Organization and Significant Accounting Policies, Basic and Diluted Net Income (Loss) per Share (Details) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	3 Months Ended																12 Months Ended
	Dec. 31, 2017		Sep. 30, 2017		Jun. 30, 2017		Mar. 31, 2017		Dec. 31, 2016		Sep. 30, 2016		Jun. 30, 2016	[2]	Mar. 31, 2016	[2]	Dec. 31, 2017	Dec. 31, 2016	Dec. 31, 2015
Basic Net Income (Loss) per Share [Abstract]
Basic net income (loss) per share (in dollars per share)	$ 0.02	[1],[2]	$ 0.00	[1],[2]	$ (0.09)	[2]	$ 0.03	[2]	$ 0.21	[2]	$ 0.06	[2]	$ (0.47)		$ (0.52)		$ 0.08	$ (0.72)	$ (0.74)
Net income (loss)	$ 2,744		$ (976)		$ (11,206)		$ 3,468										$ (5,970)	$ (86,556)	$ (88,278)
Net income available to Ionis common stockholders	$ 2,717		$ (419)				$ 3,468		$ 25,865		$ 7,351						$ 9,661
Shares used in computing basic net income per share (in shares)	124,818		124,370				122,861		121,340		120,989						124,016	120,933	119,719
Income available to Ionis common shareholders, plus assumed conversions	$ 2,717						$ 3,468		$ 25,865		$ 7,351						$ 9,661
Shares issuable related to our ESPP																	4
Shares used in computing diluted net income per share (in shares)	126,862						124,972		123,953		123,378						126,098	120,933	119,719
Diluted net income per share (in dollars per share)	$ 0.02	[2]	$ 0.00	[2]	$ (0.09)	[2]	$ 0.03	[2],[3]	$ 0.21	[2],[4]	$ 0.06	[2],[5]	$ (0.47)		$ (0.52)		$ 0.08	$ (0.72)	$ (0.74)
1 Percent Convertible Senior Notes [Member]
Basic Net Income (Loss) per Share [Abstract]
Interest rate on convertible senior notes	1.00%						1.00%		1.00%		1.00%						1.00%	1.00%	1.00%
2 3/4 Percent Convertible Senior Notes [Member]
Basic Net Income (Loss) per Share [Abstract]
Interest rate on convertible senior notes	2.75%						2.75%		2.75%		2.75%						2.75%	2.75%	2.75%
Stock Options [Member]
Basic Net Income (Loss) per Share [Abstract]
Shares issuable related to stock-based compensation (in shares)	1,532						1,674		2,189		2,129						1,619
Restricted Stock Awards [Member]
Basic Net Income (Loss) per Share [Abstract]
Shares issuable related to stock-based compensation (in shares)	507						377		403		202						459
Ionis [Member]
Basic Net Income (Loss) per Share [Abstract]
Net income (loss)	$ 18,672		$ 9,168														$ 92,336
Akcea [Member]
Basic Net Income (Loss) per Share [Abstract]
Net income (loss)	$ (15,955)		$ (9,587)														$ (82,676)
Akcea [Member] | Common Stock [Member]
Basic Net Income (Loss) per Share [Abstract]
Weighted average shares owned in Akcea (in shares)	45,448		36,556														20,669
Basic net income (loss) per share (in dollars per share)	$ (0.35)		$ (0.27)														$ (2.82)
Net income (loss)	$ (15,955)		$ (9,870)														$ (58,332)
Akcea [Member] | Series A Convertible Preferred Stock [Member]
Basic Net Income (Loss) per Share [Abstract]
Dividend rate																	6.00%
Conversion ratio																	converted into common stock on a 1:1 basis
Weighted average shares owned in Akcea (in shares)			5,651														15,748
Basic net income (loss) per share (in dollars per share)			$ 0.05														$ (1.55)
Net income (loss)			$ 283														$ (24,344)

[1] As discussed in Note 1, Organization and Significant Accounting Policies, we compute basic net income (loss) per share by dividing the total net income (loss) attributable to our common stockholders by our weighted-average number of common shares outstanding during the period. The calculation of total net income (loss) attributable to our common stockholders for the three months ended December 31, 2017 and September 30, 2017 considered our net income for Ionis on a stand-alone basis plus our share of Akcea's net loss for the periods. To calculate the portion of Akcea's net loss attributable to our ownership, we multiplied Akcea's income (loss) per share by the weighted average shares we owned in Akcea during the period. For the three months ended December 31, 2017, we had net income available to Ionis common stockholders. As a result, we computed diluted net income per share using the weighted-average number of common shares and dilutive common equivalent shares outstanding during those periods. For the three months ended December 31, 2017, the calculation excluded the 1 percent and 2.75 percent notes because the effect on diluted earnings per share was anti-dilutive. Prior to Akcea's IPO, we owned Akcea series A convertible preferred stock, which included a six percent cumulative dividend. Upon completion of Akcea's IPO in July 2017, our preferred stock was converted into common stock on a 1:1 basis. The preferred stock dividend was not paid at the IPO because it was not a liquidation event or a change in control. During the three months ended September 30, 2017, Akcea used a two-class method to compute its net income (loss) per share because it had both common and preferred shares outstanding during the periods. The two-class method required Akcea to calculate its net income (loss) per share for each class of stock by dividing total distributable losses applicable to preferred and common stock, including the six percent cumulative dividend contractually due to series A convertible preferred shareholders, by the weighted-average of preferred and common shares outstanding during the requisite period. Since Akcea used the two-class method, accounting rules required us to include our portion of Akcea's net income (loss) per share for both Akcea's common and preferred shares which we owned in our calculation of basic and diluted net income (loss) per share for three months ended September 30, 2017. As a result of this calculation, our total net income (loss) available to Ionis common stockholders for the calculation of net income (loss) per share is different than net income (loss) attributable to Ionis Pharmaceuticals, Inc. common stockholders in the consolidated statements of operations.

[2] We computed net income (loss) per share independently for each of the quarters presented. Therefore, the sum of the quarterly net income (loss) per share will not necessarily equal the total for the year.

[3] For the three months ended March 31, 2017 we had net income. As a result, we computed diluted net income per share using the weighted-average number of common shares and dilutive common equivalent shares outstanding during the period. For the three months ended March 31, 2017, the calculation excludes the 1 percent and 2 3/4 percent notes because the effect on diluted earnings per share was anti-dilutive.

[4] For the three months ended December, 2016, we had net income. As a result, we computed diluted net income per share using the weighted-average number of common shares and dilutive common equivalent shares outstanding during the period. For the three months ended December 31, 2016, the calculation excludes the 1 percent and 2 3/4 percent notes because the effect on diluted earnings per share would be anti-dilutive.

[5] For the three months ended September 30, 2016, we had net income. As a result, we computed diluted net income per share using the weighted-average number of common shares and dilutive common equivalent shares outstanding during the period. For the three months ended September 30, 2016, the calculation excludes the 1 percent and 2 3/4 percent notes because the effect on diluted earnings per share would be anti-dilutive.