Company materials provided to Ziopharm during the ECC. Subject to certain expense allocations, Ziopharm will pay the Company 50% of the quarterly net profits derived from the sale of products developed from the ECC. Ziopharm is responsible for conducting preclinical and clinical development of product candidates, as well as for other aspects of commercialization or manufacturing of product candidates. The term of the ECC commenced on January 6, 2011 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 Ziopharm upon 90 days written notice to the Company.
See Note 15 for further discussion related to Ziopharm.
Synthetic Biologics, Inc. Collaborations
Effective November 18, 2011, the Company entered into a worldwide ECC with Synthetic Biologics, Inc. (“Synthetic Biologics”), a publicly traded company focused on the development of innovative disease-modifying medicines for serious illnesses. Pursuant to the ECC, at the transaction effective date, Synthetic Biologics received a license to the Company’s technology platform within a designated field (“Field One”). Upon execution of the ECC, the Company received 3,123,558 shares of Synthetic Biologics’ common stock valued at $1,687 as upfront consideration. The Company is entitled to additional shares of common stock representing the lesser of (i) the original shares received or (ii) the number of shares representing 9.995% of Synthetic Biologics’ outstanding shares at the date of the dosing of the first patient in a Phase II clinical trial of a product candidate created, produced or developed by Synthetic Biologics using the Company’s technology. The Company will receive reimbursement payments for research and development services provided pursuant to the agreement and manufacturing services for Company materials provided to Synthetic Biologics during the ECC. Subject to certain expense allocations, Synthetic Biologics will pay the Company 50% of the quarterly net profits derived from the sale of products developed from the ECC. Synthetic Biologics is responsible for conducting preclinical and clinical development of product candidates, as well as for other aspects of commercialization or manufacturing of the product candidates. The term of the ECC commenced on November 18, 2011 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 Synthetic Biologics upon 90 days written notice to the Company. On April 16, 2013, the Company terminated its ECC with Synthetic Biologics in Field One. As a result of this termination, all licenses granted by the Company under the ECC for use in Field One reverted back to the Company and the Company recognized the balance of deferred revenue associated with the upfront consideration as collaboration revenue in April 2013.
On August 6, 2012, the Company entered into its second worldwide ECC with Synthetic Biologics. Pursuant to this ECC, at the transaction effective date, Synthetic Biologics received a license to the Company’s technology platform within a second designated field (“Field Two”). Upon Synthetic Biologics’ shareholders’ approval on October 5, 2012, the Company received a technology access fee of 3,552,210 shares of Synthetic Biologics common stock valued at $7,815 as upfront consideration. Upon the filing by Synthetic Biologics of an investigational new drug application with the U.S. Food and Drug Administration (“U.S. FDA”), the Company will receive cash or common stock at the option of Synthetic Biologics valued at $2,000. Upon the first to occur of either the first commercial sale of a product developed under the ECC or the granting of regulatory approval of a product developed under the ECC, the Company will receive cash or common stock at the option of Synthetic Biologics valued at $3,000. The ECC initially targets three infectious diseases and Synthetic Biologics may elect to target up to five more infectious diseases by paying the Company a field expansion fee of $2,000 in either cash or common stock for each additional infectious disease selected. The Company receives reimbursement payments for research and development services provided pursuant to the agreement and manufacturing services for preclinical Company materials provided to Synthetic Biologics during the ECC. The Company has the option to propose, and Synthetic Biologics can select, the Company to be the bulk manufacturer of products developed from the ECC. On a quarterly basis, Synthetic Biologics will pay the Company royalties with percentages ranging from upper-single digits to lower double digits of net sales of products developed from the ECC. Synthetic Biologics is responsible for conducting preclinical and clinical development of product candidates, as well as for other aspects of commercialization and manufacturing of the product candidates. The term of the ECC commenced on August 6, 2012 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 Synthetic Biologics upon 90 days written notice to the Company.
On December 17, 2012, the Company received $2,500 from Synthetic Biologics as a prepayment of research and development services to be provided in conjunction with either of the two ECCs. The Company recorded this amount as deferred revenue and recognizes collaboration revenue as services are performed. Any remaining balance of this prepayment is refundable to Synthetic Biologics in the event both ECCs are terminated.
See Note 15 for further discussion related to Synthetic Biologics.
Oragenics Collaborations
Effective June 5, 2012, the Company entered into a worldwide ECC with Oragenics, a publicly traded company focused on becoming the world leader in novel antibiotics against infectious disease and probiotics for oral health for humans and pets. Pursuant to the ECC, at the transaction effective date, Oragenics received a license to the Company’s technology platform within the field of lantibiotics for the treatment of infectious diseases in humans and companion animals as defined more specifically in the agreement. Upon execution of the ECC, the Company received a technology access fee of 4,392,425 shares of Oragenics’ common stock valued at $6,588 as upfront consideration. The Company is entitled to receive additional shares of common stock, or at Oragenics’ option, receive a cash payment based upon the fair market value of the shares, upon the separate achievement of certain regulatory milestones of the first product candidate developed from the ECC (“Oragenics ECC 1 Milestones”). The Oragenics ECC 1 Milestones include: (i) 1% of Oragenics’ outstanding shares as defined in the ECC agreement at the date of the filing of the first Investigative New Drug Application with the U.S. FDA for a product candidate created, produced or developed using the Company’s technology (“Oragenics ECC 1 Product”); (ii) 1.5% of Oragenics’ outstanding shares as defined in the ECC agreement at the date of the dosing of the first patient in the first Phase II clinical trial of an Oragenics ECC 1 Product; (iii) 2% of Oragenics’ outstanding shares as defined in the ECC agreement at the date of the dosing of the first patient in the first Phase III clinical trial of an Oragenics ECC 1 Product; (iv) 2.5% of Oragenics’ outstanding shares as defined in the ECC agreement at the date of the first New Drug Application or Biologics License Application with the U.S. FDA for an Oragenics ECC 1 Product, or alternatively the first equivalent regulatory filing with a foreign agency; and (v) 3% of Oragenics’ outstanding shares as defined in the ECC agreement at the date of the granting of the first regulatory approval of an Oragenics ECC 1 Product. The Company receives reimbursement payments for research and development services provided pursuant to the agreement during the ECC and manufacturing services for Company materials provided to Oragenics during the ECC. Oragenics will pay the Company 25% of the quarterly profits derived from the sale of products developed from the ECC.
Oragenics is responsible for funding the further development of lantibiotics toward the goal of commercialization, conducting preclinical and clinical development of product candidates, as well as for other aspects of commercialization or manufacturing of the product candidates. The term of the ECC commenced on June 5, 2012 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 Oragenics upon 90 days written notice to the Company.
Effective September 30, 2013, the Company entered into its second worldwide ECC with Oragenics (“ECC 2”). Pursuant to ECC 2, at the transaction effective date, Oragenics received a license to the Company’s technology platform to develop and commercialize probiotics, specifically the direct administration to humans of genetically modified probiotics for the treatment of diseases of the oral cavity, throat, sinus and esophagus as defined more specifically in the agreement. Upon execution of ECC 2, the Company received a technology access fee of 1,348,000 shares of Oragenics’ common stock valued at $3,503 and a $1,956 convertible promissory note maturing on or before December 31, 2013 as upfront consideration. Prior to the maturity date, Oragenics had the right to convert the promissory note into shares of Oragenics’ common stock subject to its shareholders’ approval. The conversion price is equal to the closing price of Oragenics’ common stock on the last trading day immediately prior to the date of conversion. On December 18, 2013, Oragenics converted the promissory note into 698,241 shares of Oragenics’ common stock. The Company is entitled to receive additional shares of common stock, or at Oragenics’ option, receive a cash payment based upon the fair market value of the shares, upon the first instance of attainment of certain commercialization milestones of a product candidate developed from ECC 2 (“Oragenics ECC 2 Milestones”). The Oragenics ECC 2 Milestones include: (i) $2,000 within thirty days of the first instance of the achievement of the first dosing of a patient in a phase II clinical trial for an Oragenics product developed from ECC 2 (“Oragenics ECC 2 Product”); (ii) $5,000 within thirty days of the first instance of the achievement of the meeting of the primary endpoint in a phase III clinical trial for an Oragenics ECC 2 Product; and (iii) $10,000 within thirty days of the first instance of the achievement of the first to occur of (a) the first commercial sale of an Oragenics ECC 2 Product anywhere in the world, or (b) the regulatory approval for an Oragenics ECC 2 Product. The Company receives reimbursement payments for research and development services provided pursuant to the agreement during the ECC and manufacturing services for Company materials provided to Oragenics during ECC 2. Oragenics will pay the Company 10% of the net sales derived from the sale of products developed from ECC 2.
Oragenics is responsible for funding the further development of probiotics toward the goal of commercialization, conducting preclinical and clinical development of product candidates, as well as for other aspects of commercialization or manufacturing of the product candidates. The term of ECC 2 commenced on September 30, 2013 and continues until terminated pursuant to ECC 2. ECC 2 may be terminated by either party in the event of certain material breaches defined in the agreement and following full payment of the technology access fee may be terminated voluntarily by Oragenics upon 90 days written notice to the Company.
See Note 15 for further discussion related to Oragenics.
Fibrocell Science, Inc. Collaboration
Effective October 5, 2012, the Company entered into an ECC with Fibrocell Science, Inc. (“Fibrocell”), a publicly traded, autologous cellular therapeutic company focused on the development of innovative products for aesthetic, medical and scientific applications. Pursuant to the ECC, at the transaction effective date, Fibrocell received a license to the Company’s technology platform to develop and commercialize genetically modified and non-genetically modified autologous fibroblasts and autologous dermal cells in the United States of America. Upon execution of the ECC, the Company received a technology access fee of 1,317,520 shares of Fibrocell’s common stock valued at $7,576 as upfront consideration. The number of shares received reflects a 1-for-25 reverse stock split of Fibrocell’s common stock effective April 30, 2013. The Company receives reimbursement payments for research and development services provided pursuant to the agreement during the ECC and manufacturing services for Company materials provided to Fibrocell during the ECC. On a quarterly basis, Fibrocell will pay the Company royalties of 7% of net sales up to $25,000 and 14% of net sales above $25,000 on each product developed from the ECC. If Fibrocell uses the Company’s technology platform to improve the production of a current or new Fibrocell product not developed from the ECC, Fibrocell will pay the Company a quarterly royalty equal to 33% of the cost of goods sold savings generated by the improvement. Fibrocell is responsible for conducting preclinical and clinical development of product candidates, as well as for other aspects of commercialization and manufacturing of the product candidates. The term of the ECC commenced on October 5, 2012 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 Fibrocell upon 90 days written notice to the Company.
Effective June 28, 2013, the Company entered into an amendment to the ECC with Fibrocell. The amendment expands the field of use defined in the ECC agreement. Under the terms of the amendment to the ECC, the Company received 1,243,781 shares of Fibrocell’s common stock valued at $7,612 as a supplemental technology access fee. The Company allocated this additional consideration to the appropriate unit of accounting and is recognizing it consistent with the unit of accounting.
Effective January 10, 2014, the Company entered into a second amendment to the ECC with Fibrocell. The second amendment further expanded the field of use defined in the ECC agreement. Under the terms of the second amendment to the ECC, the Company received 1,024,590 shares of Fibrocell’s common stock valued at $5,225 as a technology access fee. The Company allocated this additional consideration to the appropriate unit of accounting and is recognizing it consistent with the unit of accounting.
See Note 15 for further discussion related to Fibrocell.
Genopaver Collaboration
Effective March 29, 2013, the Company entered into a worldwide ECC with Genopaver, a limited liability company formed by affiliates of Third Security (Note 15). Genopaver was formed for the purpose of entering into the ECC and developing and commercializing products in the field of the fermentative production of alkaloids through genetically modified cell-lines and substrate feeds for use as active pharmaceutical ingredients or as commercially sold intermediates in the manufacture of active pharmaceutical ingredients. Upon execution of the ECC, the Company received a technology access fee of $3,000 as upfront consideration. The Company receives reimbursement payments for research and development services provided pursuant to the agreement during the ECC. Genopaver will pay the Company a royalty as a percentage in the lower-double digits on the quarterly gross profits of product sales from products developed under the ECC. Genopaver is responsible for the development and commercialization of the product candidates. The term of the ECC commenced on March 29, 2013 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 Genopaver upon 90 days written notice to the Company.
AquaBounty Collaboration
On February 14, 2013, the Company entered into an ECC with AquaBounty. The Company will be reimbursed for research and development services as provided for in the ECC agreement. In the event of product sales from a product developed from the ECC, the Company will receive 16.66% of quarterly gross profits for each product. All revenues and expenses related to this ECC are eliminated in consolidation (Note 4).
S & I Ophthalmic Collaboration
On September 30, 2013, the Company entered into a worldwide ECC with S & I Ophthalmic, a joint venture between the Company and Sun Pharmaceutical Subsidiary, an indirect subsidiary of Sun Pharmaceutical, an international specialty pharmaceutical company focused on chronic diseases (Note 5). The ECC grants S & I Ophthalmic an exclusive worldwide license to the Company’s technology platform to develop and commercialize therapies in humans for the treatment of ocular diseases defined more specifically in the agreement. The Company will be reimbursed for research and development services pursuant to the agreement and manufacturing services for Company materials provided to S & I Ophthalmic during the ECC. Subject to certain expense allocations, S & I Ophthalmic will pay the Company royalties with percentages ranging from mid-single digits and above of the net sales derived from the sale of products developed under the ECC. The term of the ECC commenced on September 30, 2013 and continues until terminated by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by S & I Ophthalmic upon 90 days written notice to the Company.
BioPop Collaboration
On October 1, 2013, the Company entered into a worldwide ECC with BioPop. The ECC grants BioPop an exclusive, worldwide license to the Company’s technology platform to develop and commercialize artwork, children’s toys and novelty goods that are derived from living organisms or are enabled by synthetic biology. The Company will be reimbursed for research and development services and manufacturing services as provided for in the ECC agreement. The Company is entitled to royalties in the mid-single digits as a percentage of the net product sales of a product developed under the ECC. All revenues and expenses related to this ECC are eliminated in consolidation (Note 4).
OvaXon Collaboration
On December 18, 2013, the Company entered into a worldwide ECC with OvaXon, a joint venture between the Company and OvaScience, a life sciences company focused on infertility treatments (Note 5). The ECC grants OvaXon an exclusive, worldwide license to the Company’s technology platform to create new applications for improving human and animal health. OvaScience also licensed certain technology to OvaXon pursuant to a separate license agreement. The Company will be reimbursed for research and development services and manufacturing services as provided for in the ECC agreement. The term of the ECC commenced on December 18, 2013 and continues until terminated by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by OvaXon upon 90 days written notice to the Company.
Intrexon Energy Partners Collaboration
On March 26, 2014, the Company entered into a worldwide ECC with Intrexon Energy Partners, a joint venture between the Company and certain investors, including an affiliate of Third Security (Note 5). The ECC grants Intrexon Energy Partners an exclusive, worldwide license to the Company’s technology platform to optimize and scale-up the Company’s gas-to-liquid bioconversion platform for the production of certain fuels and lubricants. Upon execution of the ECC, the Company received a technology access fee of $25,000 as upfront consideration. The Company will be reimbursed for research and development services as provided for in the ECC agreement. The term of the ECC commenced on March 26, 2014 and continues until March 26, 2034 unless terminated prior to that date by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by Intrexon Energy Partners upon 90 days written notice to the Company.
Deferred Revenue
Deferred revenue primarily consists of consideration received for upfront and milestone payments in connection with the Company’s collaborations and prepayments for research and development services performed for collaborators pursuant to the terms of the collaborations. Deferred revenue consists of the following:
	June 30,		December 31,
	2014		2013
Upfront and milestone payments	$	98,233	$	72,207
Prepaid research and development services		1,207		1,319
Other		13		45
Total	$	99,453	$	73,571
Current portion of deferred revenue	$	10,706	$	7,793
Long-term portion of deferred revenue		88,747		65,778
Total	$	99,453	$	73,571

Shortterm_and_Longterm_Investm

Short-term and Long-term Investments	6 Months Ended
	Jun. 30, 2014
Investments Debt And Equity Securities [Abstract]	'
Short-term and Long-term Investments	'
	7. Short-term and Long-term Investments
	The Company’s investments are classified as available-for-sale. The following table summarizes the amortized cost, gross unrealized gains and losses and fair value of available-for-sale investments as of June 30, 2014:
		Amortized		Gross		Gross			Aggregate
		Cost		Unrealized		Unrealized			Fair Value
				Gains		Losses
	U.S. government debt securities	$	172,960	$	113	$	(1	)	$	173,072
	Certificates of deposit		1,519		—		—			1,519
	Total	$	174,479	$	113	$	(1	)	$	174,591
	The following table summarizes the amortized cost, gross unrealized gains and losses and fair value of available-for-sale investments as of December 31, 2013:
		Amortized		Gross		Gross			Aggregate
		Cost		Unrealized		Unrealized			Fair Value
				Gains		Losses
	U.S. government debt securities	$	178,277	$	35	$	(13	)	$	178,299
	Commercial paper		7,997		—		—			7,997
	Certificates of deposit		2,266		—		(1	)		2,265
	Total	$	188,540	$	35	$	(14	)	$	188,561
	For more information on our method for determining the fair value of our assets, see Note 2 – “Fair Value of Financial Instruments”.
	The estimated fair value of available-for-sale investments classified by their contractual maturities as of June 30, 2014 was as follows:
	Due within one year	$	101,046
	After one year through three years		73,545
	Total	$	174,591
	Changes in market interest rates and bond yields cause certain investments to fall below their cost basis, resulting in unrealized losses on investments. The unrealized losses of the Company’s investments were primarily a result of unfavorable changes in interest rates subsequent to the initial purchase of these investments and have been in a loss position for less than 12 months.
	As of June 30, 2014, the Company did not consider any of its investments to be other-than-temporarily impaired. When evaluating its investments for other-than-temporary impairment, the Company reviews factors such as the length of time and extent to which fair value has been below its cost basis, the financial condition of the issuer, the Company’s ability and intent to hold the security and whether it is more likely than not that it will be required to sell the investment before recovery of its cost basis.

Fair_Value_Measurements

Fair Value Measurements	6 Months Ended
	Jun. 30, 2014
Fair Value Disclosures [Abstract]	'
Fair Value Measurements	'
	8. Fair Value Measurements
	The carrying amount of cash and cash equivalents, receivables, prepaid expenses and other current assets, accounts payable, accrued compensation and benefits, other accrued liabilities, and related party payables approximate fair value due to the short maturity of these instruments.
	The following table presents the placement in the fair value hierarchy of financial assets that are measured at fair value on a recurring basis, including the items for which the fair value option has been elected, at June 30, 2014:
		Quoted		Significant		Significant		June 30,
		prices in		other		unobservable		2014
		active		observable		inputs
		markets		inputs		(level 3)
		(level 1)		(level 2)
	Assets
	U.S. government debt securities (Note 7)	$	—	$	173,072	$	—	$	173,072
	Certificates of deposit (Note 7)		—		1,519		—		1,519
	Equity securities (Note 6)		109,665		25,230		—		134,895
	Total	$	109,665	$	199,821	$	—	$	309,486
	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, 2013:
		Quoted		Significant		Significant		December 31,
		prices		other		unobservable		2013
		in active		observable		inputs
		markets		inputs		(level 3)
		(level 1)		(level 2)
	Assets
	U.S. government debt securities (Note 7)	$	—	$	178,299	$	—	$	178,299
	Commercial paper (Note 7)		—		7,997		—		7,997
	Certificates of deposit (Note 7)		—		2,265		—		2,265
	Equity securities (Note 6)		110,297		31,228		—		141,525
	Total	$	110,297	$	219,789	$	—	$	330,086
	Financial liabilities measured on a recurring basis were not significant at June 30, 2014 and December 31, 2013.
	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 quote prices in active markets. The method used to estimate the fair value of the Level 2 equity securities in the tables above is based on the quoted market price of the publicly-traded security, adjusted for a discount for lack of marketability.
	There were no transfers between levels of the fair value hierarchy in the six months ended June 30, 2014 and 2013.

Property_Plant_and_Equipment_n

Property, Plant and Equipment, net	6 Months Ended
	Jun. 30, 2014
Property Plant And Equipment [Abstract]	'
Property, Plant and Equipment, net	'
	9. Property, Plant and Equipment, net
	Property, plant and equipment consist of the following:
		June 30,			December 31,
		2014			2013
	Land	$	55		$	55
	Building		945			945
	Furniture and fixtures		975			876
	Lab equipment		24,295			22,275
	Leasehold improvements		5,629			5,147
	Computer hardware		3,513			3,286
	Construction in progress		140			314
	Software		1,344			1,008
			36,896			33,906
	Less: Accumulated depreciation and amortization		(19,507	)		(17,277	)
	Property, plant and equipment, net	$	17,389		$	16,629
	Depreciation expense was $1,281 and $1,114 for the three months ended June 30, 2014 and 2013, respectively, and $2,399 and $2,260 for the six months ended June 30, 2014 and 2013, respectively

Goodwill_and_Intangible_Assets

Goodwill and Intangible Assets, net	6 Months Ended
	Jun. 30, 2014
Goodwill And Intangible Assets Disclosure [Abstract]	'
Goodwill and Intangible Assets, net	'
	10. Goodwill and Intangible Assets, net
	The changes in the carrying amount of goodwill for the six months ended June 30, 2014 are as follows:
	Balance as of December 31, 2013	$	13,823
	Acquisitions		21,042
	Balance as of June 30, 2014	$	34,865
	No goodwill or accumulated impairment losses existed as of June 30, 2014 and December 31, 2013.
	Intangible assets consist of the following at June 30, 2014:
		Gross		Accumulated			Net
		Carrying		Amortization
		Amount
	Patents and related technologies	$	34,772	$	(9,090	)	$	25,682
	In-process research and development		19,724		—			19,724
	Total	$	54,496	$	(9,090	)	$	45,406
	No in-process research and development or accumulated impairment losses existed as of June 30, 2014.
	Intangible assets consist of the following at December 31, 2013:
		Gross		Accumulated			Net
		Carrying		Amortization
		Amount
	Patents and related technologies	$	34,772	$	(7,716	)	$	27,056
	In-process research and development		14,900		—			14,900
	Total	$	49,672	$	(7,716	)	$	41,956
	No in-process research and development or accumulated impairment losses existed as of December 31, 2013.
	Amortization expense was $687 and $709 for the three months ended June 30, 2014 and 2013, respectively, and $1,374 and $1,434 for the six months ended June 30, 2014 and 2013, respectively. At June 30, 2014, the weighted average useful life for patents and related technology was 12.3 years.

Income_Taxes

Income Taxes	6 Months Ended
	Jun. 30, 2014
Income Tax Disclosure [Abstract]	'
Income Taxes	'
	11. Income Taxes
	Tax provisions for interim periods are calculated using an estimate of actual taxable income or loss for the respective period, rather than estimating the Company’s annual effective income tax rate, as the Company is currently unable to reliably estimate its income for the full year. For the three months ended June 30, 2014 the Company had a taxable loss of approximately $14,100, which resulted in an income tax benefit of $283 that was recognized to offset income tax expense recognized for the three months ended March 31, 2014. For the six months ended June 30, 2014 the Company had taxable income of approximately $1,200, which, after offset by available loss carryforwards, resulted in $23 of current tax expense due to the corporate alternative minimum tax. The associated deferred tax asset is 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. For the three and six months ended June 30, 2013, there is no income tax benefit recognized. 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. Due to the Company’s history of net losses incurred from inception, no deferred income tax benefit has been recorded and the corresponding deferred tax assets have been fully reserved as the Company cannot sufficiently be assured that these deferred tax assets will be realized.
	At June 30, 2014, the Company has loss carryforwards for federal income tax purposes of approximately $249,600 available to offset future taxable income and federal and state research and development tax credits of approximately $7,000, 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 $6,800 relate to benefits from stock compensation deductions that will be recorded as a component of paid-in capital when realized.

Shareholders_Equity

Shareholders' Equity	6 Months Ended
	Jun. 30, 2014
Equity [Abstract]	'
Shareholders' Equity	'
	12. Shareholders’ Equity
	On March 26, 2014 and concurrent with the formation of Intrexon Energy Partners, the Company entered into securities purchase agreements with each of the Investors in Intrexon Energy Partners for the private placement of 972,004 shares of the Company’s common stock at a price per share of $25.72 for gross proceeds of $25,000. Each Investor purchased an amount proportionate to its investment in Intrexon Energy Partners, including 243,001 shares, or $6,250, purchased by an affiliate of Third Security (Note 15).

Stock_Option_Plans

Stock Option Plans	6 Months Ended
	Jun. 30, 2014
Disclosure Of Compensation Related Costs Sharebased Payments [Abstract]	'
Stock Option Plans	'
	13. Stock Option Plans
	Intrexon Stock Option Plan
	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 cost that has been included in research and development expenses and general and administrative expenses amounted to $1,343 and $5,429, respectively, for the three months ended June 30, 2014, and $147 and $641, respectively, for the three months ended June 30, 2013. Stock-based compensation cost that has been included in research and development expenses and general and administrative expenses amounted to $1,670 and $8,799, respectively, for the six months ended June 30, 2014, and $299 and $896, respectively, for the six months ended June 30, 2013.
	On April 18, 2008, the Company adopted the 2008 Equity Incentive Plan (the “2008 Plan”) for employees and nonemployees pursuant to which the Company’s board of directors may grant share based awards to officers, key employees and nonemployees. During 2011, the 2008 Plan was amended to increase the number of authorized awards under the 2008 plan from 2,857,142 to 5,714,285. Upon the effectiveness of the 2013 Omnibus Incentive Plan (the “2013 Plan”), no new awards may be granted under the 2008 Plan. As of June 30, 2014, there are 2,200,779 stock options outstanding under the 2008 Plan.
	On July 26, 2013, the Company adopted the 2013 Plan for employees and nonemployees pursuant to which the Company’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 IPO. On June 9, 2014, the Company’s shareholders voted to amend the 2013 Plan to increase the numbers of shares authorized for issuance under the 2013 Plan from 7,000,000 to 10,000,000. As of June 30, 2014, there were 6,421,800 stock options outstanding under the 2013 Plan, and there were 3,559,727 remaining shares available for the Company to grant under the 2013 Plan.
	Stock option activity under the Company’s award plans during the period indicated is as follows:
			Number			Weighted			Weighted
			of			average			average
			shares			exercise			remaining
						price			contractual
									term
	Balances at December 31, 2013			2,840,648		$	8.27			7.75
	Granted			6,273,300			28.57
	Exercised			(235,438	)		(4.30	)
	Forfeited			(255,646	)		(19.51	)
	Expired			(285	)		(7.12	)
	Balances at June 30, 2014			8,622,579			22.82			9
	Exercisable at June 30, 2014			1,242,345			7.86			6.39
	Vested and Expected to Vest at June 30, 2014(1)			6,657,224			21.72			8.84
	-1	The number of stock options expected to vest takes into account an estimate of expected forfeitures.
	Total unrecognized compensation costs related to nonvested awards at June 30, 2014 and December 31, 2013 were $74,570 and $9,639, respectively, and are expected to be recognized over a weighted-average period of approximately three years.
	The Company currently uses authorized and unissued shares to satisfy share award exercises.
	AquaBounty Stock Option Plan
	The AquaBounty 2006 Equity Incentive Plan (the “AquaBounty Plan”) provides for the issuance of incentive stock options to employees of AquaBounty and non-qualified stock options and awards of restricted and direct stock purchases to its directors, officers, employees and consultants of AquaBounty. Unless otherwise indicated, options issued to employees, directors and non-employees are vested over one to three years and are exercisable for a term of ten years from the date of issuance. As of June 30, 2014, there were 7,359,000 options outstanding under the AquaBounty Plan at a weighted average exercise price of $0.31 per share of which 6,255,520 were exercisable. Stock-based compensation cost that has been included in research and development expenses and general and administrative expenses amounted to $21 and $55, respectively, for the three months ended June 30, 2014. Stock-based compensation cost that has been included in research and development expenses and general and administrative expenses amounted to $42 and $111, respectively, for the six months ended June 30, 2014. Stock- based compensation cost that has been included in general and administrative expenses amounted to $21 and $1 for the three and six months ended June 30, 2013, respectively.

Commitments_and_Contingencies

Commitments and Contingencies	6 Months Ended
	Jun. 30, 2014
Commitments And Contingencies Disclosure [Abstract]	'
Commitments and Contingencies	'
	14. Commitments and Contingencies
	Operating Leases
	The Company leases its facilities and certain equipment under noncancelable operating leases. The equipment leases are renewable at the option of the Company. At June 30, 2014, future minimum lease payments under noncancelable operating leases having initial or remaining noncancelable lease terms in excess of one year are as follows:
	2014	$	1,919
	2015		4,397
	2016		4,072
	2017		2,607
	2018		1,295
	2019		1,259
	Thereafter		2,406
	Total	$	17,955
	Rent expense, including other facility expenses, was $1,361 and $1,766 in the three months ended June 30, 2014 and 2013, respectively, and $2,731 and $3,039 in the six months ended June 30, 2014 and 2013, respectively.
	The Company maintains subleases for certain of its facilities. Rental income under sublease agreements was $171 and $91 for the three months ended June 30, 2014 and 2013, respectively, and $262 and $182 for the six months ended June 30, 2014 and 2013, respectively. Future minimum rental payments receivable under noncancelable operating subleases having initial or remaining noncancelable lease terms in excess of one year are $357 for 2014, $725 for 2015, $384 for 2016, and $11 for 2017.
	Long Term Debt
	In January 2009, the Atlantic Canada Opportunities Agency (“ACOA”), a Canadian government agency, awarded AquaBounty a grant to provide funding of a research and development project. The total amount available under the award is $2,691, which AquaBounty can claim 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 regulatory approval, the timing of repayment is uncertain. As of the acquisition date, AquaBounty had claimed $1,952 of the available funds and this amount was recorded at its acquisition date fair value of $1,107 (Note 4). 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 and through June 30, 2014, AquaBounty has made subsequent claims of $767 resulting in total long-term debt of $2,001 as of June 30, 2014.
	In November 1999, Technology Partnership Canada (“TPC”), a Canadian government agency, agreed to provide AquaBounty funding up to $2,778, to support AquaBounty’s research and development. This amount is repayable to TPC in the form of a 5.2% royalty on revenues generated from AquaBounty’s technology through June 30, 2014. There were no revenues generated from AquaBounty’s technology through June 30, 2014. Therefore, no amounts are required to be repaid.
	Contingencies
	The Company may become subject to claims and assessments from time to time in the ordinary course of business. Such matters are subject to many uncertainties and outcomes are not predictable with assurance. The Company accrues liabilities for such matters when it is probable that future expenditures will be made and such expenditures can be reasonably estimated. As of June 30, 2014 and December 31, 2013, the Company does not believe that any such matters, individually or in the aggregate, will have a material adverse effect on the Company’s business, financial condition, results of operations, or cash flows.

Related_Party_Transactions

Related Party Transactions	6 Months Ended
	Jun. 30, 2014
Related Party Transactions [Abstract]	'
Related Party Transactions	'
	15. Related Party Transactions
	Third Security and Affiliates
	The Company reimburses Third Security for certain documented out-of-pocket expenses incurred on the Company’s behalf. The total amount of expenses reimbursed by the Company for the three months ended June 30, 2014 and 2013 was approximately $64 and $167, respectively, and the total amount of expenses reimbursed by the Company for the six months ended June 30, 2014 and 2013 was approximately $88 and $248, respectively.
	On June 6, 2011, the Company entered into a worldwide exclusive licensing agreement with Halozyme Therapeutics, Inc. (“Halozyme”) for the use of Halozyme’s proprietary enzyme in one of the Company’s targeted therapeutics. The Company and Halozyme are related parties through common ownership by affiliates of Third Security. The Company’s CEO also serves on Halozyme’s board of directors. Under the terms of the agreement, the Company paid a license fee of $9,000 upon execution of the agreement, which is recorded in research and development expenses on the accompanying consolidated statement of operations. The Company was required to pay an annual exclusivity fee of $1,000 commencing June 6, 2012 and on each anniversary of the effective date of the agreement thereafter until a certain development event occurs. If the Company successfully developed a product candidate using the license in the exclusive field of use and achieves an established sales target, the Company could pay up to $54,000 in milestone payments. The Company was obligated to pay tiered royalties on net sales of the approved product. The Company terminated the agreement effective May 2014 and no payments after that date are required.
	The Manager of Third Security is also the Chief Executive Officer (“CEO”) and Chairman of the Board of Directors of the Company. The CEO has not received compensation for his services as CEO, and as a result, the Company recorded $507 and $387 in compensation expense for each of the three months ended June 30, 2014 and 2013, respectively, and $977 and $775 in compensation expense for each of the six months ended June 30, 2014 and 2013, respectively, based on the estimated salary and benefits appropriate for the role.
	Transactions with ECC Parties
	In conjunction with the ECC with Ziopharm (Note 6), the Company agreed to purchase up to an additional $50,000 of common stock in conjunction with securities offerings that may be conducted by Ziopharm in the future, subject to certain conditions and limitations. Between February 2011 and October 2013, the Company purchased an aggregate of $30,982 of Ziopharm securities. At June 30, 2014, the Company had approximately $19,018 remaining on its purchase commitment.
	In conjunction with the ECC with Synthetic Biologics (Note 6), the Company is entitled to, at its election, purchase up to 19.99% of securities offerings that may be conducted by Synthetic Biologics in the future, subject to certain conditions and limitations. On December 17, 2013, the Company purchased 2,000,000 shares of Synthetic Biologics common stock at $1.00 per share in a securities offering under this right. The Company has been granted the right to make purchases of Synthetic Biologics’ common stock in the open market up to an additional 10% of Synthetic Biologics’ common stock, but has made no such purchases.
	In conjunction with the ECC with Oragenics (Note 6), 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. On November 20, 2013, the Company purchased 1,100,000 shares of Oragenics common stock at $2.50 per share under this right. On September 30, 2013, the Company purchased 1,300,000 shares of Oragenics common stock at $3.00 per share in a private transaction.
	On October 1, 2013, the Company purchased 2,439,024 shares of Fibrocell common stock at $4.10 per share.

Net_Loss_per_Share

Net Loss per Share	6 Months Ended
	Jun. 30, 2014
Earnings Per Share [Abstract]	'
Net Loss per Share	'
	16. Net Loss per Share
	The following table presents the computation of basic and diluted net loss per share for the three and six months ended June 30, 2014 and 2013:
		Three months ended						Six months ended
		June 30,						June 30,
		2014			2013			2014			2013
	Historical net loss per share:
	Numerator:
	Net loss attributable to Intrexon	$	(52,043	)	$	(5,963	)	$	(47,928	)	$	(42,274	)
	Accretion of dividends on redeemable convertible preferred stock		—			(7,942	)		—			(14,347	)
	Net loss attributable to common shareholders	$	(52,043	)	$	(13,905	)	$	(47,928	)	$	(56,621	)
	Denominator:
	Weighted average shares outstanding, basic and diluted		98,892,601			5,667,557			98,113,493			5,664,665
	Net loss attributable to common shareholders per share, basic and diluted	$	(0.53	)	$	(2.45	)	$	(0.49	)	$	(10.00	)
	The following potentially dilutive securities as of June 30, 2014 and 2013, have been excluded from the above computations of diluted weighted average shares outstanding as they would have been anti-dilutive:
		June 30,
		2014			2013
	Common shares issuable upon conversion of all Series Preferred		—			75,402,332
	Options		8,622,579			2,856,905
	Warrants		373,102			511,098
	Total		8,995,681			78,770,335
	In addition to the potentially dilutive securities in the table above, preferred stock cumulative dividends convertible into common shares at a price per share equal to the fair market value of a common share at the time of conversion have been excluded from the computation of diluted weighted-average shares outstanding as of June 30, 2013.

Subsequent_Events

Subsequent Events	6 Months Ended
	Jun. 30, 2014
Subsequent Events [Abstract]	'
Subsequent Events	'
	17. Subsequent Events
	Effective August 8, 2014 (the “Closing Date”), the Company acquired 100% of the membership interests of Trans Ova Genetics, L.C. (“Trans Ova”), an industry-leading provider of bovine reproductive technologies, pursuant to an Amended and Restated Membership Interest Purchase Agreement (the “Purchase Agreement”) dated as of August 8, 2014. The Company and Trans Ova intend to build upon Trans Ova’s current platform with new capabilities to allow for even higher levels of delivered value to dairy and beef cattle producers. The consideration paid at closing for all the membership interests in Trans Ova consisted of $60,000 in cash and the issuance of 1,444,388 shares of the Company’s common stock. In addition, $20,000 in deferred cash is payable in three equal installments upon the first, second, and third anniversaries of the Closing Date (the “Base Consideration”). The Purchase Agreement also provides for (i) the payment to former equity holders of Trans Ova of the aggregate amounts of certain debts, together with accrued interest, currently owed by Trans Ova to governmental entities in the event and to the extent that those debts are forgiven by the relevant governmental entities; and (ii) the payment to such former equity holders of a portion of certain cash proceeds in the event there is an award under currently pending litigation matters to which Trans Ova is a party (together with the Base Consideration, the “Purchase Agreement Consideration”). The Purchase Agreement Consideration is subject to further adjustment as described in the Purchase Agreement.

Summary_of_Significant_Account1

Summary of Significant Accounting Policies (Policies)

6 Months Ended

Jun. 30, 2014

Accounting Policies [Abstract]

'

Principles of Consolidation

'

Principles of Consolidation

The accompanying consolidated financial statements reflect the operations of the Company and its subsidiaries. All intercompany accounts and transactions have been eliminated.

Unaudited Financial Information

'

Unaudited Financial Information

The accompanying interim consolidated financial statements are unaudited and have been prepared in accordance with U.S. GAAP. Certain information and footnote disclosures normally included in the Company’s annual financial statements have been condensed or omitted. These interim consolidated financial statements, in the opinion of management, reflect all normal recurring adjustments necessary for fair statement of the Company’s financial position as of June 30, 2014 and results of operations and cash flows for the interim periods ended June 30, 2014 and 2013. These interim financial results are not necessarily indicative of the results to be expected for the year ending December 31, 2014, 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, 2013.

Revenue Recognition

'

Revenue Recognition

The Company generates revenue through contractual agreements with collaborators (known as exclusive channel collaborations, “ECC” or “ECCs”) whereby the collaborators 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. Generally, the terms of these collaborative agreements provide that the Company receives some or all of the following: (i) upfront payments upon consummation of the agreement, (ii) reimbursements for costs incurred by the Company for research and development and/or manufacturing efforts related to specific applications provided for in the agreement, (iii) milestone payments upon the achievement of specified development, regulatory and commercial activities, and (iv) royalties on sales of products arising from the collaboration.

The Company’s collaboration agreements typically contain multiple elements, or deliverables, including technology licenses, research and development services, and in certain cases manufacturing services. The Company applies the provisions of Accounting Standards Update (“ASU”) No. 2009-13, Revenue Recognition (Topic 605): Multiple Deliverable Revenue Arrangements (“ASU 2009-13”). In accordance with the provisions of ASU 2009-13, the Company identifies the deliverables within the agreements and evaluates which deliverables represent separate units of accounting. Analyzing the agreements to identify deliverables requires the use of judgment. A deliverable is considered a separate unit of accounting when the deliverable has value to the collaborative partner on a standalone basis based on the consideration of the relevant facts and circumstances for each agreement.

Consideration received is allocated at the inception of the agreement to all identified units of accounting based on their relative selling price. When available, the relative selling price for each deliverable is determined using vendor specific objective evidence (“VSOE”) of the selling price or third-party evidence of the selling price, if VSOE does not exist. If neither VSOE nor third-party evidence of the selling price exists, the Company uses its best estimate of the selling price (“BESP”) for the deliverable. The amount of allocable consideration is limited to amounts that are fixed or determinable. The consideration received is allocated among the separate units of accounting, and the applicable revenue recognition criteria are applied to each of the separate units. The Company recognizes the revenue allocated to each unit of accounting as the Company delivers the related goods or services. If the Company determines that certain deliverables should be treated as a single unit of accounting, then the revenue is recognized using either a proportional performance or straight-line method, depending on whether the Company can reasonably estimate the level of effort required to complete its performance obligations under an arrangement and whether such performance obligations are provided on a best-efforts basis. As the Company cannot reasonably estimate its performance obligations related to its collaborators, the Company recognizes revenue on a straight-line basis over the period it expects to complete its performance obligations.

The terms of the Company’s agreements may provide for milestone payments upon achievement of certain defined events. The Company applies ASU No. 2010-17, Revenue Recognition — Milestone Method (“ASU 2010-17” or “Milestone Method”). Under the Milestone Method, the Company recognizes consideration that is contingent upon the achievement of a milestone in its entirety as revenue in the period in which the milestone is achieved only if the milestone is substantive in its entirety. A milestone is considered substantive when it meets all of the following criteria:

-1

The consideration is commensurate with either the entity’s performance to achieve the milestone or the enhancement of the value of the delivered item or items as a result of a specific outcome resulting from the entity’s performance to achieve the milestone;

-2

The consideration relates solely to past performance; and

-3

The consideration is reasonable relative to all of the deliverables and payment terms within the arrangement.

In the event that a milestone is not considered substantive, the Company recognizes the milestone consideration as revenue using the same method applied to upfront payments.

Research and development services are a deliverable satisfied by the Company in accordance with the terms of the collaboration agreements and the Company considers these services to be inseparable from the license to the core technology; therefore, reimbursements of services performed are recognized as revenue. Because reimbursement (i) is contingent upon performance of the services by the Company, (ii) does not include a profit component, and (iii) does not relate to any future deliverable, the revenue is recognized during the period in which the related services are performed and collection of such amounts is reasonably assured. Payments received for manufacturing services will be recognized when the earnings process related to the manufactured materials has been completed. Royalties to be received under the agreements will be recognized as earned.

Research and Development

'

Research and Development

The Company considers that regulatory and other uncertainties inherent in the research and development of new products preclude it from capitalizing such costs. Research and development expenses include salaries and related costs of research and development personnel, and the costs of consultants, facilities, materials and supplies associated with research and development projects as well as various laboratory studies. Indirect research and development costs include depreciation, amortization and other indirect overhead expenses.

The Company has research and development arrangements with third parties that include upfront and milestone payments. At June 30, 2014 and December 31, 2013, the Company had research and development commitments with third parties totaling $2,647 and $2,445, respectively, of which $1,049 and $957, respectively, had not yet been incurred. The commitments are generally cancellable by the Company at any time upon written notice.

Cash and Cash Equivalents

'

Cash and Cash Equivalents

All highly liquid investments with an original maturity of three months or less at the date of purchase are considered to be cash equivalents. Cash balances at a limited number of banks may periodically exceed insurable amounts. The Company believes that it mitigates its risk by investing in or through major financial institutions with high quality credit ratings. Recoverability of investments is dependent upon the performance of the issuer. At June 30, 2014 and December 31, 2013, the Company had cash equivalent investments in highly liquid money market accounts at major financial institutions of $67,792 and $43,733, respectively.

Short-term and Long-term Investments

'

Short-term and Long-term Investments

Short-term and long-term investments include U.S. government debt securities, commercial paper and certificates of deposit. The Company determines the appropriate classification as short-term or long-term at the time of purchase based on original maturities and management’s reasonable expectation of sales and redemption. The Company reevaluates such classification at each balance sheet date. The Company’s written investment policy requires investments to be explicitly rated by two of the three following rating services: Standard & Poor’s, Moody’s and/or Fitch and to have a minimum rating of A1, P1 and/or F-1, respectively, from those agencies. In addition, the investment policy limits the amount of credit exposure to any one issuer.

Equity Securities

'

Equity Securities

The Company holds equity securities received and/or purchased from certain collaborators. Other than investments accounted for using the equity method, the Company elected the fair value option to account for its equity securities held in these collaborators. These equity securities are recorded at fair value at each reporting date and are subject to market price volatility. Unrealized gains and losses resulting from fair value adjustments are reported in the consolidated statement of operations. The fair value of these equity securities is subject to fluctuation in the future due to the volatility of the stock market, changes in general economic conditions and changes in the financial conditions of these collaborators. These equity securities are classified as noncurrent in the consolidated balance sheet since the Company does not intend to sell these equity securities within one year. The Company has not sold any of these equity securities to date.

The Company records the fair value of securities received on the date the collaboration is consummated or the milestone is achieved using the closing, quoted price of the collaborator’s security on that date, assuming the transfer of consideration is considered perfunctory. If the transfer of the consideration is not considered perfunctory, the Company considers the specific facts and circumstances to determine the appropriate date on which to evaluate fair value. The Company also evaluates whether any discounts for trading restrictions or other basis for lack of marketability should be applied to the fair value of the securities at inception of the collaboration. In the event the Company concludes that a discount should be applied, the fair value of the securities is adjusted at inception of the collaboration and re-evaluated at each reporting period thereafter.

Fair Value of Financial Instruments

'

Fair Value of Financial Instruments

Fair value is the price that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date. As such, fair value is a market-based measurement that should be determined based on assumptions that market participants would use in pricing an asset and liability. As a basis for considering such assumptions, the Company uses a three-tier fair value hierarchy that prioritizes the inputs used in its fair value measurements. The hierarchy gives the highest priority to unadjusted quoted prices in active markets for identical assets or liabilities (Level 1 measurements) and the lowest priority to unobservable inputs (Level 3 measurements). The three levels of the fair value hierarchy are as follows:

Level 1:

Quoted prices in active markets for identical assets and liabilities;

Level 2:

Other than quoted prices included in Level 1 inputs that are observable for the asset or liability, either directly or indirectly; and

Level 3:

Unobservable inputs for the asset or liability used to measure fair value to the extent that observable inputs are not available.

Concentrations of Risk

'

Concentrations of Risk

Due to the Company’s mix of fixed and variable rate securities holdings, the Company’s investment portfolio is susceptible to changes in interest rates. As of June 30, 2014, gross unrealized losses on the Company’s investments were not material. From time to time, the Company may liquidate some or all of its investments to fund operational needs or other activities, such as capital expenditures or business acquisitions. Depending on which investments the Company liquidates to fund these activities, the Company could recognize a portion, or all, of the gross unrealized losses.

Equity Method Investments

'

Equity Method Investments

Through March 15, 2013, the Company accounted for its investment in AquaBounty using the equity method of accounting since the Company had the ability to exercise significant influence, but not control, over the operating activities of AquaBounty. The excess of the investment over the Company’s pro-rata share of AquaBounty’s net assets represented identifiable intangible assets and equity-method goodwill. On March 15, 2013, the Company acquired additional ownership interests in AquaBounty which resulted in the Company gaining control over AquaBounty, thereby requiring consolidation effective on that date (Note 4).

The Company has entered into three strategic joint ventures (Note 5). The Company accounts for its investments in these joint ventures using the equity method of accounting since the Company has the ability to exercise significant influence, but not control, over the operating activities of these entities.

The Company determined that it has significant influence over two of its collaborators, Ziopharm Oncology, Inc. (“Ziopharm”) and Oragenics, Inc. (“Oragenics”), as of June 30, 2014 and December 31, 2013, based on its ownership interests, representation on the board of directors of the collaborators and other qualitative factors. The Company accounts for its investments in Ziopharm and Oragenics using the fair value option. The fair value of the Company’s equity securities of Ziopharm was $66,053 and $71,134 as of June 30, 2014 and December 31, 2013, respectively, and is included as equity securities in the respective consolidated balance sheets. The Company’s ownership percentage of Ziopharm is 16.3% and 16.4% at June 30, 2014 and December 31, 2013, respectively. Unrealized appreciation (depreciation) in the fair value of the Company’s equity securities held in Ziopharm was $(9,015) and $3,789 for the three months ended June 30, 2014 and 2013, respectively, and $(5,081) and $(27,743) for the six months ended June 30, 2014 and 2013, respectively. Summarized unaudited financial information for Ziopharm for the three and six months ended June 30, 2014 and 2013 are as follows:

Three months ended

Six months ended

June 30,

June 30,

2014

2013

2014

2013

Revenues

$

200

$

200

$

400

$

400

Operating expenses

11,377

18,496

21,361

42,279

Loss from operations

(11,177

)

(18,296

)

(20,961

)

(41,879

)

Other

5,601

(396

)

5,674

10,388

Net loss

$

(5,576

)

$

(18,692

)

$

(15,287

)

$

(31,491

)

In September 2013, the Company increased its investment in Oragenics, upon which the Company concluded it had significant influence over the operations of Oragenics. The fair value of the Company’s equity securities of Oragenics was $15,758 and $22,161 as of June 30, 2014 and December 31, 2013, respectively, and is included as equity securities in the respective consolidated balance sheets. The Company’s ownership interest in Oragenics was 24.4% and 24.6% at June 30, 2014 and December 31, 2013, respectively. Unrealized appreciation (depreciation) in the fair value of the Company’s equity securities held in Oragenics was $(7,113) and $(865) for the three months ended June 30, 2014 and 2013, respectively, and $(6,403) and $2,028 for the six months ended June 30, 2014 and 2013, respectively. Summarized unaudited financial information for Oragenics for the three and six months ended June 30, 2014 and 2013 are as follows:

Three months ended

Six months ended

June 30,

June 30,

2014

2013

2014

2013

Revenues, net

$

304

$

168

$

518

$

344

Gross profit

178

81

313

194

Operating expenses

2,081

2,156

3,864

4,005

Loss from operations

(1,903

)

(2,075

)

(3,551

)

(3,811

)

Other

7

1

15

147

Net loss

$

(1,896

)

$

(2,074

)

$

(3,536

)

$

(3,664

)

Variable Interest Entities

'

Variable Interest Entities

The Company identifies entities that (1) do not have sufficient equity investment at risk to permit the entity to finance its activities without additional subordinated financial support or (2) in which the equity investors lack an essential characteristic of a controlling financial interest as variable interest entities (“VIE” or “VIEs”). The Company performs an initial and on-going evaluation of the entities with which the Company has variable interests to determine if any of these entities are a VIE. If an entity is identified as a VIE, the Company performs an assessment to determine whether the Company has both (1) the power to direct activities that most significantly impact the VIE’s economic performance and (2) have the obligation to absorb losses from or the right to receive benefits of the VIE that could potentially be significant to the VIE. If both of these criteria are satisfied, the Company is identified as the primary beneficiary of the VIE.

As of June 30, 2014, the Company determined that Genopaver, LLC (“Genopaver”) and Intrexon Energy Partners, LLC (“Intrexon Energy Partners”) were 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. As of December 31, 2013, the Company determined that Genopaver was a VIE. The Company was not the primary beneficiary for this entity since it did not have the power to direct the activities that most significantly impact the economic performance of the VIE.

Property, Plant and Equipment

'

Property, Plant and Equipment

Property, plant and equipment are stated at cost, less accumulated depreciation and amortization. Major additions or betterments are capitalized and repairs and maintenance are generally expensed as incurred. Depreciation and amortization is calculated using the straight-line method over the estimated useful lives of the assets. The estimated useful lives of these assets are as follows:

Years

Building

13

Furniture and fixtures

7

Lab equipment

2–7

Computer hardware

5–7

Software

3–5

Leasehold improvements are amortized over the shorter of the useful life of the asset or the applicable lease term, generally one to four years.

Goodwill

'

Goodwill

Goodwill represents the future economic benefits arising from other assets acquired in a business combination that are not individually identified and separately recognized (Notes 3 and 10). Goodwill is reviewed for impairment at least annually. The Company performs a qualitative assessment to determine whether it is more-likely-than-not that the fair value of a reporting unit is less than its carrying amount prior to performing the two-step goodwill impairment test. If this is the case, the two-step goodwill impairment test is required. If it is more-likely-than-not that the fair value of a reporting unit is greater than the carrying amount, the two-step goodwill impairment test is not required.

If the two-step goodwill impairment test is required, first, the fair value of the reporting unit is compared with its carrying amount (including goodwill). If the fair value of the reporting unit is less than its carrying amount, an indication of goodwill impairment exists for the reporting unit and the entity must perform step two of the impairment test. Under step two, an impairment loss is recognized for any excess of the carrying amount of the reporting unit’s goodwill over the implied fair value of that goodwill. The implied fair value of goodwill is determined by allocating the fair value of the reporting unit in a manner similar to a purchase price allocation and the residual fair value after this allocation is the implied fair value of the reporting unit goodwill. Fair value of the reporting unit is determined using a discounted cash flow analysis. If the fair value of the reporting unit exceeds its carrying amount, step two does not need to be performed.

The Company performs its annual impairment review of goodwill in the fourth quarter, or sooner if a triggering event occurs prior to the annual impairment review.

Intangible Assets

'

Intangible Assets

Intangible assets subject to amortization consist of patents and related technologies acquired as a result of mergers and acquisitions (Note 3). These intangible assets are subject to amortization, were recorded at fair value at the date of acquisition and are stated net of accumulated amortization. Indefinite-lived intangible assets consist of in-process research and development acquired in mergers and acquisitions (Notes 3 and 4) and was recorded at fair value at the dates of the respective acquisitions.

The Company applies the provisions of ASC Topic 350, Intangibles, Goodwill and Other, which requires the amortization of long-lived intangible assets to reflect the pattern in which the economic benefits of the intangible asset are expected to be realized. The intangible assets are amortized over their remaining estimated useful lives, ranging from seven to fourteen years for the patents and related technologies.

Impairment of Long-Lived Assets

'

Impairment of Long-Lived Assets

Long-lived assets to be held and used, including property, plant and equipment and intangible assets subject to amortization, are reviewed for impairment whenever events or changes in circumstances indicate that the carrying amount of the assets may not be recoverable. Conditions that would necessitate an impairment assessment include a significant decline in the observable market value of an asset, a significant change in the extent or manner in which an asset is used, or a significant adverse change that would indicate that the carrying amount of an asset or group of assets is not recoverable.

Indefinite-lived intangible assets, including in-process research and development, are tested for impairment annually, or more frequently if events or circumstances between annual tests indicate that the asset may be impaired. Impairment losses on indefinite-lived intangible assets are recognized based solely on a comparison of their fair value to carrying value, without consideration of any recoverability test. The Company monitors the progression of its in-process research and development, as the likelihood of success is contingent upon commercial development or regulatory approval.

Foreign Currency Translation

'

Foreign Currency Translation

The assets and liabilities of foreign subsidiaries, where the local currency is the functional currency, are translated from their respective functional currencies into United States dollars at the exchange rates in effect at the balance sheet date, with resulting foreign currency translation adjustments recorded in the consolidated statement of comprehensive loss. Revenue and expense amounts are translated at average rates during the period.

Income Taxes

'

Income Taxes

Income taxes are accounted for under the asset and liability method. Deferred tax assets and liabilities are recognized for the future tax consequences attributable to both differences between the financial statement carrying amounts of existing assets and liabilities and their respective tax bases as well as operating loss and tax credit carryforwards. Deferred tax assets and liabilities are measured using enacted tax rates expected to apply to taxable income in the years in which those temporary differences are expected to be recovered or settled. The effect on deferred tax assets and liabilities of a change in tax rates is recognized in income in the period that includes the enactment date of the change. Valuation allowances are established when necessary to reduce deferred tax assets to the amount expected to be realized.

The Company identifies any uncertain income tax positions and recognizes the effect of income tax positions only if those positions are more likely than not of being sustained. Recognized income tax positions are measured at the largest amount that is greater than 50% likely of being realized. Changes in recognition or measurement are reflected in the period in which the change in judgment occurs. The Company records interest, if any, related to unrecognized tax benefits as a component of interest expense. Penalties, if any, are recorded in general and administrative expenses.

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, preferred stock, 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

The Company has determined that it operates as one segment. The Company uses synthetic biology for the creation of distinct products developed in collaboration with third parties. For the three and six months ended June 30, 2014 and 2013, substantially all of the Company’s revenues are derived in the United States of America. As of June 30, 2014 and December 31, 2013, substantially all of the Company’s assets are located in the United States of America. As of June 30, 2014, the Company has $1,390 of property and equipment in Hungary.

Recently Issued Accounting Pronouncements

'

Recently Issued Accounting Pronouncements

In May 2014, the Financial Accounting Standards Board (“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 is effective for fiscal years and interim periods within those years beginning after December 15, 2016, which 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 June 2014, the FASB issued ASU 2014-10, Development Stage Entities (Topic 915): Elimination of Certain Financial Reporting Requirements, Including an Amendment to Variable Interest Entities Guidance in Topic 810, Consolidation (“ASU 2014-10”). The provisions of ASU 2014-10 related to Topic 915 will not have a significant impact to the Company. ASU 2014-10 removes an exception provided to development-stage entities in Consolidation (Topic 810) for determining whether an entity is a variable interest entity. The revisions to Consolidation (Topic 810) are effective for interim and annual periods beginning after December 15, 2015, which are effective for the Company for the year ending December 31, 2016. The Company is currently evaluating the impact that the implementation of this standard will have on the Company’s consolidated financial statements.

Reclassifications

'

Reclassifications

Certain insignificant reclassifications have been made to the prior interim period consolidated financial statements to conform to the current interim period presentation.

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.

Summary_of_Significant_Account2

Summary of Significant Accounting Policies (Tables)	6 Months Ended
	Jun. 30, 2014
Estimated Useful Lives	'
	The estimated useful lives of these assets are as follows:
		Years
	Building	13
	Furniture and fixtures	7
	Lab equipment	2–7
	Computer hardware	5–7
	Software	3–5
Ziopharm Oncology, Inc.	'
Summarized Unaudited Financial Information	'
	Summarized unaudited financial information for Ziopharm for the three and six months ended June 30, 2014 and 2013 are as follows:
		Three months ended						Six months ended
		June 30,						June 30,
		2014			2013			2014			2013
	Revenues	$	200		$	200		$	400		$	400
	Operating expenses		11,377			18,496			21,361			42,279
	Loss from operations		(11,177	)		(18,296	)		(20,961	)		(41,879	)
	Other		5,601			(396	)		5,674			10,388
	Net loss	$	(5,576	)	$	(18,692	)	$	(15,287	)	$	(31,491	)
Oragenics, Inc.	'
Summarized Unaudited Financial Information	'
	Summarized unaudited financial information for Oragenics for the three and six months ended June 30, 2014 and 2013 are as follows:
		Three months ended						Six months ended
		June 30,						June 30,
		2014			2013			2014			2013
	Revenues, net	$	304		$	168		$	518		$	344
	Gross profit		178			81			313			194
	Operating expenses		2,081			2,156			3,864			4,005
	Loss from operations		(1,903	)		(2,075	)		(3,551	)		(3,811	)
	Other		7			1			15			147
	Net loss	$	(1,896	)	$	(2,074	)	$	(3,536	)	$	(3,664	)

Mergers_and_Acquisitions_Table

Mergers and Acquisitions (Tables)	6 Months Ended
	Jun. 30, 2014
Medistem, Inc.	'
Acquisition Date Fair Value Consideration Transferred	'
	The fair value of the total consideration transferred was $24,995. The acquisition date fair value of each class of consideration transferred was as follows:
	Cash	$	4,920
	Common shares		19,368
	Settlement of promissory notes		707
		$	24,995
Estimated Fair Value of Assets Acquired and Liabilities Assumed at Acquisition Date	'
	The preliminary estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown below:
	Cash	$	8
	Intangible assets		4,824
	Total assets acquired		4,832
	Accounts payable		644
	Accrued compensation and benefits		85
	Other accrued expenses		150
	Total liabilities assumed		879
	Net assets acquired		3,953
	Goodwill		21,042
	Total consideration	$	24,995
Condensed Pro forma Financial Information	'
	The following unaudited condensed pro forma financial information for the three months ended June 30, 2013 and the six months ended June 30, 2014 and 2013 is presented as if the acquisition had been consummated on January 1, 2013:
		Three Months Ended			Six Months Ended
		June 30,			June 30,
		2013			2014			2013
		Pro forma
	Revenues	$	6,690		$	19,641		$	10,575
	Loss before income taxes		(6,839	)		(50,245	)		(43,470	)
	Net loss		(6,839	)		(50,268	)		(43,470	)
	Net loss attributable to the noncontrolling interests		556			1,758			607
	Net loss attributable to Intrexon		(6,283	)		(48,510	)		(42,863	)
	Accretion of dividends on redeemable convertible preferred stock	$	(7,942	)	$	—		$	(14,347	)
	Net loss attributable to common shareholders	$	(14,225	)	$	(48,510	)	$	(57,210	)
AquaBounty	'
Acquisition Date Fair Value Consideration Transferred	'
	The fair value of the consideration transferred included:
	Consideration paid	$	4,907
	Fair value of noncontrolling interest		15,153
	Fair value of the Company’s investment in affiliate held before the business combination		12,751
	Fair value of the consideration transferred	$	32,811
Estimated Fair Value of Assets Acquired and Liabilities Assumed at Acquisition Date	'
	The estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown in the table below along with subsequent adjustments during the measurement period to the fair value of assets acquired and liabilities assumed. The adjustments were due to the completed valuation of intangible assets and long-term debt.
		Initial			Adjustments			Adjusted
		estimated						fair
		fair						value
		value
	Cash	$	5,419		$	—		$	5,419
	Short-term investments		14			—			14
	Trade receivables		4			—			4
	Other receivables		9			—			9
	Prepaid expenses and other		200			—			200
	Property, plant and equipment		1,241			—			1,241
	Intangible assets		14,900			—			14,900
	Other assets		22			—			22
	Total assets acquired		21,809			—			21,809
	Accounts payable		156			—			156
	Accrued compensation		94			—			94
	Other accrued liabilities		395			—			395
	Long term debt		2,199			(845	)		1,354
	Total liabilities assumed		2,844			(845	)		1,999
	Net assets acquired		18,965			845			19,810
	Goodwill		13,846			(845	)		13,001
	Total consideration	$	32,811		$	—		$	32,811
Condensed Pro forma Financial Information	'
	The following unaudited condensed pro forma financial information for the six months ended June 30, 2013 is presented as if the acquisition had been consummated on January 1, 2012:
		Six Months Ended
		June 30,
		2013
		Pro forma
	Revenues	$	10,575
	Net loss		(50,418	)
	Net loss attributable to noncontrolling interest		989
	Net loss attributable to Intrexon		(49,429	)
	Accretion of dividends on redeemable convertible preferred stock		(14,347	)
	Net loss attributable to Intrexon common shareholders	$	(63,776	)

Collaboration_Revenue_Tables

Collaboration Revenue (Tables)	6 Months Ended
	Jun. 30, 2014
Organization Consolidation And Presentation Of Financial Statements [Abstract]	'
Summarized Collaboration Revenues	'
	The following table summarizes the amounts recorded in the consolidated statements of operations for each significant collaboration for the three and six months ended June 30, 2014 and 2013.
		Three months ended June 30, 2014
		Collaboration		Collaboration		Total
		revenue recognized		revenue recognized
		from upfront and		from research and
		milestone		development
		payments		services
	ZIOPHARM Oncology, Inc.	$	644	$	3,697	$	4,341
	Synthetic Biologics, Inc.		163		30		193
	Oragenics, Inc.		261		52		313
	Fibrocell Science, Inc.		448		883		1,331
	Genopaver, LLC		68		423		491
	S & I Ophthalmic, LLC		—		607		607
	OvaXon, LLC		—		579		579
	Intrexon Energy Partners, LLC		625		1,210		1,835
	Other		308		1,766		2,074
	Total	$	2,517	$	9,247	$	11,764
		Three months ended June 30, 2013
		Collaboration		Collaboration		Total
		revenue recognized		revenue recognized
		from upfront and		from research and
		milestone		development
		payments		services
	ZIOPHARM Oncology, Inc.	$	644	$	2,291	$	2,935
	Synthetic Biologics, Inc.		1,666		314		1,980
	Oragenics, Inc.		137		334		471
	Fibrocell Science, Inc.		158		615		773
	Genopaver, LLC		68		213		281
	Other		78		156		234
	Total	$	2,751	$	3,923	$	6,674
		Six months ended June 30, 2014
		Collaboration		Collaboration		Total
		revenue recognized		revenue recognized
		from upfront and		from research and
		milestone		development
		payments		services
	ZIOPHARM Oncology, Inc.	$	1,288	$	5,733	$	7,021
	Synthetic Biologics, Inc.		325		227		552
	Oragenics, Inc.		523		585		1,108
	Fibrocell Science, Inc.		896		1,745		2,641
	Genopaver, LLC		137		844		981
	S & I Ophthalmic, LLC		—		1,486		1,486
	OvaXon, LLC		—		748		748
	Intrexon Energy Partners, LLC		625		1,210		1,835
	Other		605		2,624		3,229
	Total	$	4,399	$	15,202	$	19,601
		Six months ended June 30, 2013
		Collaboration		Collaboration		Total
		revenue recognized		revenue recognized
		from upfront and		from research and
		milestone		development
		payments		services
	ZIOPHARM Oncology, Inc.	$	1,288	$	3,721	$	5,009
	Synthetic Biologics, Inc.		1,861		689		2,550
	Oragenics, Inc.		274		713		987
	Fibrocell Science, Inc.		316		1,045		1,361
	Genopaver, LLC		68		213		281
	Other		81		269		350
	Total	$	3,888	$	6,650	$	10,538
Summary of Deferred Revenue	'
	Deferred revenue consists of the following:
		June 30,		December 31,
		2014		2013
	Upfront and milestone payments	$	98,233	$	72,207
	Prepaid research and development services		1,207		1,319
	Other		13		45
	Total	$	99,453	$	73,571
	Current portion of deferred revenue	$	10,706	$	7,793
	Long-term portion of deferred revenue		88,747		65,778
	Total	$	99,453	$	73,571

Shortterm_and_Longterm_Investm1

Short-term and Long-term Investments (Tables)	6 Months Ended
	Jun. 30, 2014
Investments Debt And Equity Securities [Abstract]	'
Summary of Amortized Cost, Gross Unrealized Gains and Losses and Fair Value of Investments	'
	The following table summarizes the amortized cost, gross unrealized gains and losses and fair value of available-for-sale investments as of June 30, 2014:
		Amortized		Gross		Gross			Aggregate
		Cost		Unrealized		Unrealized			Fair Value
				Gains		Losses
	U.S. government debt securities	$	172,960	$	113	$	(1	)	$	173,072
	Certificates of deposit		1,519		—		—			1,519
	Total	$	174,479	$	113	$	(1	)	$	174,591
	The following table summarizes the amortized cost, gross unrealized gains and losses and fair value of available-for-sale investments as of December 31, 2013:
		Amortized		Gross		Gross			Aggregate
		Cost		Unrealized		Unrealized			Fair Value
				Gains		Losses
	U.S. government debt securities	$	178,277	$	35	$	(13	)	$	178,299
	Commercial paper		7,997		—		—			7,997
	Certificates of deposit		2,266		—		(1	)		2,265
	Total	$	188,540	$	35	$	(14	)	$	188,561
Summary of Estimated Fair Value of Available-for-Sale Investments Classified by Contractual Maturities	'
	The estimated fair value of available-for-sale investments classified by their contractual maturities as of June 30, 2014 was as follows:
	Due within one year	$	101,046
	After one year through three years		73,545
	Total	$	174,591

Fair_Value_Measurements_Tables

Fair Value Measurements (Tables)	6 Months Ended
	Jun. 30, 2014
Fair Value Disclosures [Abstract]	'
Summary of Placement in the Fair Value Hierarchy of Financial Assets that are Measured at Fair Value on a Recurring Basis	'
	The following table presents the placement in the fair value hierarchy of financial assets that are measured at fair value on a recurring basis, including the items for which the fair value option has been elected, at June 30, 2014:
		Quoted		Significant		Significant		June 30,
		prices in		other		unobservable		2014
		active		observable		inputs
		markets		inputs		(level 3)
		(level 1)		(level 2)
	Assets
	U.S. government debt securities (Note 7)	$	—	$	173,072	$	—	$	173,072
	Certificates of deposit (Note 7)		—		1,519		—		1,519
	Equity securities (Note 6)		109,665		25,230		—		134,895
	Total	$	109,665	$	199,821	$	—	$	309,486
	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, 2013:
		Quoted		Significant		Significant		December 31,
		prices		other		unobservable		2013
		in active		observable		inputs
		markets		inputs		(level 3)
		(level 1)		(level 2)
	Assets
	U.S. government debt securities (Note 7)	$	—	$	178,299	$	—	$	178,299
	Commercial paper (Note 7)		—		7,997		—		7,997
	Certificates of deposit (Note 7)		—		2,265		—		2,265
	Equity securities (Note 6)		110,297		31,228		—		141,525
	Total	$	110,297	$	219,789	$	—	$	330,086

Property_Plant_and_Equipment_n1

Property, Plant and Equipment, net (Tables)	6 Months Ended
	Jun. 30, 2014
Property Plant And Equipment [Abstract]	'
Schedule of Property, Plant and Equipment	'
	Property, plant and equipment consist of the following:
		June 30,			December 31,
		2014			2013
	Land	$	55		$	55
	Building		945			945
	Furniture and fixtures		975			876
	Lab equipment		24,295			22,275
	Leasehold improvements		5,629			5,147
	Computer hardware		3,513			3,286
	Construction in progress		140			314
	Software		1,344			1,008
			36,896			33,906
	Less: Accumulated depreciation and amortization		(19,507	)		(17,277	)
	Property, plant and equipment, net	$	17,389		$	16,629

Goodwill_and_Intangible_Assets1

Goodwill and Intangible Assets, net (Tables)	6 Months Ended
	Jun. 30, 2014
Goodwill And Intangible Assets Disclosure [Abstract]	'
Schedule of Changes in Carrying Amount of Goodwill	'
	The changes in the carrying amount of goodwill for the six months ended June 30, 2014 are as follows:
	Balance as of December 31, 2013	$	13,823
	Acquisitions		21,042
	Balance as of June 30, 2014	$	34,865
Schedule of Intangible Assets	'
	Intangible assets consist of the following at June 30, 2014:
		Gross		Accumulated			Net
		Carrying		Amortization
		Amount
	Patents and related technologies	$	34,772	$	(9,090	)	$	25,682
	In-process research and development		19,724		—			19,724
	Total	$	54,496	$	(9,090	)	$	45,406
	Intangible assets consist of the following at December 31, 2013:
		Gross		Accumulated			Net
		Carrying		Amortization
		Amount
	Patents and related technologies	$	34,772	$	(7,716	)	$	27,056
	In-process research and development		14,900		—			14,900
	Total	$	49,672	$	(7,716	)	$	41,956

Stock_Option_Plans_Tables

Stock Option Plans (Tables)	6 Months Ended
	Jun. 30, 2014
Disclosure Of Compensation Related Costs Sharebased Payments [Abstract]	'
Schedule of Stock Option Activity	'
	Stock option activity under the Company’s award plans during the period indicated is as follows:
			Number			Weighted			Weighted
			of			average			average
			shares			exercise			remaining
						price			contractual
									term
	Balances at December 31, 2013			2,840,648		$	8.27			7.75
	Granted			6,273,300			28.57
	Exercised			(235,438	)		(4.30	)
	Forfeited			(255,646	)		(19.51	)
	Expired			(285	)		(7.12	)
	Balances at June 30, 2014			8,622,579			22.82			9
	Exercisable at June 30, 2014			1,242,345			7.86			6.39
	Vested and Expected to Vest at June 30, 2014(1)			6,657,224			21.72			8.84
	-1	The number of stock options expected to vest takes into account an estimate of expected forfeitures.

Commitments_and_Contingencies_

Commitments and Contingencies (Tables)	6 Months Ended
	Jun. 30, 2014
Commitments And Contingencies Disclosure [Abstract]	'
Future Minimum Lease Payments Under Noncancelable Operating Leases	'
	At June 30, 2014, future minimum lease payments under noncancelable operating leases having initial or remaining noncancelable lease terms in excess of one year are as follows:
	2014	$	1,919
	2015		4,397
	2016		4,072
	2017		2,607
	2018		1,295
	2019		1,259
	Thereafter		2,406
	Total	$	17,955

Net_Loss_per_Share_Tables

Net Loss per Share (Tables)	6 Months Ended
	Jun. 30, 2014
Earnings Per Share [Abstract]	'
Computation of Basic and Diluted Net Loss per Share	'
	The following table presents the computation of basic and diluted net loss per share for the three and six months ended June 30, 2014 and 2013:
		Three months ended						Six months ended
		June 30,						June 30,
		2014			2013			2014			2013
	Historical net loss per share:
	Numerator:
	Net loss attributable to Intrexon	$	(52,043	)	$	(5,963	)	$	(47,928	)	$	(42,274	)
	Accretion of dividends on redeemable convertible preferred stock		—			(7,942	)		—			(14,347	)
	Net loss attributable to common shareholders	$	(52,043	)	$	(13,905	)	$	(47,928	)	$	(56,621	)
	Denominator:
	Weighted average shares outstanding, basic and diluted		98,892,601			5,667,557			98,113,493			5,664,665
	Net loss attributable to common shareholders per share, basic and diluted	$	(0.53	)	$	(2.45	)	$	(0.49	)	$	(10.00	)
Potentially Dilutive Securities Excluded from Calculation of Net Loss per Share	'
	The following potentially dilutive securities as of June 30, 2014 and 2013, have been excluded from the above computations of diluted weighted average shares outstanding as they would have been anti-dilutive:
		June 30,
		2014			2013
	Common shares issuable upon conversion of all Series Preferred		—			75,402,332
	Options		8,622,579			2,856,905
	Warrants		373,102			511,098
	Total		8,995,681			78,770,335

Organization_and_Basis_of_Pres1

Organization and Basis of Presentation - Additional Information (Detail) (USD $)

0 Months Ended

0 Months Ended

0 Months Ended

In Thousands, except Share data, unless otherwise specified

Mar. 26, 2014

Aug. 13, 2013

Jul. 26, 2013

Jun. 30, 2014

Mar. 26, 2014

Dec. 31, 2013

Aug. 13, 2013

Jun. 30, 2014

Jun. 30, 2014

Oct. 01, 2013

Aug. 13, 2013

Aug. 13, 2013

Aug. 13, 2013

AquaBounty

BioPop

BioPop

IPO

IPO

Exercise of Overallotment Option by Underwriters

Organization, Consolidation and Presentation of Financial Statements Disclosure [Line Items]

'

'

'

'

'

'

'

'

'

'

'

'

'

Percentage of outstanding common stock acquired

'

'

'

'

'

'

'

60.00%

51.00%

51.00%

'

'

'

Reverse stock split ratio

'

'

'1-for-1.75

'

'

'

'

'

'

'

'

'

'

Reverse stock split ratio

'

'

0.57143

'

'

'

'

'

'

'

'

'

'

Shares of common stock

972,004

'

'

'

'

'

'

'

'

'

11,499,998

'

1,499,999

Price per share of common stock

'

'

'

'

$25.72

'

'

'

'

'

'

$16

'

Aggregate proceeds from the IPO

'

'

'

'

'

'

'

'

'

'

$168,300

'

'

Underwriting discounts and commissions

'

'

'

'

'

'

'

'

'

'

12,900

'

'

Offering Expense paid

'

'

'

'

'

'

'

'

'

'

2,800

'

'

Capitalized expenses

'

'

'

'

'

'

'

'

'

'

$2,300

'

'

Shares of common stock issued upon the conversion of redeemable convertible preferred stock, including accrued but unpaid dividends

'

79,705,130

'

'

'

'

'

'

'

'

'

'

'

Number of authorized shares of common stock

'

'

'

200,000,000

'

200,000,000

200,000,000

'

'

'

'

'

'

Number of authorized shares of preferred stock

'

'

'

'

'

'

25,000,000

'

'

'

'

'

'

Summary_of_Significant_Account3

Summary of Significant Accounting Policies - Additional Information (Detail) (USD $)	3 Months Ended		6 Months Ended		12 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013	Dec. 31, 2013
	Entity		Segment		Entity
			Entity
Organization And Significant Accounting Policies [Line Items]	'	'	'	'	'
Research and development commitments with third parties	'	'	$2,647	'	$2,445
Research and development commitments with third parties not incurred	1,049	'	1,049	'	957
Maturity period of liquid investment	'	'	'3 months	'	'
Cash equivalent investments in highly liquid money market accounts	67,792	'	67,792	'	43,733
Number of collaborators over which the Company has significant influence	2	'	2	'	2
Fair value of financial assets measured at fair value on a recurring basis	309,486	'	309,486	'	330,086
Unrealized appreciation (depreciation) in the fair value of the Company's equity securities	-33,777	7,734	-11,855	-21,635	'
Percentage of recognized income tax positions	'	'	50.00%	'	'
Number of segment	'	'	1	'	'
Property and equipment	17,389	'	17,389	'	16,629
HUNGARY	'	'	'	'	'
Organization And Significant Accounting Policies [Line Items]	'	'	'	'	'
Property and equipment	1,390	'	1,390	'	'
Equity Securities	'	'	'	'	'
Organization And Significant Accounting Policies [Line Items]	'	'	'	'	'
Fair value of financial assets measured at fair value on a recurring basis	134,895	'	134,895	'	141,525
Oragenics, Inc.	'	'	'	'	'
Organization And Significant Accounting Policies [Line Items]	'	'	'	'	'
Company's ownership percentage	24.40%	'	24.40%	'	24.60%
Oragenics, Inc. | Equity Securities	'	'	'	'	'
Organization And Significant Accounting Policies [Line Items]	'	'	'	'	'
Fair value of financial assets measured at fair value on a recurring basis	15,758	'	15,758	'	22,161
Unrealized appreciation (depreciation) in the fair value of the Company's equity securities	-7,113	-865	-6,403	2,028	'
Ziopharm Oncology, Inc.	'	'	'	'	'
Organization And Significant Accounting Policies [Line Items]	'	'	'	'	'
Company's ownership percentage	16.30%	'	16.30%	'	16.40%
Ziopharm Oncology, Inc. | Equity Securities	'	'	'	'	'
Organization And Significant Accounting Policies [Line Items]	'	'	'	'	'
Fair value of financial assets measured at fair value on a recurring basis	66,053	'	66,053	'	71,134
Unrealized appreciation (depreciation) in the fair value of the Company's equity securities	($9,015)	$3,789	($5,081)	($27,743)	'
Minimum | Patents and Related Technologies	'	'	'	'	'
Organization And Significant Accounting Policies [Line Items]	'	'	'	'	'
Expected useful life of intangible asset	'	'	'7 years	'	'
Minimum | Leasehold Improvements	'	'	'	'	'
Organization And Significant Accounting Policies [Line Items]	'	'	'	'	'
Property plant and equipment, useful life	'	'	'1 year	'	'
Maximum | Patents and Related Technologies	'	'	'	'	'
Organization And Significant Accounting Policies [Line Items]	'	'	'	'	'
Expected useful life of intangible asset	'	'	'14 years	'	'
Maximum | Leasehold Improvements	'	'	'	'	'
Organization And Significant Accounting Policies [Line Items]	'	'	'	'	'
Property plant and equipment, useful life	'	'	'4 years	'	'

Summarized_Financial_Data_Deta

Summarized Financial Data (Detail) (USD $)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Oragenics, Inc.	'	'	'	'
Schedule of Equity Method Investments [Line Items]	'	'	'	'
Revenues	$304	$168	$518	$344
Gross profit	178	81	313	194
Operating expenses	2,081	2,156	3,864	4,005
Loss from operations	-1,903	-2,075	-3,551	-3,811
Other	7	1	15	147
Net loss	-1,896	-2,074	-3,536	-3,664
Ziopharm Oncology, Inc.	'	'	'	'
Schedule of Equity Method Investments [Line Items]	'	'	'	'
Revenues	200	200	400	400
Operating expenses	11,377	18,496	21,361	42,279
Loss from operations	-11,177	-18,296	-20,961	-41,879
Other	5,601	-396	5,674	10,388
Net loss	($5,576)	($18,692)	($15,287)	($31,491)

Summary_of_Significant_Account4

Summary of Significant Accounting Policies - Estimated Useful Lives of Property, Plant and Equipment (Detail)	6 Months Ended
	Jun. 30, 2014
Building	'
Property, Plant and Equipment [Line Items]	'
Property plant and equipment, useful life	'13 years
Furniture and Fixtures	'
Property, Plant and Equipment [Line Items]	'
Property plant and equipment, useful life	'7 years
Minimum | Lab Equipment	'
Property, Plant and Equipment [Line Items]	'
Property plant and equipment, useful life	'2 years
Minimum | Computer hardware	'
Property, Plant and Equipment [Line Items]	'
Property plant and equipment, useful life	'5 years
Minimum | Software	'
Property, Plant and Equipment [Line Items]	'
Property plant and equipment, useful life	'3 years
Maximum | Lab Equipment	'
Property, Plant and Equipment [Line Items]	'
Property plant and equipment, useful life	'7 years
Maximum | Computer hardware	'
Property, Plant and Equipment [Line Items]	'
Property plant and equipment, useful life	'7 years
Maximum | Software	'
Property, Plant and Equipment [Line Items]	'
Property plant and equipment, useful life	'5 years

Business_Acquisitions_Medistem

Business Acquisitions - Medistem, Inc. - Additional Information (Detail) (Medistem, Inc., USD $)	0 Months Ended	6 Months Ended		0 Months Ended	3 Months Ended	6 Months Ended
In Thousands, except Share data, unless otherwise specified	Mar. 06, 2014	Jun. 30, 2014	Mar. 06, 2014	Mar. 06, 2014	Jun. 30, 2014	Jun. 30, 2014
			Note	Settlement of Promissory Notes	General and Administrative Expense	General and Administrative Expense
Business Acquisition [Line Items]	'	'	'	'	'	'
Percentage of outstanding common stock acquired	'	'	100.00%	'	'	'
Cash	$4,920	'	'	'	'	'
Business acquisition, consideration paid, shares issued	714,144	'	'	'	'	'
Number of promissory notes settled upon the closing of the merger	'	'	2	'	'	'
Fair value of total consideration transferred	24,995	'	'	707	'	'
Shares of merger consideration surrendered by acquiree management to reimburse for required payroll tax withholdings	17,695	'	'	'	'	'
Business combination, acquisition related cost	'	$680	'	'	$20	$310

Fair_Value_of_Consideration_Tr

Fair Value of Consideration Transferred - Medistem, Inc. (Detail) (Medistem, Inc., USD $)	0 Months Ended
In Thousands, unless otherwise specified	Mar. 06, 2014
Business Acquisition [Line Items]	'
Cash	$4,920
Common shares	19,368
Fair value of consideration transferred	24,995
Settlement of Promissory Notes	'
Business Acquisition [Line Items]	'
Fair value of consideration transferred	$707

Fair_Value_of_Assets_Acquired_

Fair Value of Assets Acquired and Liabilities Assumed - Medistem, Inc. (Detail) (USD $)	Jun. 30, 2014	Dec. 31, 2013	Mar. 06, 2014
In Thousands, unless otherwise specified			Medistem, Inc.
			Scenario, Plan
Business Acquisition [Line Items]	'	'	'
Cash	'	'	$8
Intangible assets	'	'	4,824
Total assets acquired	'	'	4,832
Accounts payable	'	'	644
Accrued compensation and benefits	'	'	85
Other accrued expenses	'	'	150
Total liabilities assumed	'	'	879
Net assets acquired	'	'	3,953
Goodwill	34,865	13,823	21,042
Total consideration	'	'	$24,995

Pro_Forma_Financial_Informatio

Pro Forma Financial Information (Detail) (USD $)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Business Acquisition, Pro Forma Information, Nonrecurring Adjustment [Line Items]	'	'	'	'
Loss before income taxes	($53,218)	($6,519)	($49,663)	($42,881)
Net loss	-52,935	-6,519	-49,686	-42,881
Net loss attributable to the noncontrolling interests	892	556	1,758	607
Accretion of dividends on redeemable convertible preferred stock	'	-7,942	'	-14,347
Net loss attributable to common shareholders	-52,043	-13,905	-47,928	-56,621
Medistem, Inc. | Pro Forma	'	'	'	'
Business Acquisition, Pro Forma Information, Nonrecurring Adjustment [Line Items]	'	'	'	'
Revenues	'	6,690	19,641	10,575
Loss before income taxes	'	-6,839	-50,245	-43,470
Net loss	'	-6,839	-50,268	-43,470
Net loss attributable to the noncontrolling interests	'	556	1,758	607
Net loss attributable to Intrexon	'	-6,283	-48,510	-42,863
Accretion of dividends on redeemable convertible preferred stock	'	-7,942	'	-14,347
Net loss attributable to common shareholders	'	($14,225)	($48,510)	($57,210)

Consolidated_MajorityOwned_Sub1

Consolidated Majority-Owned Subsidiaries - Additional Information (Detail) (USD $)

3 Months Ended

6 Months Ended

0 Months Ended

3 Months Ended

6 Months Ended

In Thousands, except Share data, unless otherwise specified

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Mar. 20, 2014

Mar. 15, 2013

Nov. 29, 2012

Nov. 16, 2012

Feb. 28, 2013

Mar. 20, 2014

Mar. 15, 2013

Nov. 16, 2012

Jun. 30, 2013

Jun. 30, 2014

AquaBounty

AquaBounty

AquaBounty

AquaBounty

AquaBounty

AquaBounty

AquaBounty

AquaBounty

AquaBounty

AquaBounty

Pro Forma

In- Process Research and Development

Business Acquisition [Line Items]

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Number of shares acquired

'

'

'

'

'

'

'

'

'

19,040,366

18,714,814

48,631,444

'

'

Percentage of outstanding shares

'

'

'

'

'

'

'

'

'

'

'

47.56%

'

'

Definitive purchase agreement amount

'

'

'

'

'

'

'

$6,000

'

'

'

'

'

'

Amount of loan allowed in promissory note

'

'

'

'

'

'

500

'

'

'

'

'

'

'

Annual interest rate

'

'

'

'

'

'

3.00%

'

'

'

'

'

'

'

Amount drawn on promissory note

'

'

'

'

'

'

'

'

500

'

'

'

'

'

Promissory note repaid

'

'

'

500

'

500

'

'

'

'

'

'

'

'

Maturity date of promissory note

'

'

'

'

'

'

'May 28, 2013

'

'

'

'

'

'

'

Amount from private subscription offering

'

'

'

'

10,000

4,907

'

'

'

'

'

'

'

'

Aggregate percentage of ownership

'

'

'

'

'

'

'

'

'

59.85%

53.82%

'

'

'

Gain recognized

$0

$0

$0

$7,415

'

$7,415

'

'

'

'

'

'

$7,415

'

Percentage of equity interest previously held

'

'

'

'

'

'

'

'

'

'

47.56%

'

'

'

Expected useful life of intangible asset

'

'

'

'

'

'

'

'

'

'

'

'

'

'15 years

Consolidated_MajorityOwned_Sub2

Consolidated Majority-Owned Subsidiaries - Summary of Fair Value of the Consideration Transferred (Detail) (AquaBounty, USD $)	0 Months Ended
In Thousands, unless otherwise specified	Mar. 20, 2014	Mar. 15, 2013	Mar. 15, 2013
AquaBounty	'	'	'
Business Acquisition [Line Items]	'	'	'
Consideration paid	$10,000	$4,907	'
Fair value of noncontrolling interest	'	'	15,153
Fair value of the Company's investment in affiliate held before the business combination	'	12,751	'
Fair value of the consideration transferred	'	$32,811	'

Consolidated_MajorityOwned_Sub3

Consolidated Majority-Owned Subsidiaries - Summary of Estimated Fair Value of Assets Acquired and Liabilities Assumed at the Acquisition Date (Detail) (USD $)	Jun. 30, 2014	Dec. 31, 2013	Mar. 15, 2013	Mar. 15, 2013	Mar. 15, 2013
In Thousands, unless otherwise specified			Scenario, Plan	Scenario, Adjustment	Scenario, Actual
			AquaBounty	AquaBounty	AquaBounty
Business Acquisition [Line Items]	'	'	'	'	'
Cash	'	'	$5,419	'	$5,419
Short-term investments	'	'	14	'	14
Trade receivables	'	'	4	'	4
Other receivables	'	'	9	'	9
Prepaid expenses and other	'	'	200	'	200
Property, plant and equipment	'	'	1,241	'	1,241
Intangible assets	'	'	14,900	'	14,900
Other assets	'	'	22	'	22
Total assets acquired	'	'	21,809	'	21,809
Accounts payable	'	'	156	'	156
Accrued compensation	'	'	94	'	94
Other accrued liabilities	'	'	395	'	395
Long term debt	'	'	2,199	-845	1,354
Total liabilities assumed	'	'	2,844	-845	1,999
Net assets acquired	'	'	18,965	845	19,810
Goodwill	34,865	13,823	13,846	-845	13,001
Total consideration	'	'	$32,811	'	$32,811

Consolidated_MajorityOwned_Sub4

Consolidated Majority-Owned Subsidiaries - Summary of Unaudited Condensed Pro Forma Financial Information (Detail) (USD $)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Business Acquisition, Pro Forma Information [Line Items]	'	'	'	'
Net loss	($52,935)	($6,519)	($49,686)	($42,881)
Net loss attributable to noncontrolling interests	892	556	1,758	607
Accretion of dividends on redeemable convertible preferred stock	'	-7,942	'	-14,347
Net loss attributable to common shareholders	-52,043	-13,905	-47,928	-56,621
AquaBounty | Pro Forma	'	'	'	'
Business Acquisition, Pro Forma Information [Line Items]	'	'	'	'
Revenues	'	'	'	10,575
Net loss	'	'	'	-50,418
Net loss attributable to noncontrolling interests	'	'	'	989
Net loss attributable to Intrexon	'	'	'	-49,429
Accretion of dividends on redeemable convertible preferred stock	'	'	'	-14,347
Net loss attributable to common shareholders	'	'	'	($63,776)

Business_Acquisitions_BioPop_A

Business Acquisitions - BioPop Acquisition - Additional Information (Detail) (USD $)	Jun. 30, 2014	Dec. 31, 2013	Oct. 01, 2013	Jun. 30, 2014	Oct. 01, 2013	Oct. 01, 2013
In Thousands, unless otherwise specified			BioPop	BioPop	BioPop	BioPop
						Patents and Related Technologies
Business Combination, Transactions [Line Items]	'	'	'	'	'	'
Cash	'	'	$1,300	'	'	'
Percentage of outstanding shares acquired	'	'	'	51.00%	51.00%	'
Goodwill	34,865	13,823	'	'	822	'
Intangible Asset	'	'	'	'	$430	'
Acquired Intangible Assets, useful life	'	'	'	'	'	'4 years

Investments_in_Joint_Ventures_

Investments in Joint Ventures - Additional Information (Detail) (USD $)

Jun. 30, 2014

Dec. 31, 2013

Mar. 26, 2014

Jun. 30, 2014

Mar. 26, 2014

Mar. 26, 2014

Mar. 26, 2014

Jan. 31, 2014

Jun. 30, 2014

Jun. 30, 2014

Oct. 31, 2013

Jun. 30, 2014

Jun. 30, 2014

Dec. 31, 2013

In Thousands, unless otherwise specified

Intrexon Energy Partners, LLC

Intrexon Energy Partners, LLC

Intrexon Energy Partners, LLC

Intrexon Energy Partners, LLC

Intrexon Energy Partners, LLC

OvaXon, LLC

OvaXon, LLC

OvaXon, LLC

S & I Ophthalmic, LLC

S & I Ophthalmic, LLC

S & I Ophthalmic, LLC

S & I Ophthalmic, LLC

Research And Development Services

Investors

Maximum

Maximum

Investors

Schedule Of Investments In Joint Venture [Line Items]

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Initial capital contribution

'

'

'

'

$25,000

'

'

$1,500

'

'

$5,000

'

'

'

Membership interest

'

'

50.00%

'

'

'

'

50.00%

'

'

50.00%

'

'

'

Additional capital contribution

'

'

'

'

'

25,000

25,000

'

'

'

'

'

'

'

Net loss

'

'

'

1,210

'

'

'

'

590

784

'

910

1,788

'

Net assets

'

'

'

'

'

'

'

'

2,216

2,216

'

7,779

7,779

9,567

Investment

$4,997

$6,284

'

'

'

'

'

'

$1,108

$1,108

'

$3,889

$3,889

$4,784

Summarized_Amount_of_Collabora

Summarized Amount of Collaboration Recorded in Consolidated Statement of Operations (Detail) (USD $)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'
Collaboration revenues	$11,764	$6,674	$19,601	$10,538
Ziopharm Oncology, Inc.	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'
Collaboration revenues	4,341	2,935	7,021	5,009
Synthetic Biologics, Inc.	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'
Collaboration revenues	193	1,980	552	2,550
Oragenics, Inc.	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'
Collaboration revenues	313	471	1,108	987
Fibrocell Science, Inc.	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'
Collaboration revenues	1,331	773	2,641	1,361
Genopaver, LLC	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'
Collaboration revenues	491	281	981	281
S & I Ophthalmic, LLC	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'
Collaboration revenues	607	'	1,486	'
OvaXon, LLC	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'
Collaboration revenues	579	'	748	'
Intrexon Energy Partners, LLC	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'
Collaboration revenues	1,835	'	1,835	'
Other Collaborations	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'
Collaboration revenues	2,074	234	3,229	350
Upfront and Milestone Payments	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'
Collaboration revenues	2,517	2,751	4,399	3,888
Upfront and Milestone Payments | Ziopharm Oncology, Inc.	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'
Collaboration revenues	644	644	1,288	1,288
Upfront and Milestone Payments | Synthetic Biologics, Inc.	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'
Collaboration revenues	163	1,666	325	1,861
Upfront and Milestone Payments | Oragenics, Inc.	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'
Collaboration revenues	261	137	523	274
Upfront and Milestone Payments | Fibrocell Science, Inc.	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'
Collaboration revenues	448	158	896	316
Upfront and Milestone Payments | Genopaver, LLC	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'
Collaboration revenues	68	68	137	68
Upfront and Milestone Payments | Intrexon Energy Partners, LLC	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'
Collaboration revenues	625	'	625	'
Upfront and Milestone Payments | Other Collaborations	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'
Collaboration revenues	308	78	605	81
Research And Development Services	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'
Collaboration revenues	9,247	3,923	15,202	6,650
Research And Development Services | Ziopharm Oncology, Inc.	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'
Collaboration revenues	3,697	2,291	5,733	3,721
Research And Development Services | Synthetic Biologics, Inc.	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'
Collaboration revenues	30	314	227	689
Research And Development Services | Oragenics, Inc.	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'
Collaboration revenues	52	334	585	713
Research And Development Services | Fibrocell Science, Inc.	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'
Collaboration revenues	883	615	1,745	1,045
Research And Development Services | Genopaver, LLC	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'
Collaboration revenues	423	213	844	213
Research And Development Services | S & I Ophthalmic, LLC	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'
Collaboration revenues	607	'	1,486	'
Research And Development Services | OvaXon, LLC	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'
Collaboration revenues	579	'	748	'
Research And Development Services | Intrexon Energy Partners, LLC	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'
Collaboration revenues	1,210	'	1,210	'
Research And Development Services | Other Collaborations	'	'	'	'
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'
Collaboration revenues	$1,766	$156	$2,624	$269

Collaboration_Revenue_Addition

Collaboration Revenue - Additional Information (Detail) (USD $)

0 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

0 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

0 Months Ended

0 Months Ended

0 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

0 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

0 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

0 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

0 Months Ended

0 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

0 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

0 Months Ended

0 Months Ended

In Thousands, except Share data, unless otherwise specified

Jul. 26, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Dec. 31, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Dec. 31, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Aug. 06, 2012

Aug. 06, 2012

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Dec. 17, 2012

Jun. 05, 2012

Jun. 05, 2012

Sep. 30, 2013

Sep. 30, 2013

Apr. 30, 2013

Oct. 05, 2012

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Oct. 05, 2012

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Mar. 29, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Feb. 14, 2013

Mar. 26, 2014

Jun. 30, 2014

Jun. 30, 2014

Jun. 30, 2014

Jun. 30, 2014

Jun. 30, 2014

Jun. 30, 2014

Jan. 06, 2011

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Jan. 06, 2011

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Nov. 18, 2011

Nov. 18, 2011

Sep. 30, 2013

Jun. 30, 2014

Jun. 30, 2014

Jun. 30, 2014

Jun. 30, 2014

Dec. 18, 2013

Jun. 30, 2014

Jun. 30, 2014

Jun. 30, 2014

Jun. 30, 2014

Oct. 05, 2012

Jun. 05, 2012

Dec. 18, 2013

Sep. 30, 2013

Oct. 05, 2012

Mar. 29, 2013

Mar. 26, 2014

Jan. 06, 2011

Jan. 06, 2011

Jan. 06, 2011

Nov. 18, 2011

Jan. 10, 2014

Jun. 28, 2013

Oct. 24, 2012

Upfront and Milestone Payments

Upfront and Milestone Payments

Upfront and Milestone Payments

Upfront and Milestone Payments

Upfront and Milestone Payments

Research And Development Services

Research And Development Services

Research And Development Services

Research And Development Services

Synthetic Biologics Field Two ECC

Synthetic Biologics Field Two ECC

Synthetic Biologics, Inc.

Synthetic Biologics, Inc.

Synthetic Biologics, Inc.

Synthetic Biologics, Inc.

Synthetic Biologics, Inc.

Synthetic Biologics, Inc.

Synthetic Biologics, Inc.

Synthetic Biologics, Inc.

Synthetic Biologics, Inc.

Synthetic Biologics, Inc.

Synthetic Biologics, Inc.

Synthetic Biologics, Inc.

Synthetic Biologics, Inc.

Oragenics ECC

Oragenics ECC

Oragenics Second ECC

Oragenics Second ECC

Fibrocell Science, Inc.

Fibrocell Science, Inc.

Fibrocell Science, Inc.

Fibrocell Science, Inc.

Fibrocell Science, Inc.

Fibrocell Science, Inc.

Fibrocell Science, Inc.

Fibrocell Science, Inc.

Fibrocell Science, Inc.

Fibrocell Science, Inc.

Fibrocell Science, Inc.

Fibrocell Science, Inc.

Fibrocell Science, Inc.

Fibrocell Science, Inc.

Fibrocell Science, Inc.

Genopaver, LLC

Genopaver, LLC

Genopaver, LLC

Genopaver, LLC

Genopaver, LLC

Genopaver, LLC

Genopaver, LLC

Genopaver, LLC

Genopaver, LLC

Genopaver, LLC

Genopaver, LLC

Genopaver, LLC

Genopaver, LLC

AquaBounty ECC

Intrexon Energy Partners, LLC

Intrexon Energy Partners, LLC

Intrexon Energy Partners, LLC

Intrexon Energy Partners, LLC

Intrexon Energy Partners, LLC

Intrexon Energy Partners, LLC

Intrexon Energy Partners, LLC

Ziopharm Oncology, Inc.

Ziopharm Oncology, Inc.

Ziopharm Oncology, Inc.

Ziopharm Oncology, Inc.

Ziopharm Oncology, Inc.

Ziopharm Oncology, Inc.

Ziopharm Oncology, Inc.

Ziopharm Oncology, Inc.

Ziopharm Oncology, Inc.

Ziopharm Oncology, Inc.

Ziopharm Oncology, Inc.

Ziopharm Oncology, Inc.

Ziopharm Oncology, Inc.

Ziopharm Oncology, Inc.

Synthetic Biologics Field One ECC

Synthetic Biologics Field One ECC

S & I Ophthalmic, LLC

S & I Ophthalmic, LLC

S & I Ophthalmic, LLC

S & I Ophthalmic, LLC

S & I Ophthalmic, LLC

OvaXon, LLC

OvaXon, LLC

OvaXon, LLC

OvaXon, LLC

OvaXon, LLC

Upfront

Upfront

Upfront

Upfront

Upfront

Upfront

Upfront

Upfront

Upfront

Upfront

Upfront

Supplemental Upfront

Supplemental Upfront

Milestone One

Upfront and Milestone Payments

Upfront and Milestone Payments

Upfront and Milestone Payments

Upfront and Milestone Payments

Research And Development Services

Research And Development Services

Research And Development Services

Research And Development Services

Research And Development Services

Upfront and Milestone Payments

Upfront and Milestone Payments

Upfront and Milestone Payments

Upfront and Milestone Payments

Research And Development Services

Research And Development Services

Research And Development Services

Research And Development Services

Upfront and Milestone Payments

Upfront and Milestone Payments

Upfront and Milestone Payments

Upfront and Milestone Payments

Research And Development Services

Research And Development Services

Research And Development Services

Research And Development Services

Upfront and Milestone Payments

Upfront and Milestone Payments

Research And Development Services

Research And Development Services

Upfront and Milestone Payments

Upfront and Milestone Payments

Upfront and Milestone Payments

Upfront and Milestone Payments

Research And Development Services

Research And Development Services

Research And Development Services

Research And Development Services

Research And Development Services

Research And Development Services

Research And Development Services

Research And Development Services

Synthetic Biologics Field Two ECC

Oragenics ECC

Oragenics Second ECC

Oragenics Second ECC

Fibrocell Science, Inc.

Genopaver, LLC

Intrexon Energy Partners, LLC

Ziopharm Oncology, Inc.

Ziopharm Oncology ECC Separate Unit of Accounting

Ziopharm Oncology ECC Unit of Accounting One

Synthetic Biologics Field One ECC

Fibrocell Science, Inc.

Fibrocell Science, Inc.

Ziopharm Oncology, Inc.

Upfront and Milestone Payments

Upfront and Milestone Payments

Upfront and Milestone Payments

Upfront and Milestone Payments

Upfront and Milestone Payments

Upfront and Milestone Payments

Upfront and Milestone Payments

Upfront and Milestone Payments

Upfront and Milestone Payments

Upfront and Milestone Payments

Upfront and Milestone Payments

Upfront and Milestone Payments

Upfront and Milestone Payments

Upfront and Milestone Payments

Collaboration Agreements [Line Items]

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Collaborative arrangement consideration received, shares

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

3,552,210

4,392,425

'

1,348,000

1,317,520

'

'

3,636,926

'

'

3,123,558

1,024,590

1,243,781

3,636,926

Collaborative arrangement consideration received, value

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

$7,815

$6,588

'

$3,503

$7,576

$3,000

$25,000

$17,457

'

'

$1,687

$5,225

$7,612

$18,330

Collaboration revenue

'

11,764

6,674

19,601

10,538

'

2,517

2,751

4,399

3,888

'

9,247

3,923

15,202

6,650

'

'

193

1,980

552

2,550

163

1,666

325

1,861

30

314

227

689

'

'

'

'

'

'

'

1,331

773

2,641

1,361

'

448

158

896

316

883

615

1,745

1,045

'

491

281

981

281

68

68

137

68

423

213

844

213

'

'

1,835

1,835

625

625

1,210

1,210

'

4,341

2,935

7,021

5,009

'

644

644

1,288

1,288

3,697

2,291

5,733

3,721

'

'

'

607

1,486

607

1,486

'

579

748

579

748

'

'

'

'

'

'

'

'

1,115

'

'

'

'

'

Deferred revenue

'

99,453

'

99,453

'

73,571

98,233

'

98,233

'

72,207

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

2,500

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

16,342

'

'

'

'

Percent of shares outstanding at the date of achievement of future milestone

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

1.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

7.50%

'

'

'

'

'

'

'

'

'

10.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Royalty rate as a percentage of net profit

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

25.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

50.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

50.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Required notice period for voluntary termination of collaborative agreement

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'90 days

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'90 days

'

'90 days

'

'

'90 days

'

'

'

'

'

'

'

'

'

'

'

'

'

'90 days

'

'

'

'

'

'

'

'

'

'

'

'

'

'90 days

'

'

'

'

'

'

'90 days

'

'

'

'

'

'

'

'

'

'

'

'

'

'90 days

'

'90 days

'

'

'

'

'90 days

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Consideration to be received upon achievement of future milestone 1

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

2,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

2,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Consideration to be received upon achievement of future milestone 2

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

3,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

5,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Field expansion fee

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

2,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Percentage of shares outstanding at the date of achievement of future milestone 2

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

1.50%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Percentage of shares outstanding at the date of achievement of future milestone 3

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

2.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Percentage of shares outstanding at the date of achievement of future milestone 4

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

2.50%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Percentage of shares outstanding at the date of achievement of future milestone 5

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

3.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Maturity date of promissory note

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'December 31, 2013

'

'

'

'

'

'

'

'

'

'

Collaborative arrangement consideration received, value of convertible promissory note

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

1,956

'

'

'

'

'

'

'

'

'

'

Consideration to be received upon achievement of future milestone 3

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

10,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Royalty rate as a percentage of net sales, tier 1

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

10.00%

'

'

7.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Conversion of promissory note into Common stock

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

698,241

'

'

'

'

'

'

'

'

'

'

'

Reverse stock split ratio

'1-for-1.75

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'1-for-25

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Reverse stock split ratio

0.57143

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

0.04

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Royalty rate as a percentage of net sales, tier 2

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

14.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Royalty rate of savings from improvement

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

33.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Level of net sales at which royalty rate changes to tier 2

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

$25,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Royalty rate as a percentage of gross profit

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

16.66%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Collaboration_Revenue_Summary_

Collaboration Revenue - Summary of Deferred Revenue (Detail) (USD $)	Jun. 30, 2014	Dec. 31, 2013
In Thousands, unless otherwise specified
Deferred Revenue Arrangement [Line Items]	'	'
Current portion of deferred revenue	$10,706	$7,793
Long-term portion of deferred revenue	88,747	65,778
Deferred revenue	99,453	73,571
Upfront and Milestone Payments	'	'
Deferred Revenue Arrangement [Line Items]	'	'
Deferred revenue	98,233	72,207
Prepaid Research And Development Services	'	'
Deferred Revenue Arrangement [Line Items]	'	'
Deferred revenue	1,207	1,319
Other	'	'
Deferred Revenue Arrangement [Line Items]	'	'
Deferred revenue	$13	$45

Shortterm_and_Longterm_Investm2

Short-term and Long-term Investments - Summary of Amortized Cost, Gross Unrealized Gains and Losses and Fair Value of Short-term Investments (Detail) (USD $)	Jun. 30, 2014	Dec. 31, 2013
In Thousands, unless otherwise specified
Schedule of Available-for-sale Securities [Line Items]	'	'
Amortized Cost	$174,479	$188,540
Gross Unrealized Gains	113	35
Gross Unrealized Losses	-1	-14
Aggregate Fair Value	174,591	188,561
US Government Debt Securities	'	'
Schedule of Available-for-sale Securities [Line Items]	'	'
Amortized Cost	172,960	178,277
Gross Unrealized Gains	113	35
Gross Unrealized Losses	-1	-13
Aggregate Fair Value	173,072	178,299
Commercial Paper	'	'
Schedule of Available-for-sale Securities [Line Items]	'	'
Amortized Cost	'	7,997
Aggregate Fair Value	'	7,997
Certificates of Deposit	'	'
Schedule of Available-for-sale Securities [Line Items]	'	'
Amortized Cost	1,519	2,266
Gross Unrealized Losses	'	-1
Aggregate Fair Value	$1,519	$2,265

Shortterm_and_Longterm_Investm3

Short-term and Long-term Investments - Summary of Estimated Fair Value of Available-for-Sale Investments Classified by Contractual Maturities (Detail) (USD $)	Jun. 30, 2014	Dec. 31, 2013
In Thousands, unless otherwise specified
Amortized Cost And Fair Value Debt Securities [Abstract]	'	'
Due within one year	$101,046	'
After one year through three years	73,545	'
Aggregate Fair Value	$174,591	$188,561

Shortterm_and_Longterm_Investm4

Short-term and Long-term Investments - Additional Information (Detail) (USD $)	Jun. 30, 2014
Investments Debt And Equity Securities [Abstract]	'
Other-than-temporarily impaired	$0

Fair_Value_Measurements_Summar

Fair Value Measurements - Summary of Placement in the Fair Value Hierarchy of Financial Assets that are Measured at Fair Value on a Recurring Basis (Detail) (USD $)	Jun. 30, 2014	Dec. 31, 2013
In Thousands, unless otherwise specified
Assets	'	'
Fair value of assets	$309,486	$330,086
US Government Debt Securities	'	'
Assets	'	'
Fair value of assets	173,072	178,299
Commercial Paper	'	'
Assets	'	'
Fair value of assets	'	7,997
Certificates of Deposit	'	'
Assets	'	'
Fair value of assets	1,519	2,265
Equity Securities	'	'
Assets	'	'
Fair value of assets	134,895	141,525
Quoted prices in active markets (level 1)	'	'
Assets	'	'
Fair value of assets	109,665	110,297
Quoted prices in active markets (level 1) | Equity Securities	'	'
Assets	'	'
Fair value of assets	109,665	110,297
Significant other observable inputs (level 2)	'	'
Assets	'	'
Fair value of assets	199,821	219,789
Significant other observable inputs (level 2) | US Government Debt Securities	'	'
Assets	'	'
Fair value of assets	173,072	178,299
Significant other observable inputs (level 2) | Commercial Paper	'	'
Assets	'	'
Fair value of assets	'	7,997
Significant other observable inputs (level 2) | Certificates of Deposit	'	'
Assets	'	'
Fair value of assets	1,519	2,265
Significant other observable inputs (level 2) | Equity Securities	'	'
Assets	'	'
Fair value of assets	$25,230	$31,228

Fair_Value_Measurements_Additi

Fair Value Measurements - Additional Information (Detail) (USD $)	6 Months Ended
	Jun. 30, 2014	Jun. 30, 2013
Fair Value Disclosures [Abstract]	'	'
Transfers between levels of fair value hierarchy	$0	$0

Recovered_Sheet1

Property, Plant and Equipment, Net - Schedule of Property Plant and Equipment (Detail) (USD $)	Jun. 30, 2014	Dec. 31, 2013
In Thousands, unless otherwise specified
Property Plant And Equipment [Abstract]	'	'
Land	$55	$55
Building	945	945
Furniture and fixtures	975	876
Lab equipment	24,295	22,275
Leasehold improvements	5,629	5,147
Computer hardware	3,513	3,286
Construction in progress	140	314
Software	1,344	1,008
Property, plant and equipment, gross	36,896	33,906
Less: Accumulated depreciation and amortization	-19,507	-17,277
Property, plant and equipment, net	$17,389	$16,629

Recovered_Sheet2

Property, Plant and Equipment, Net - Additional Information (Detail) (USD $)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Property Plant And Equipment [Abstract]	'	'	'	'
Depreciation expense	$1,281	$1,114	$2,399	$2,260

Goodwill_and_Intangible_Assets2

Goodwill and Intangible Assets, Net - Schedule of Changes in Carrying Amount of Goodwill (Detail) (USD $)	6 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014
Goodwill And Intangible Assets Disclosure [Abstract]	'
Beginning Balance	$13,823
Acquisitions	21,042
Ending Balance	$34,865

Goodwill_and_Intangible_Assets3

Goodwill and Intangible Assets, Net - Additional Information (Detail) (USD $)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013	Dec. 31, 2013
Goodwill And Intangible Assets [Line Items]	'	'	'	'	'
Accumulated impairment losses	$0	'	$0	'	$0
In-process research and development or accumulated impairment losses	0	'	0	'	0
Amortization expense	$687	$709	$1,374	$1,434	'
Weighted Average | Patents and Related Technologies	'	'	'	'	'
Goodwill And Intangible Assets [Line Items]	'	'	'	'	'
Weighted average useful life	'	'	'12 years 3 months 18 days	'	'

Intangible_Assets_Net_Schedule

Intangible Assets, Net - Schedule of Intangible Assets (Detail) (USD $)	Jun. 30, 2014	Dec. 31, 2013
In Thousands, unless otherwise specified
Finite-Lived Intangible Assets [Line Items]	'	'
Gross Carrying Amount	$54,496	$49,672
Accumulated Amortization	-9,090	-7,716
Net	45,406	41,956
Patents and Related Technologies	'	'
Finite-Lived Intangible Assets [Line Items]	'	'
Gross Carrying Amount	34,772	34,772
Accumulated Amortization	-9,090	-7,716
Net	25,682	27,056
In- Process Research and Development	'	'
Finite-Lived Intangible Assets [Line Items]	'	'
Gross Carrying Amount	19,724	14,900
Net	$19,724	$14,900

Income_Taxes_Additional_Inform

Income Taxes - Additional Information (Detail) (USD $)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Income Tax Disclosure [Abstract]	'	'	'	'
Taxable income (loss)	($14,100)	'	$1,200	'
Income tax benefit (expense)	283	0	-23	0
Operating loss carryforwards	249,600	'	249,600	'
Expiration date of Federal income tax loss carryforwards	'	'	'2022	'
Stock Compensation Deductions	'	'	'	'
Income Tax Disclosure [Abstract]	'	'	'	'
Operating loss carryforwards	6,800	'	6,800	'
INTREXON CORP	'	'	'	'
Income Tax Disclosure [Abstract]	'	'	'	'
Federal and state research and development tax credits	$7,000	'	$7,000	'

Shareholders_Equity_Additional

Shareholders' Equity - Additional Information (Detail) (USD $)	0 Months Ended	6 Months Ended
In Thousands, except Share data, unless otherwise specified	Mar. 26, 2014	Jun. 30, 2014	Mar. 26, 2014
Temporary Equity [Line Items]	'	'	'
Securities purchase agreements, share	972,004	'	'
Price per share of common stock	'	'	$25.72
Securities purchase agreements gross proceed	$25,000	$25,000	'
Securities purchase agreements, value	'	25,000	'
Affiliates Of Third Security	'	'	'
Temporary Equity [Line Items]	'	'	'
Securities purchase agreements, share	243,001	'	'
Securities purchase agreements, value	$6,250	'	'

Stock_Option_Plans_Additional_

Stock Option Plans - Additional Information (Detail) (USD $)

6 Months Ended

12 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

In Thousands, except Share data, unless otherwise specified

Jun. 30, 2014

Dec. 31, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Dec. 31, 2011

Dec. 31, 2010

Jun. 30, 2014

Jun. 09, 2014

Jul. 26, 2013

Jun. 30, 2014

Jun. 30, 2014

Jun. 30, 2014

Jun. 30, 2014

Jun. 30, 2014

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Intrexon Stock Option Plans

Intrexon Stock Option Plans

Intrexon Stock Option Plans

Intrexon Stock Option Plans

Intrexon Stock Option Plans

Intrexon Stock Option Plans

Intrexon Stock Option Plans

Intrexon Stock Option Plans

Intrexon Stock Option Plans

Intrexon Stock Option Plans

Intrexon Stock Option Plans

Intrexon Stock Option Plans

Intrexon Stock Option Plans

Intrexon Stock Option Plans

Intrexon Stock Option Plans

Intrexon Stock Option Plans

AquaBounty Stock Option Plan

AquaBounty Stock Option Plan

AquaBounty Stock Option Plan

AquaBounty Stock Option Plan

AquaBounty Stock Option Plan

AquaBounty Stock Option Plan

AquaBounty Stock Option Plan

AquaBounty Stock Option Plan

AquaBounty Stock Option Plan

Research and Development Expense

Research and Development Expense

Research and Development Expense

Research and Development Expense

General and Administrative Expense

General and Administrative Expense

General and Administrative Expense

General and Administrative Expense

2008 Equity Incentive Plan

2008 Equity Incentive Plan

2008 Equity Incentive Plan

2013 Omnibus Incentive Plan

2013 Omnibus Incentive Plan

2013 Omnibus Incentive Plan

Minimum

Maximum

Research and Development Expense

Research and Development Expense

General and Administrative Expense

General and Administrative Expense

General and Administrative Expense

General and Administrative Expense

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

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Stock based compensation cost

'

'

$1,343

$147

$1,670

$299

$5,429

$641

$8,799

$896

'

'

'

'

'

'

'

'

'

$21

$42

$55

$21

$111

$1

Number of authorized awards

'

'

'

'

'

'

'

'

'

'

'

5,714,285

2,857,142

'

10,000,000

7,000,000

'

'

'

'

'

'

'

'

'

Options outstanding

8,622,579

2,840,648

'

'

'

'

'

'

'

'

2,200,779

'

'

6,421,800

'

'

7,359,000

'

'

'

'

'

'

'

'

Remaining shares available to grant

'

'

'

'

'

'

'

'

'

'

'

'

'

3,559,727

'

'

'

'

'

'

'

'

'

'

'

Unrecognized compensation costs related to nonvested awards

$74,570

$9,639

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Recognized over weighted-average period

'3 years

'3 years

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Option issued, vesting period

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'1 year

'3 years

'

'

'

'

'

'

Term of issuance of option

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'10 years

'

'

'

'

'

'

'

'

Weighted average price of option

$22.82

$8.27

'

'

'

'

'

'

'

'

'

'

'

'

'

'

$0.31

'

'

'

'

'

'

'

'

Options exercisable

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

6,255,520

'

'

'

'

'

'

'

'

Stock_Option_Plans_Schedule_of

Stock Option Plans - Schedule of Stock Option Activity (Detail) (Intrexon Stock Option Plans, USD $)	6 Months Ended		12 Months Ended
	Jun. 30, 2014		Dec. 31, 2013
Intrexon Stock Option Plans	'		'
Number of shares	'		'
Balances at beginning of period, Number of shares	2,840,648		'
Granted, Number of shares	6,273,300		'
Exercised, Number of shares	-235,438		'
Forfeited, Number of shares	-255,646		'
Expired, Number of shares	-285		'
Balances at period end, Number of shares	8,622,579		2,840,648
Exercisable, Number of shares	1,242,345		'
Vested and Expected to Vest, Number of shares	6,657,224	[1]	'
Weighted average exercise price	'		'
Balances at beginning of period, Weighted average exercise price	$8.27		'
Granted, Weighted average exercise price	$28.57		'
Exercised, Weighted average exercise price	($4.30)		'
Forfeited, Weighted average exercise price	($19.51)		'
Expired, Weighted average exercise price	($7.12)		'
Balances at period end, Weighted average exercise price	$22.82		$8.27
Exercisable, Weighted average exercise price	$7.86		'
Vested and Expected to Vest, Weighted average exercise price	$21.72	[1]	'
Weighted average remaining contractual term	'		'
Balances at period end, weighted average remaining contractual period	'9 years		'7 years 9 months
Exercisable at period end, weighted average remaining contractual period	'6 years 4 months 21 days		'
Vested and Expected to Vest at period end, weighted average remaining contractual period	'8 years 10 months 2 days	[1]	'
[1]	The number of stock options expected to vest takes into account an estimate of expected forfeitures.

Commitments_and_Contingencies_1

Commitments and Contingencies - Future Minimum Lease Payments Under Noncancelable Operating Leases (Detail) (USD $)	Jun. 30, 2014
In Thousands, unless otherwise specified
Operating Leases Future Minimum Payments Due [Abstract]	'
2014	$1,919
2015	4,397
2016	4,072
2017	2,607
2018	1,295
2019	1,259
Thereafter	2,406
Operating Leases, Future Minimum Payments Due, Total	$17,955

Commitments_and_Contingencies_2

Commitments and Contingencies - Additional Information (Detail) (USD $)	3 Months Ended		6 Months Ended			6 Months Ended	15 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013	Dec. 31, 2013	Jun. 30, 2014	Jun. 30, 2014	Mar. 15, 2013
						AquaBounty	AquaBounty	AquaBounty
Commitment And Contingencies [Line Items]	'	'	'	'	'	'	'	'
Rent expenses	$1,361	$1,766	$2,731	$3,039	'	'	'	'
Rental income under sublease agreement	171	91	262	182	'	'	'	'
Future rental income for the sublease agreement in 2014	357	'	357	'	'	'	'	'
Future rental income for the sublease agreement in 2015	725	'	725	'	'	'	'	'
Future rental income for the sublease agreement in 2016	384	'	384	'	'	'	'	'
Future rental income for the sublease agreement in 2017	11	'	11	'	'	'	'	'
Amount available under the grant for Research and Development	'	'	'	'	'	2,691	2,691	'
Claims period	'	'	'	'	'	'5 years	'	'
Royalty on products	'	'	'	'	'	10.00%	'	'
Amount claimed	'	'	'	'	'	'	'	1,952
Amount claimed fair value	'	'	'	'	'	'	'	1,107
Long term debt	2,001	'	2,001	'	1,653	2,001	2,001	'
Accreted difference between face value of amount drawn and acquisition date fair value	'	'	'	'	'	845	845	'
Subsequent claims of research and development grant	'	'	'	'	'	'	767	'
AquaBounty funding	'	'	'	'	'	$2,778	$2,778	'
Percentage of royalty on revenues	'	'	'	'	'	5.20%	'	'

Related_Party_Transactions_Add

Related Party Transactions - Additional Information (Detail) (USD $)

6 Months Ended

0 Months Ended

12 Months Ended

3 Months Ended

6 Months Ended

33 Months Ended

0 Months Ended

0 Months Ended

0 Months Ended

0 Months Ended

3 Months Ended

6 Months Ended

In Thousands, except Share data, unless otherwise specified

Jun. 30, 2014

Jun. 30, 2013

Jun. 06, 2011

Jun. 06, 2012

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Oct. 31, 2013

Jun. 30, 2014

Dec. 17, 2013

Jun. 30, 2014

Dec. 17, 2013

Sep. 30, 2013

Jun. 30, 2014

Sep. 30, 2013

Nov. 20, 2013

Nov. 20, 2013

Oct. 01, 2013

Oct. 01, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Affiliates Of Third Security

Affiliates Of Third Security

Chief Executive Officer

Chief Executive Officer

Chief Executive Officer

Chief Executive Officer

Ziopharm Oncology, Inc.

Ziopharm Oncology, Inc.

Synthetic Biologics, Inc.

Synthetic Biologics, Inc.

Synthetic Biologics, Inc.

Oragenics, Inc.

Oragenics, Inc.

Oragenics, Inc.

Oragenics, Inc.

Oragenics, Inc.

Fibrocell Science, Inc.

Fibrocell Science, Inc.

Third Security

Third Security

Third Security

Third Security

Share Purchase Rights Plan

Share Purchase Rights Plan

Related Party Transaction [Line Items]

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Total amount of expenses reimbursed

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

$64

$167

$88

$248

Payment of license fee

'

'

9,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Annual exclusivity fee

'

'

'

1,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Milestone payments

'

'

'

54,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Compensation expense

977

775

'

'

507

387

977

775

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Purchase of additional common stock

'

'

'

'

'

'

'

'

'

50,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Shares of common stock purchased from collaborative partners

'

'

'

'

'

'

'

'

30,982

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Purchase commitment

'

'

'

'

'

'

'

'

'

$19,018

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Maximum percentage of shares of future securities offerings of collaborative partners to which the entity is entitled to purchase

'

'

'

'

'

'

'

'

'

'

'

19.99%

'

'

30.00%

'

'

'

'

'

'

'

'

'

Additional shares of collaborative partner to which the entity is entitled to purchase on the open market

'

'

'

'

'

'

'

'

'

'

'

10.00%

'

'

'

'

'

'

'

'

'

'

'

'

Shares of common stock purchased from collaborative partners

'

'

'

'

'

'

'

'

'

'

2,000,000

'

'

1,300,000

'

'

1,100,000

'

2,439,024

'

'

'

'

'

Price per share of common shares

'

'

'

'

'

'

'

'

'

'

'

'

$1

'

'

$3

'

$2.50

'

$4.10

'

'

'

'

Net_Loss_Per_Share_Historical_

Net Loss Per Share - Historical Computation of Basic and Diluted Net Loss Per Share (Detail) (USD $)	3 Months Ended		6 Months Ended
In Thousands, except Share data, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Numerator:	'	'	'	'
Net loss attributable to Intrexon	($52,043)	($5,963)	($47,928)	($42,274)
Accretion of dividends on redeemable convertible preferred stock	'	-7,942	'	-14,347
Net loss attributable to common shareholders	($52,043)	($13,905)	($47,928)	($56,621)
Denominator:	'	'	'	'
Weighted average shares outstanding, basic and diluted	98,892,601	5,667,557	98,113,493	5,664,665
Net loss attributable to common shareholders per share, basic and diluted	($0.53)	($2.45)	($0.49)	($10)

Net_Loss_Per_Share_Potentially

Net Loss Per Share - Potentially Dilutive Securities Excluded from Calculation of Net Loss per Share (Detail)	6 Months Ended
	Jun. 30, 2014	Jun. 30, 2013
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'
Antidilutive securities excluded from computation of earnings per share, amount	8,995,681	78,770,335
Common Shares Issuable Upon Conversion of All Series Preferred	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'
Antidilutive securities excluded from computation of earnings per share, amount	'	75,402,332
Options	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'
Antidilutive securities excluded from computation of earnings per share, amount	8,622,579	2,856,905
Warrant	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'
Antidilutive securities excluded from computation of earnings per share, amount	373,102	511,098

Subsequent_Events_Additional_I

Subsequent Events - Additional Information (Detail) (Subsequent Event, Trans Ova Genetics, L.C., USD $)	0 Months Ended
In Thousands, except Share data, unless otherwise specified	Aug. 08, 2014	Aug. 08, 2014
Subsequent Event | Trans Ova Genetics, L.C.	'	'
Subsequent Event [Line Items]	'	'
Business acquisition, percentage of ownership acquired	'	100.00%
Business acquisition, consideration paid in cash	$60,000	'
Business acquisition, consideration paid in shares, number shares of common stock issued	1,444,388	'
Business acquisition, maximum deferred cash payment payable in three equal installments upon the first, second and third anniversaries of closing dates	'	$20,000