CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME (LOSS) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2018	Dec. 31, 2017	Dec. 31, 2016
CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME (LOSS) [Abstract]
Net income (loss)	$ 214,985	$ (10,783)	$ (60,400)
Unrealized losses on investments, net of tax	(280)	(960)	(17,219)
Reclassification adjustment for realized (gains) losses included in net loss	0	(374)	447
Currency translation adjustment	23	(67)	(21)
Comprehensive income (loss)	214,728	(12,184)	(77,193)
Comprehensive loss attributable to noncontrolling interest in Akcea Therapeutics, Inc.	(58,781)	(11,224)	0
Comprehensive income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders	$ 273,509	$ (960)	$ (77,193)