CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS (Unaudited) - USD ($) shares in Thousands, $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2020	Jun. 30, 2019	Jun. 30, 2020	Jun. 30, 2019
Revenue:
Revenue	$ 145,537	$ 163,813	$ 278,905	$ 461,026
Expenses:
Cost of products sold	3,012	1,364	5,561	2,406
Research, development and patent	122,264	106,165	239,214	212,582
Selling, general and administrative	72,015	75,111	147,009	143,332
Total operating expenses	197,291	182,640	391,784	358,320
Income (loss) from operations	(51,754)	(18,827)	(112,879)	102,706
Other income (expense):
Investment income	9,243	13,735	19,459	25,880
Interest expense	(11,173)	(11,802)	(22,163)	(23,402)
Gain on investments	9,625	0	9,887	0
Other income (expenses)	(149)	(45)	(249)	(192)
Income (loss) before income tax (expense) benefit	(44,208)	(16,939)	(105,945)	104,992
Income tax (expense) benefit	439	6,927	3,696	(24,119)
Net income (loss)	(43,769)	(10,012)	(102,249)	80,873
Net loss attributable to noncontrolling interest in Akcea Therapeutics, Inc.	11,924	9,136	22,178	2,694
Net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders	$ (31,845)	$ (876)	$ (80,071)	$ 83,567
Basic net income (loss) per share (in dollars per share)	$ (0.23)	$ (0.01)	$ (0.58)	$ 0.62
Shares used in computing basic net income (loss) per share (in shares)	139,352	140,247	139,391	139,419
Diluted net income (loss) per share (in dollars per share)	$ (0.23)	$ (0.01)	$ (0.58)	$ 0.61
Shares used in computing diluted net income (loss) per share (in shares)	139,352	140,247	139,391	142,499
Commercial Revenue [Member]
Revenue:
Revenue	$ 89,734	$ 88,299	$ 173,696	$ 156,386
SPINRAZA Royalties [Member]
Revenue:
Revenue	71,746	70,502	137,754	130,212
Product Sales, Net [Member]
Revenue:
Revenue	16,364	9,865	31,523	16,619
Licensing and Other Royalty Revenue [Member]
Revenue:
Revenue	1,624	7,932	4,419	9,555
Research and Development Revenue Under Collaborative Agreements [Member]
Revenue:
Revenue	$ 55,803	$ 75,514	$ 105,209	$ 304,640