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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 | 6 Months Ended | 12 Months Ended
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Dec. 31, 2018 | Sep. 30, 2018 | Jun. 30, 2018 | Mar. 31, 2018 | Dec. 31, 2017 | Sep. 30, 2017 | Jun. 30, 2017 | Mar. 31, 2017 | Jun. 30, 2017 | Dec. 31, 2018 | Dec. 31, 2017 | Dec. 31, 2016
Basic Net Income (Loss) per Share [Abstract] |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Basic net income (loss) per share (in dollars per share) | $ 2.32 | [1],[2] | $ (0.03) | [1],[2] | $ (0.29) | [1],[2] | $ (0.01) | [1],[2] | $ (0.03) | [1],[2] | $ (0.02) | [1],[2],[3] | $ (0.02) | [2] | $ 0.07 | [2] |  | $ 2.09 | $ 0.15 | $ (0.50)
Net income (loss) | $ 320,078 |  | $ (4,559) |  | $ (40,358) |  | $ (1,420) |  | $ (2,922) |  | $ (2,611) |  | $ (3,085) |  | $ 8,964 |  |  | $ 273,741 | $ 346 | $ (60,400)
Net income available to Ionis common stockholders | $ 319,694 |  | $ (4,563) |  | $ (37,932) |  | $ (1,212) |  | $ (3,124) |  | $ (1,976) |  |  |  | $ 8,964 |  |  | $ 276,868 | $ 18,792 |
Shares used in computing basic net income per share (in shares) | 137,699 |  | 137,346 |  | 128,712 |  | 125,330 |  | 124,818 |  | 124,370 |  |  |  | 122,861 |  |  | 132,320 | 124,016 | 120,933
Income available to Ionis common shareholders, plus assumed conversions | $ 330,439 |  |  |  |  |  |  |  |  |  |  |  |  |  | $ 8,964 |  |  | $ 276,868 | $ 18,792 |
Shares issuable related to our ESPP (in shares) |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | 6 | 4 |
Shares used in computing diluted net income per share (in shares) | 149,856 |  |  |  |  |  |  |  |  |  |  |  |  |  | 124,972 |  |  | 134,056 | 126,098 | 120,933
Diluted net income per share (in dollars per share) | $ 2.21 | [2],[4] | $ (0.03) | [2] | $ (0.29) | [2] | $ (0.01) | [2] | $ (0.03) | [2] | $ (0.02) | [2],[3] | $ (0.02) | [2] | $ 0.07 | [2],[5],[6] |  | $ 2.07 | $ 0.15 | $ (0.50)
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%
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%
Stock Options [Member] |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Basic Net Income (Loss) per Share [Abstract] |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Shares issuable related to stock-based compensation (in shares) | 1,254 |  |  |  |  |  |  |  |  |  |  |  |  |  | 1,674 |  |  | 1,216 | 1,619 |
Restricted Stock Awards [Member] |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Basic Net Income (Loss) per Share [Abstract] |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Shares issuable related to stock-based compensation (in shares) | 636 |  |  |  |  |  |  |  |  |  |  |  |  |  | 377 |  |  | 514 | 459 |
Ionis [Member] |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Basic Net Income (Loss) per Share [Abstract] |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Net income (loss) | $ 372,913 |  | $ 43,226 |  | $ 5,882 |  | $ 18,785 |  | $ 10,510 |  | $ 10,144 |  |  |  |  |  |  | $ 440,806 | $ 110,776 |
Akcea [Member] |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Basic Net Income (Loss) per Share [Abstract] |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Percentage ownership |  |  |  |  |  |  |  |  |  |  |  |  |  |  | 100.00% |  | 100.00% |  |  | 100.00%
Net income (loss) | $ (53,219) |  | $ (47,789) |  | $ (43,814) |  | $ (19,997) |  | $ (13,634) |  | $ (12,120) |  |  |  |  |  |  | $ (163,938) | $ (91,984) |
Akcea [Member] | Common Stock [Member] |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Basic Net Income (Loss) per Share [Abstract] |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Weighted average shares owned in Akcea (in shares) | 67,130 |  | 65,538 |  | 60,832 |  | 45,448 |  | 45,448 |  | 36,556 |  |  |  |  |  |  | 59,812 | 20,669 |
Basic net income (loss) per share (in dollars per share) | $ (0.79) |  | $ (0.73) |  | $ (0.72) |  | $ (0.44) |  | $ (0.30) |  | $ (0.33) |  |  |  |  |  |  | $ (2.74) | $ (3.08) |
Net income (loss) | $ (53,219) |  | $ (47,789) |  | $ (43,814) |  | $ (19,997) |  | $ (13,634) |  | $ (12,063) |  |  |  |  |  |  | $ (163,938) | $ (63,638) |
Akcea [Member] | 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) |  |  |  |  |  |  |  |  |  |  | $ (0.01) |  |  |  |  |  |  |  | $ (1.80) |
Net income (loss) |  |  |  |  |  |  |  |  |  |  | $ (57) |  |  |  |  |  |  |  | $ (28,346) |
[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. Our basic net income (loss) per share calculation for each of the quarters in 2018 and for the third and fourth quarters of 2017 considered our net income for Ionis on a stand-alone basis plus our share of Akcea's net loss for the period. To calculate the portion of Akcea's net loss attributable to our ownership, we multiplied Akcea's loss per share by the weighted average shares we owned in Akcea during the period. 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] | Prior to Akcea's IPO in July 2017, 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 the IPO 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 that we owned in our calculation of basic and diluted net income (loss) per share for the three months ended September 30, 2017.
[4] | For the three months ended December 31, 2018, 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.
[5] | For the three months ended March 31, 2017, the calculation excluded the 1 percent and 2.75 percent notes because the effect on diluted earnings per share was anti-dilutive.
[6] | For the three months ended March 31, 2017, we owned 100 percent of Akcea. As a result, we did not have to adjust our earnings per share calculation. 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 those periods.

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