SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 Isis Pharmaceuticals, Inc. -------------------------- (Name of Issuer) Common Stock (Title of Class of Securities) 464330-1-09 (CUSIP Number) August 29, 2001 --------------------- (Date of Event Which Requires Filing of this Statement) Check the appropriate box to designate the rule pursuant to which this Schedule is filed: ____ Rule 13d-1(b) X Rule 13d-1(c) ---- ____ Rule 13d-1(d) *The remainder of this cover page shall be filled out for a reporting person's initial filing on this form with respect to the subject class of securities, and for any subsequent amendment containing information which would alter disclosures provided in a prior cover page. The information required in the remainder of this cover page shall not be deemed to be "filed" for the purpose of Section 18 of the Securities Exchange Act of 1934 ("Act") or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes). Page 1 of 5 Pages
CUSIP No. 464330-1-09 1. NAME OF REPORTING PERSON: I.R.S. IDENTIFICATION NO. OF ABOVE PERSON Eli Lily and Company 35-0470950 2. CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (a) [_] (b) [_] Not Applicable 3. SEC USE ONLY 4. CITIZENSHIP OR PLACE OF ORGANIZATION Indiana - ------------------------------------------------------------ NUMBER OF 5. SOLE VOTING POWER SHARES BENEFICIALLY OWNED BY 4,166,167 EACH REPORTING 6. SHARED VOTING POWER PERSON WITH None 7. SOLE DISPOSITIVE POWER 4,166,167 8. SHARED DISPOSITIVE POWER None - ------------------------------------------------------------ 9. AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 4,166,167 10. CHECK IF THE AGGREGATE AMOUNT IN ROW (9) EXCLUDES CERTAIN SHARES [_] Not Applicable 11. PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW 9 9.0% 12. TYPE OF REPORTING PERSON CO Page 2 of 5 Pages
Item 1(a). Name of Issuer: Isis Pharmaceuticals, Inc. Item 1(b). Address of Issuer's Principal Executive Offices: 2292 Faraday Avenue Carlsbad, CA 92008 Item 2(a). Name of Person Filing: Eli Lilly and Company Item 2(b). Address of Principal Business Office or, if None, Residence: Lilly Corporate Center Indianapolis, IN 46285 Item 2(c). Citizenship: Indiana Item 2(d). Title of Class of Securities: Common Stock Item 2(e). CUSIP Number: 464330-1-09 Item 3. If this statement is filed pursuant to Rule 13d-1(b), or 13d-2(b) or (c), check whether the person filing is a: (a)-(j) Not applicable If this statement is filed pursuant to Rule 13d-1(c), check this box. [ X ] Page 3 of 5 Pages
Item 4. Ownership. (a) Amount Beneficially Owned: 4,166,167 (b) Percent of Class: 9.0% (c) Number of shares as to which the person has: Sole voting power 4,166,167 Shared voting power None Sole dispositive power 4,166,167 Shared dispositive power None Item 5. Ownership of Five Percent or Less of a Class. Not applicable Item 6. Ownership of More Than Five Percent on Behalf of Another Person. Not applicable Item 7. Identification and Classification of the Subsidiary which Acquired the Security Being Reported on by the Parent Holding Company. Not applicable Item 8. Identification and Classification of Members of the Group. Not applicable Item 9. Notice of Dissolution of Group. Not applicable Page 4 of 5 Pages
Item 10. Certifications. By signing below, I certify that, to the best of my knowledge and belief, the securities referred to above were not acquired and are not held for the purpose of or with the effect of changing or influencing control of the issuer of the securities and were not acquired and are not held in connection with or as a participant in any transaction having that purpose or effect. SIGNATURE After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct. ELI LILLY AND COMPANY By:/s/ Charles E. Golden ----------------------------- Charles E. Golden Executive Vice President and Chief Financial Officer Date: August 30, 2001 Page 5 of 5 Pages