IONIS PHARMACEUTICALS INC — Director's Dealing 2012

Jan 5, 2012

SEC Form 4 — Statement of Changes in Beneficial Ownership

Issuer: ISIS PHARMACEUTICALS INC (ISIS)
CIK: 0000874015
Period of Report: 2012-01-04

Reporting Person: KLEIN JOSEPH III (Director)

Derivative Transactions

Date	Security	Exercise Price	Code	Shares	A/D	Expiration	Underlying	Ownership
2012-01-04	Employee Stock Option (right to buy)	$9.77	G	12500	Disposed	2017-07-01	Common Stock (12500)	Direct
2012-01-04	Employee Stock Option (right to buy)	$13.88	G	11250	Disposed	2018-06-30	Common Stock (11250)	Direct
2012-01-04	Employee Stock Option (right to buy)	$16.32	G	7500	Disposed	2019-06-30	Common Stock (7500)	Direct
2012-01-04	Employee Stock Option (right to buy)	$9.22	G	3750	Disposed	2020-06-30	Common Stock (3750)	Direct
2012-01-04	Employee Stock Option (right to buy)	$9.77	G	4166	Acquired	2017-07-01	Common Stock (4166)	Indirect
2012-01-04	Employee Stock Option (right to buy)	$13.88	G	3750	Acquired	2018-06-30	Common Stock (3750)	Indirect
2012-01-04	Employee Stock Option (right to buy)	$16.32	G	2500	Acquired	2019-06-30	Common Stock (2500)	Indirect
2012-01-04	Employee Stock Option (right to buy)	$9.22	G	1250	Acquired	2020-06-30	Common Stock (1250)	Indirect
2012-01-04	Employee Stock Option (right to buy)	$9.77	G	4167	Acquired	2017-07-01	Common Stock (4167)	Indirect
2012-01-04	Employee Stock Option (right to buy)	$13.88	G	3750	Acquired	2018-06-30	Common Stock (3750)	Indirect
2012-01-04	Employee Stock Option (right to buy)	$16.32	G	2500	Acquired	2019-06-30	Common Stock (2500)	Indirect
2012-01-04	Employee Stock Option (right to buy)	$9.22	G	1250	Acquired	2020-06-30	Common Stock (1250)	Indirect
2012-01-04	Employee Stock Option (right to buy)	$9.77	G	4167	Acquired	2017-07-01	Common Stock (4167)	Indirect
2012-01-04	Employee Stock Option (right to buy)	$13.88	G	3750	Acquired	2018-06-30	Common Stock (3750)	Indirect
2012-01-04	Employee Stock Option (right to buy)	$16.32	G	2500	Acquired	2019-06-30	Common Stock (2500)	Indirect
2012-01-04	Employee Stock Option (right to buy)	$9.22	G	1250	Acquired	2020-06-30	Common Stock (1250)	Indirect

Footnotes

F1: The reporting person transfrerred options to trusts for his three children who share the reporting person's household

F2: Grant of 7/1/08 to reporting person of stock options under the Isis Pharmaceuticals, Inc. 2002 Non-Employee Directors' Stock Option Plan. The option vests and becomes exercisable in four equal annual installments, with the first installment vesting on 7/1/09. The option shall be fully vested and exercisable on 7-1-12. The option was exercisable as to 11,250 shares on 1/4/12.

F3: Grant of 7/1/09 to reporting person of stock options under the Isis Pharmaceuticals, Inc. 2002 Non-Employee Directors' Stock Option Plan. The option vests and becomes exercisable in four equal annual installments, with the first installment vesting on 7/1/10. The option shall be fully vested and exercisable on 7-1-13. The option was exercisable as to 7,500 shares on 1/4/12.

F4: Grant of 7/1/10 to reporting person of stock options under the Isis Pharmaceuticals, Inc. 2002 Non-Employee Directors' Stock Option Plan. The option vests and becomes exercisable in four equal annual installments, with the first installment vesting on 7/1/11. The option shall be fully vested and exercisable on 7-1-14. The option was exercisable as to 3,750 shares on 1/4/12.