Related Party Transactions	9 Months Ended
Sep. 30, 2015
Related Party Transactions [Abstract]
Related Party Transactions	Related Party Transactions Third Security and Affiliates The Company reimburses Third Security for certain administrative services and out-of-pocket expenses incurred on the Company's behalf. The total amount of expenses incurred by the Company for the three months ended September 30, 2015 and 2014 was $142 and $85, respectively and $294 and $173 for the nine months ended September 30, 2015 and 2014, respectively. The Manager of Third Security is also the Chief Executive Officer ("CEO") and Chairman of the Board of Directors of the Company. Prior to 2015, the CEO did not receive compensation for his services as CEO, and as a result, the Company recorded $508 and $1,485 in compensation expense for the three and nine months ended September 30, 2014, respectively, based on the estimated salary and benefits appropriate for the role. The Company anticipates that the CEO will participate in the Company's executive annual incentive compensation plan beginning in 2015. See additional discussion related to Third Security and the Company's CEO at Note 19. Transactions with ECC Parties In addition to entities controlled by Third Security, any entity in which the Company holds equity securities, including securities received as upfront or milestone consideration, and which also are party to a collaboration with the Company are considered to be related parties. In July 2015, the Company purchased 375,868 shares of common stock of Fibrocell at $5.80 per share. In March 2015, the Company purchased 278,788 shares of common stock of AmpliPhi Biosciences Corporation ("AmpliPhi"), a collaborator, and 69,696 warrants for $2,300. Of the total purchase price, $1,979 was allocated to the value of the shares of common stock and $321 was allocated to the value of the warrants. The number of shares and warrants received reflects a 1-for-50 reverse stock split of AmpliPhi's common stock effective August 7, 2015. The AmpliPhi warrants have been included in other assets on the consolidated balance sheet with a value of $145 as of September 30, 2015. Between February 2011 and February 2015, the Company purchased $43,582 of ZIOPHARM securities. See Note 13 for additional discussion related to the Company's investment in ZIOPHARM. The Company entered into an ECC with Histogenics Corporation ("Histogenics") in September 2014 and received a $10,000 convertible promissory note as upfront consideration. The note originally matured in September 2015 and accrued interest at 6.0% per annum. Upon the closing of Histogenics' IPO in December 2014, the note, with accrued interest, was converted to Histogenics common stock. Additionally, the Company purchased 1,772,364 shares of Histogenics common stock at $11.00 per share in the IPO. In conjunction with the ECC with Oragenics (Note 5), the Company is entitled to, at its election, purchase up to 30% of securities offerings that may be conducted by Oragenics in the future, subject to certain conditions and limitations. In November 2013, the Company purchased 1,100,000 shares of Oragenics common stock at $2.50 per share. In September 2013, the Company purchased 1,300,000 shares of Oragenics common stock at $3.00 per share in a private transaction. In connection with Oragenics ECC 3 (Note 5), the Company agreed to purchase additional common stock in a qualified financing, as defined in the agreement, during the sixteen months following the effective date of the Oragenics ECC 3 in an amount up to the lesser of (i) the amount that is the proportion of such financing equal to the Company's pro rata equity holdings in Oragenics as of the effective date and (ii) $10,000, subject to certain conditions. The Company recognized $31,740 and $11,295 of collaboration revenues from related parties in the three months ended September 30, 2015 and 2014, respectively, and $59,775 and $29,613 for the nine months ended September 30, 2015 and 2014, respectively. Other Related Parties In June 2015, the Company entered into an agreement with Harvest, an investment fund sponsored by Harvest Capital Strategies, LLC, and a related party based on ownership in the fund by affiliates of Third Security. Harvest was established to invest in life science research and development opportunities that Intrexon offers to Harvest. These will be investment proposals that are suitable for pursuit by a startup venture, characterized by the agreement as "start-up opportunities." For such start-up opportunities, the Company will provide Harvest with exclusive rights of first-look and first negotiation. For any opportunities it decides to pursue, Harvest would establish new collaboration entities which would enter into an ECC with the Company in a designated field. The terms of such ECCs would be negotiated between the Company and Harvest. In addition, the agreement provides the Company the right to present to Harvest the opportunity to invest in other ventures, including investment opportunities with respect to the Company's existing collaborations. Any such opportunities would be presented at the Company's discretion on a non-exclusive basis. The agreement with Harvest does not limit the Company's ability to execute other collaborations and joint ventures with third parties. As consideration for providing exclusive rights of first look and first negotiation for start-up opportunities, the Company receives a portion of the management fee collected by Harvest. These fees are included in other income in the accompanying consolidated statements of operations and totaled $697 for the three and nine months ended September 30, 2015.

Related Party Transactions

Third Security and Affiliates

The Company reimburses Third Security for certain administrative services and out-of-pocket expenses incurred on the Company's behalf. The total amount of expenses incurred by the Company for the three months ended September 30, 2015 and 2014 was $142 and $85, respectively and $294 and $173 for the nine months ended September 30, 2015 and 2014, respectively.

The Manager of Third Security is also the Chief Executive Officer ("CEO") and Chairman of the Board of Directors of the Company. Prior to 2015, the CEO did not receive compensation for his services as CEO, and as a result, the Company recorded $508 and $1,485 in compensation expense for the three and nine months ended September 30, 2014, respectively, based on the estimated salary and benefits appropriate for the role. The Company anticipates that the CEO will participate in the Company's executive annual incentive compensation plan beginning in 2015.

See additional discussion related to Third Security and the Company's CEO at Note 19.

Transactions with ECC Parties

In addition to entities controlled by Third Security, any entity in which the Company holds equity securities, including securities received as upfront or milestone consideration, and which also are party to a collaboration with the Company are considered to be related parties.

In July 2015, the Company purchased 375,868 shares of common stock of Fibrocell at $5.80 per share.

In March 2015, the Company purchased 278,788 shares of common stock of AmpliPhi Biosciences Corporation ("AmpliPhi"), a collaborator, and 69,696 warrants for $2,300. Of the total purchase price, $1,979 was allocated to the value of the shares of common stock and $321 was allocated to the value of the warrants. The number of shares and warrants received reflects a 1-for-50 reverse stock split of AmpliPhi's common stock effective August 7, 2015. The AmpliPhi warrants have been included in other assets on the consolidated balance sheet with a value of $145 as of September 30, 2015.

Between February 2011 and February 2015, the Company purchased $43,582 of ZIOPHARM securities. See Note 13 for additional discussion related to the Company's investment in ZIOPHARM.

The Company entered into an ECC with Histogenics Corporation ("Histogenics") in September 2014 and received a $10,000 convertible promissory note as upfront consideration. The note originally matured in September 2015 and accrued interest at 6.0% per annum. Upon the closing of Histogenics' IPO in December 2014, the note, with accrued interest, was converted to Histogenics common stock. Additionally, the Company purchased 1,772,364 shares of Histogenics common stock at $11.00 per share in the IPO.

In conjunction with the ECC with Oragenics (Note 5), the Company is entitled to, at its election, purchase up to 30% of securities offerings that may be conducted by Oragenics in the future, subject to certain conditions and limitations. In November 2013, the Company purchased 1,100,000 shares of Oragenics common stock at $2.50 per share. In September 2013, the Company purchased 1,300,000 shares of Oragenics common stock at $3.00 per share in a private transaction. In connection with Oragenics ECC 3 (Note 5), the Company agreed to purchase additional common stock in a qualified financing, as defined in the agreement, during the sixteen months following the effective date of the Oragenics ECC 3 in an amount up to the lesser of (i) the amount that is the proportion of such financing equal to the Company's pro rata equity holdings in Oragenics as of the effective date and (ii) $10,000, subject to certain conditions.

The Company recognized $31,740 and $11,295 of collaboration revenues from related parties in the three months ended September 30, 2015 and 2014, respectively, and $59,775 and $29,613 for the nine months ended September 30, 2015 and 2014, respectively.

Other Related Parties

In June 2015, the Company entered into an agreement with Harvest, an investment fund sponsored by Harvest Capital Strategies, LLC, and a related party based on ownership in the fund by affiliates of Third Security. Harvest was established to invest in life science research and development opportunities that Intrexon offers to Harvest. These will be investment proposals that are suitable for pursuit by a startup venture, characterized by the agreement as "start-up opportunities." For such start-up opportunities, the Company will provide Harvest with exclusive rights of first-look and first negotiation. For any opportunities it decides to pursue, Harvest would establish new collaboration entities which would enter into an ECC with the Company in a designated field. The terms of such ECCs would be negotiated between the Company and Harvest. In addition, the agreement provides the Company the right to present to Harvest the opportunity to invest in other ventures, including investment opportunities with respect to the Company's existing collaborations. Any such opportunities would be presented at the Company's discretion on a non-exclusive basis. The agreement with Harvest does not limit the Company's ability to execute other collaborations and joint ventures with third parties. As consideration for providing exclusive rights of first look and first negotiation for start-up opportunities, the Company receives a portion of the management fee collected by Harvest. These fees are included in other income in the accompanying consolidated statements of operations and totaled $697 for the three and nine months ended September 30, 2015.