<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0203</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2009-05-01</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001463321</rptOwnerCik>
            <rptOwnerName>Mahony Susan</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, Human Resources</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>9534</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>251</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>280</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>401(k) - by husband</value>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Employee stock option 10/01 (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>79.28</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2003-10-03</value>
            </exerciseDate>
            <expirationDate>
                <value>2011-10-04</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>4250</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Employee stock option 10/01 (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>79.28</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2003-10-03</value>
            </exerciseDate>
            <expirationDate>
                <value>2011-10-04</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>1100</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>by husband</value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Employee stock option 10/99 (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>66.375</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2002-10-18</value>
            </exerciseDate>
            <expirationDate>
                <value>2009-10-16</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>2200</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>by husband</value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Employee stock option 2/01 (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>73.98</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2004-02-20</value>
            </exerciseDate>
            <expirationDate>
                <value>2011-02-18</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>4300</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Employee stock option 2/01 (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>73.98</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2004-02-20</value>
            </exerciseDate>
            <expirationDate>
                <value>2011-02-18</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>2550</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>by husband</value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Employee stock option 2/02 (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>75.92</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2005-02-18</value>
            </exerciseDate>
            <expirationDate>
                <value>2012-02-17</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>2350</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>by husband</value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Employee stock option 2/02 (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>75.92</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2005-02-18</value>
            </exerciseDate>
            <expirationDate>
                <value>2012-02-17</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>8500</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <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>10300</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <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>2350</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>by husband</value>
                </natureOfOwnership>
            </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>9000</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>3700</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>by husband</value>
                </natureOfOwnership>
            </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>1065</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>by husband</value>
                </natureOfOwnership>
            </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>8521</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>9036</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>1175</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>by husband</value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes></footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>Susan Mahony</signatureName>
        <signatureDate>2009-05-06</signatureDate>
    </ownerSignature>
</ownershipDocument>
