CONDENSED CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME (LOSS) (Unaudited) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017
CONDENSED CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME (LOSS) [Abstract]
Net loss	$ (20,365)	$ (7,493)	$ (87,747)	$ (1,616)
Unrealized gains (losses) on debt securities, net of tax	133	215	(834)	610
Reclassification adjustment for realized gains included in net income (loss)	0	0	0	(374)
Currency translation adjustment	(28)	(42)	61	(77)
Comprehensive loss	(20,260)	(7,320)	(88,520)	(1,457)
Comprehensive loss attributable to noncontrolling interests	15,797	3,952	41,455	3,952
Comprehensive income (loss) attributable to Ionis Pharmaceuticals, Inc. stockholders	$ (4,463)	$ (3,368)	$ (47,065)	$ 2,495