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Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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<SEC-DOCUMENT>0000950131-01-503237.txt : 20010906
<SEC-HEADER>0000950131-01-503237.hdr.sgml : 20010906
ACCESSION NUMBER:		0000950131-01-503237
CONFORMED SUBMISSION TYPE:	SC 13G
PUBLIC DOCUMENT COUNT:		1
FILED AS OF DATE:		20010905

SUBJECT COMPANY:	

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			ISIS PHARMACEUTICALS INC
		CENTRAL INDEX KEY:			0000874015
		STANDARD INDUSTRIAL CLASSIFICATION:	PHARMACEUTICAL PREPARATIONS [2834]
		IRS NUMBER:				330336973
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	FILING VALUES:
		FORM TYPE:		SC 13G
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	005-41771
		FILM NUMBER:		1731116

	BUSINESS ADDRESS:	
		STREET 1:		2292 FARADAY AVE
		CITY:			CARLSBAD
		STATE:			CA
		ZIP:			92008
		BUSINESS PHONE:		7609319200

	MAIL ADDRESS:	
		STREET 1:		2292 FARADAY AVE
		CITY:			CARLSBAD
		STATE:			CA
		ZIP:			92008

FILED BY:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			LILLY ELI & CO
		CENTRAL INDEX KEY:			0000059478
		STANDARD INDUSTRIAL CLASSIFICATION:	PHARMACEUTICAL PREPARATIONS [2834]
		IRS NUMBER:				350470950
		STATE OF INCORPORATION:			IN
		FISCAL YEAR END:			1231

	FILING VALUES:
		FORM TYPE:		SC 13G

	BUSINESS ADDRESS:	
		STREET 1:		LILLY CORPORATE CTR
		STREET 2:		DROP CODE 1112
		CITY:			INDIANAPOLIS
		STATE:			IN
		ZIP:			46285
		BUSINESS PHONE:		3172762000

	MAIL ADDRESS:	
		STREET 1:		LILLY CORPORATE CENTER
		STREET 2:		DROP CODE 1112
		CITY:			INDIANAPOLIS
		STATE:			IN
		ZIP:			46285
</SEC-HEADER>
<DOCUMENT>
<TYPE>SC 13G
<SEQUENCE>1
<FILENAME>dsc13g.txt
<DESCRIPTION>SCHEDULE 13-G
<TEXT>
<PAGE>

                      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
<PAGE>
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

<PAGE>

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

<PAGE>

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

<PAGE>

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


</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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