IONIS PHARMACEUTICALS INC — Director's Dealing 2013

Jan 3, 2013

SEC Form 3 — Initial Statement of Beneficial Ownership

Issuer: ISIS PHARMACEUTICALS INC (ISIS)
CIK: 0000874015
Period of Report: 2013-01-01

Reporting Person: O'NEIL PATRICK R. (SVP, Legal and General Counsel)

Holdings (Non-Derivative)

Security	Shares	Ownership
Common Stock	2328	Direct

Holdings (Derivative)

Security	Exercise Price	Expiration	Underlying	Shares	Ownership
Employee Stock Option (right to buy)	$11.12	2014-01-01	Common Stock (1350)		Direct
Employee Stock Option (right to buy)	$15.38	2015-01-01	Common Stock (14000)		Direct
Employee Stock Option (right to buy)	$14.18	2015-12-31	Common Stock (25000)		Direct
Employee Stock Option (right to buy)	$14.47	2016-01-01	Common Stock (9400)		Direct
Employee Stock Option (right to buy)	$11.27	2017-01-03	Common Stock (17400)		Direct
Employee Stock Option (right to buy)	$8.00	2017-08-31	Common Stock (6700)		Direct
Employee Stock Option (right to buy)	$10.29	2018-01-02	Common Stock (19000)		Direct
Employee Stock Option (right to buy)	$7.25	2019-01-02	Common Stock (19500)		Direct
Restricted Stock Unit	$		Common Stock (2166)		Direct

Footnotes

F1: Grant of 1/2/09 to reporting person of stock options under the Isis Pharmaceuticals, Inc. 1989 Stock Option Plan. 25% of the shares subject to the option vested and became exercisable on 1/2/10. Thereafter, the remaining shares subject to the option vested and became exerciable in 36 equal monthly installments, at the rate of 2,350 shares per year. The option is exercisable as to 9,204 on 1/1/13.

F2: Grant of 1/4/10 to reporting person of stock options under the Isis Pharmaceuticals, Inc. 1989 Stock Option Plan. 25% of the shares subject to the option vested and became exercisable on 1/4/11. Thereafter, the remaining shares subject to the option vested and became exerciable in 36 equal monthly installments, at the rate of 4,350 shares per year. The option is exercisable as to 12,687 on 1/1/13.

F3: Grant of 9/1/10 to reporting person of stock options under the Isis Pharmaceuticals, Inc. 1989 Stock Option Plan. 25% of the shares subject to the option vested and became exercisable on 9/1/11. Thereafter, the remaining shares subject to the option vested and became exerciable in 36 equal monthly installments, at the rate of 2,500 shares per year. The option is exercisable as to 2,533 on 1/1/13. SAY SOMETHING ABOUT OPTIONS ALREADY EXERCISED????

F4: Grant of 1/3/11 to reporting person of stock options under the Isis Pharmaceuticals, Inc. 1989 Stock Option Plan. 25% of the shares subject to the option vested and became exercisable on 1/3/12. Thereafter, the remaining shares subject to the option vested and became exerciable in 36 equal monthly installments, at the rate of 5,750 shares per year. The option is exercisable as to 7,020 on 1/1/13. SAY SOMETHING ABOUT OPTIONS ALREADY EXERCISED????

F5: Grant of 1/3/12 to reporting person of stock options under the Isis Pharmaceuticals, Inc. 1989 Stock Option Plan. 25% of the shares subject to the option vested and became exercisable on 1/3/13. Thereafter, the remaining shares subject to the option vested and became exerciable in 36 equal monthly installments, at the rate of 4,875 shares per year. The option is exercisable as to 0 on 1/1/13.

F6: The restricted stock units vest in four equal annual installments, the first installment vesting on January 15, 2013. Upon vesting, the restricted stock units will be paid out in whole shares of Isis common stock or cash as may be determined by the Company. The RSU shall be fully vested on January 15, 2016. The RSU is vested as to 0 shares on January 1, 2012.

F7: Each restricted stock unit represents a contingent right to receive one share of Isis common stock or its equivalent cash value.