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