<SEC-DOCUMENT>0001209191-13-002789.txt : 20130110
<SEC-HEADER>0001209191-13-002789.hdr.sgml : 20130110
<ACCEPTANCE-DATETIME>20130110162923
ACCESSION NUMBER:		0001209191-13-002789
CONFORMED SUBMISSION TYPE:	3
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20130101
FILED AS OF DATE:		20130110
DATE AS OF CHANGE:		20130110

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Harrington Michael J
		CENTRAL INDEX KEY:			0001566340

	FILING VALUES:
		FORM TYPE:		3
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-06351
		FILM NUMBER:		13523187

	MAIL ADDRESS:	
		STREET 1:		LILLY CORPORATE CENTER
		CITY:			INDIANAPOLIS
		STATE:			IN
		ZIP:			46285

ISSUER:		

	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

	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>3
<SEQUENCE>1
<FILENAME>doc3.xml
<DESCRIPTION>FORM 3 SUBMISSION
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2013-01-01</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0000059478</issuerCik>
        <issuerName>LILLY ELI &amp; CO</issuerName>
        <issuerTradingSymbol>LLY</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001566340</rptOwnerCik>
            <rptOwnerName>Harrington Michael J</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>LILLY CORPORATE CENTER</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>INDIANAPOLIS</rptOwnerCity>
            <rptOwnerState>IN</rptOwnerState>
            <rptOwnerZipCode>46285</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Senior VP and General Counsel</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>376</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>401(k)</value>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>15568</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Employee stock option 2/03 (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>57.85</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2006-02-16</value>
            </exerciseDate>
            <expirationDate>
                <value>2013-02-15</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>3800</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Employee stock option 2/04 (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>73.11</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2007-02-19</value>
            </exerciseDate>
            <expirationDate>
                <value>2014-02-14</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>5200</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Employee stock option 2/05 (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>55.65</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2008-02-11</value>
            </exerciseDate>
            <expirationDate>
                <value>2015-02-10</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>2722</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Employee stock option 2/06 (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>56.18</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2009-02-10</value>
            </exerciseDate>
            <expirationDate>
                <value>2016-02-09</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>6024</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes></footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>Michael J. Harrington</signatureName>
        <signatureDate>2013-01-10</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
