FORM 3UNITED STATES SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549

INITIAL STATEMENT OF BENEFICIAL OWNERSHIP OF SECURITIES

Filed pursuant to Section 16(a) of the Securities Exchange Act of 1934, Section 17(a) of the Public Utility Holding Company Act of 1935 or Section 30(h) of the Investment Company Act of 1940
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1. Name and Address of Reporting Person*
Geary Richard S

(Last)(First)(Middle)
C/O ISIS PHARMACEUTICALS, INC., 1896 RUTHERFORD ROAD

(Street)
CARLSBADCA92008

(City)(State)(Zip)
2. Date of Event Requiring Statement (Month/Day/Year)
08/16/2008
3. Issuer Name and Ticker or Trading Symbol
ISIS PHARMACEUTICALS INC [ISIS]
4. Relationship of Reporting Person(s) to Issuer
(Check all applicable)
Director10% Owner
XOfficer (give title below)Other (specify below)
Senior Vice President
5. If Amendment, Date of Original Filed (Month/Day/Year)
6. Individual or Joint/Group Filing (Check Applicable Line)
XForm filed by One Reporting Person
Form filed by More than One Reporting Person
Table I - Non-Derivative Securities Beneficially Owned
1. Title of Security (Instr. 4) 2. Amount of Securities Owned (Instr. 4) 3. Ownership Form: Direct (D) or Indirect (I) (Instr. 5) 4. Nature of Indirect Beneficial Ownership (Instr. 5)
No securities are beneficially owned 0
D
 
Table II - Derivative Securities Beneficially Owned
(e.g., puts, calls, warrants, options, convertible securities)
1. Title of Derivative Security (Instr. 4) 2. Date Exercisable and Expiration Date (Month/Day/Year) 3. Title and Amount of Securities Underlying Derivative Security (Instr. 4)4. Conversion or Excercise Price of Derivative Security 5. Ownership Form: Direct (D) or Indirect (I) (Instr. 5) 6. Nature of Indirect Beneficial Ownership (Instr. 5)
Date ExercisableExpiration DateTitleAmount or Number of Shares
Employee Stock Option (right to buy) 01/02/200501/01/2011 Common Stock 8,480 $ 9.625 D  
Employee Stock Option (right to buy) 01/02/200601/01/2012 Common Stock 8,000 $ 21.05 D  
Employee Stock Option (right to buy) 08/01/200407/31/2010 Common Stock 5,000 $ 11.5625 D  
Employee Stock Option (right to buy) 01/02/200801/01/2014 Common Stock 1,049 $ 6.81 D  
Employee Stock Option (right to buy) 01/03/2009(1)01/02/2012 Common Stock 5,044 $ 5.8 D  
Employee Stock Option (right to buy) 01/03/2007(2)01/02/2013 Common Stock 11,686 $ 5.25 D  
Employee Stock Option (right to buy) 01/02/2008(3)01/01/2014 Common Stock 19,042 $ 11.12 D  
Employee Stock Option (right to buy) 01/02/2009(4)01/01/2015 Common Stock 24,000 $ 15.38 D  
Employee Stock Option (right to buy) 01/01/2009(5)12/31/2014 Common Stock 10,000 $ 15.75 D  
Explanation of Responses:
1. Grant of 1-3-05 to reporting person of stock options under the Isis Pharmaceuticals, Inc. 1989 Stock Option Plan. The option is exercisable as to 3,362 shares on 8-16-08. The remaining shares subject to the option vest and become exercisable at the rate of 336.4 shares per month.
2. Grant of 1-3-06 to reporting person of stock options under the Isis Pharmaceuticals, Inc. 1989 Stock Option Plan. The option is exercisable as to 4,328 shares on 8-16-08. The remaining shares subject to the option vest and become exercisable at the rate of 432.84 shares per month.
3. Grant of 1-2-07 to reporting person of stock options under the Isis Pharmaceuticals, Inc. 1989 Stock Option Plan. The option is exercisable as to 7,538 shares on 8-16-08. The remaining shares subject to the option vest and become exercisable at the rate of 396.69 shares per month.
4. Grant of 1-2-08 to reporting person of stock options under the Isis Pharmaceuticals, Inc. 2000 Broad-Based Equity Incentive Plan. 25% of the shares subject to the option will vest and become exercisable on 1-2-09. The remaining shares subject to the option vest and become exercisable at the rate of 500 shares per month. The option is exercisable as to 0 shares on 8-16-08.
5. Grant of 1-1-08 to reporting person of stock options under the Isis Pharmaceuticals, Inc. 2000 Broad-Based Equity Incentive Plan. 25% of the shares subject to the option will vest and become exercisable on 1-1-09. The remaining shares subject to the option vest and become exercisable at the rate of 208.33 shares per month. The option is exercisable as to 0 shares on 8-16-08.
/s/Richard S. Geary08/19/2008
** Signature of Reporting PersonDate
Reminder: Report on a separate line for each class of securities beneficially owned directly or indirectly.
* If the form is filed by more than one reporting person, see Instruction 5(b)(v).
** Intentional misstatements or omissions of facts constitute Federal Criminal Violations See 18 U.S.C. 1001 and 15 U.S.C. 78ff(a).
Note: File three copies of this Form, one of which must be manually signed. If space is insufficient, see Instruction 6 for procedure.
Persons who respond to the collection of information contained in this form are not required to respond unless the form displays a currently valid OMB Number.

EX-24

Know all by these presents, that the undersigned hereby constitutes and appoints each of Stanley T. Crooke and B. Lynne Parshall, signing individually, the undersigned's true and lawful attorneys-in fact and agents to: (1) execute for and on behalf of the undersigned, an officer, director or holder of 10% or more of a registered class of securities of Isis Pharmaceuticals, Inc. (Isis), Forms 3, 4 and 5 in accordance with Section 16(a) of the Securities Exchange Act of 1934, as amended (the Exchange Act) and the rules thereunder; (2) do and perform any and all acts for and on behalf of the undersigned that may be necessary or desirable to complete and execute such Form 3, 4 or 5, complete and execute any amendment or amendments thereto, and timely file such forms or amendments with the United States Securities and Exchange Commission and any stock exchange or similar authority; and (3) take any other action of any nature whatsoever in connection with the foregoing which, in the opinion of such attorney-in-fact, may be of benefit, in the best interest of, or legally required by, the undersigned, it being understood that the documents executed by such attorney-in-fact on behalf of the undersigned pursuant to this Power of Attorney shall be in such form and shall contain such terms and conditions as such attorney-in-fact may approve in such attorney-in-fact's discretion. The undersigned hereby grants to each such attorney-in-fact full power and authority to do and perform any and every act and thing whatsoever requisite, necessary, or proper to be done in the exercise of any of the rights and powers herein granted, as fully to all intents and purposes as the undersigned might or could do if personally present, with full power of substitution or revocation, hereby ratifying and confirming all that such attorney-in-fact, or such attorney-in-fact's substitute or substitutes, will lawfully do or cause to be done by virtue of this power of attorney and the rights and powers herein granted. The undersigned acknowledges that the foregoing attorneys-in-fact, in serving in such capacity at the request of the undersigned, are not assuming, nor is Isis assuming, any of the undersigned's responsibilities to comply with Section 16 of the Exchange Act. This Power of Attorney shall remain in full force and effect until the earliest to occur of (a) the undersigned is no longer required to file Forms 3, 4 and 5 with respect to the undersigned's holdings of and transactions in securities issued by Isis, (b) revocation by the undersigned in a signed writing delivered to the foregoing attorneys-in-fact or (c) as to any attorney-in-fact individually, until such attorney-in-fact will no longer be employed by Isis. IN WITNESS WHEREOF, the undersigned has caused this Power of Attorney to be executed as of this 8th day of August, 2008. /S/Richard S. Geary



 
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