CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS (Unaudited) - USD ($) shares in Thousands, $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2018	Sep. 30, 2017	Sep. 30, 2018	Sep. 30, 2017
Revenue:
Revenue	$ 145,395	$ 118,314	$ 407,559	$ 346,387
Expenses:
Research, development and patent	95,255	80,214	301,153	246,358
Selling, general and administrative	68,712	26,788	178,563	62,782
Total operating expenses	163,967	107,002	479,716	309,140
Income (loss) from operations	(18,572)	11,312	(72,157)	37,247
Other income (expense):
Investment income	9,963	2,811	18,711	7,504
Interest expense	(11,282)	(10,825)	(33,332)	(33,966)
Loss on extinguishment of financing liability for leased facility	0	(7,689)	0	(7,689)
Other income (expenses)	(22)	(2,141)	(145)	(3,528)
Loss before income tax expense	(19,913)	(6,532)	(86,923)	(432)
Income tax expense	(452)	(961)	(824)	(1,184)
Net loss	(20,365)	(7,493)	(87,747)	(1,616)
Net loss attributable to noncontrolling interest in Akcea Therapeutics, Inc.	15,806	4,882	41,412	4,882
Net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders	$ (4,559)	$ (2,611)	$ (46,335)	$ 3,266
Basic net income (loss) per share (in dollars per share)	$ (0.03)	$ (0.02)	$ (0.33)	$ 0.13
Shares used in computing basic net income (loss) per share (in shares)	143,314	124,370	132,518	123,746
Diluted net income (loss) per share (in dollars per share)	$ (0.03)	$ (0.02)	$ (0.33)	$ 0.13
Shares used in computing diluted net income (loss) per share (in shares)	143,314	124,370	132,518	125,858
Commercial Revenue [Member]
Revenue:
Revenue	$ 82,756	$ 34,617	$ 181,975	$ 66,106
SPINRAZA Royalties [Member]
Revenue:
Revenue	70,010	32,890	167,743	60,467
Licensing and Other Royalty Revenue [Member]
Revenue:
Revenue	12,746	1,727	14,232	5,639
Research and Development Revenue Under Collaborative Agreements [Member]
Revenue:
Revenue	$ 62,639	$ 83,697	$ 225,584	$ 280,281