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

                                  Form 13F

FORM 13F COVER PAGE

Report for the Calendar Year or Quarter Ended: December 31, 2009

Check here if Amendment [  ];  Amendment Number: ________
This Amendment (check only one):  [  ] is a restatement.
                                  [  ] adds new holdings entries.

Institutional Investment Manager Filing this Report:

Name:     Lilly Endowment, Inc.
Address:  2801 North Meridian Street
          Indianapolis, IN  46208-0068

Form 13F File Number: 28-00889

The  institutional  investment manager filing this report and the person by
whom it is signed hereby  represent  that  the person signing the report is
authorized to submit it, that all information  contained  herein  is  true,
correct  and  complete,  and that it is understood that all required items,
statements, schedules, lists,  and tables, are considered integral parts of
this form.

Person Signing this Report on Behalf of Reporting Manager:
Name:   Diane M. Stenson
Title:  Treasurer
Phone:  (317) 924-5471

Signature, Place, and Date of Signing:

   /s/ Diane M. Stenson
   Indianapolis, Indiana
   January 6, 2010

Report Type (Check only one.):

[X]   13F HOLDING REPORT (Check here if all holdings of this reporting manager
      are reported in this report.)

[ ]   13F NOTICE. (Check here if no holdings reported are in this report, and
      all holdings are reported by other reporting manager(s).)

[ ]   13F COMBINATION REPORT.  (Check here if a portion of the holdings for
      this reporting manager are reported in this report and a portion are
      reported by other reporting manager(s).)

List of Other Managers Reporting for this Manager: N/A


FORM 13F SUMMARY PAGE

Report Summary:

Number of Other Included Managers:      0

Form 13F Information Table Entry Total:     1

Form 13F Information Table Value Total:  $4,844,804 (in thousands)

List of Other Included Managers:  NONE


FORM 13F INFORMATION TABLE


Column 1     Column 2  Column 3     Column 4               Column 5             Column 6    Column 7         Column 8
                                                                                                         Voting Authority
Name of      Title     CUSIP        Value        Shrs or      SH/PRN  Put/Call  Investment  Other     Sole         Shared  None
Issuer       of Class               (x$1000)     prn amt                        discretion  managers
                                                                                          
Eli Lilly    Common    532457-10-8  $4,844,804   135,670,804  SH                Sole                  135,670,804  0       0
and Company