<?xml version="1.0"?>
<ownershipDocument>
    <schemaVersion>X0201</schemaVersion>

    <documentType>3</documentType>
    <periodOfReport>2004-01-01</periodOfReport>
    <noSecuritiesOwned>0</noSecuritiesOwned>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001276038</rptOwnerCik>
            <rptOwnerName>SANTINI GINO</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>President, US Operations </officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>
  <nonDerivativeTable>
   <nonDerivativeHolding>
      <securityTitle>
          <value>Common Stock</value>
      </securityTitle>
      <postTransactionAmounts>
          <sharesOwnedFollowingTransaction>
              <value>50788.00</value>
          </sharesOwnedFollowingTransaction>
      </postTransactionAmounts>
      <ownershipNature>
          <directOrIndirectOwnership>
              <value>D</value>
          </directOrIndirectOwnership>
      </ownershipNature>
   </nonDerivativeHolding>
   <nonDerivativeHolding>
      <securityTitle>
          <value>Common Stock</value>
      </securityTitle>
      <postTransactionAmounts>
          <sharesOwnedFollowingTransaction>
              <value>1144.00</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>2070.00</value>
          </sharesOwnedFollowingTransaction>
      </postTransactionAmounts>
      <ownershipNature>
          <directOrIndirectOwnership>
              <value>I</value>
              <footnoteId id="F1" />
          </directOrIndirectOwnership>
          <natureOfOwnership>
              <value>by daughter</value>
          </natureOfOwnership>
      </ownershipNature>
   </nonDerivativeHolding>
   <nonDerivativeHolding>
      <securityTitle>
          <value>Common Stock</value>
      </securityTitle>
      <postTransactionAmounts>
          <sharesOwnedFollowingTransaction>
              <value>2070.00</value>
          </sharesOwnedFollowingTransaction>
      </postTransactionAmounts>
      <ownershipNature>
          <directOrIndirectOwnership>
              <value>I</value>
              <footnoteId id="F1" />
          </directOrIndirectOwnership>
          <natureOfOwnership>
              <value>by son</value>
          </natureOfOwnership>
      </ownershipNature>
   </nonDerivativeHolding>
   <nonDerivativeHolding>
      <securityTitle>
          <value>Common Stock</value>
      </securityTitle>
      <postTransactionAmounts>
          <sharesOwnedFollowingTransaction>
              <value>2292.00</value>
          </sharesOwnedFollowingTransaction>
      </postTransactionAmounts>
      <ownershipNature>
          <directOrIndirectOwnership>
              <value>I</value>
              <footnoteId id="F1" />
          </directOrIndirectOwnership>
          <natureOfOwnership>
              <value>by wife</value>
          </natureOfOwnership>
      </ownershipNature>
   </nonDerivativeHolding>
  </nonDerivativeTable>
  <derivativeTable>
   <derivativeHolding>
      <securityTitle>
          <value>Employee stock option (right to buy)</value>
      </securityTitle>
      <conversionOrExercisePrice>
          <value>12.3125</value>
      </conversionOrExercisePrice>
      <exerciseDate>
          <value>1997-04-21</value>
      </exerciseDate>
      <expirationDate>
          <value>2004-04-20</value>
      </expirationDate>
      <underlyingSecurity>
          <underlyingSecurityTitle>
              <value>Common Stock</value>
          </underlyingSecurityTitle>
          <underlyingSecurityShares>
              <value>15880.00</value>
          </underlyingSecurityShares>
      </underlyingSecurity>
      <ownershipNature>
          <directOrIndirectOwnership>
              <value>D</value>
          </directOrIndirectOwnership>
      </ownershipNature>
   </derivativeHolding>
   <derivativeHolding>
      <securityTitle>
          <value>Employee stock option (right to buy)</value>
      </securityTitle>
      <conversionOrExercisePrice>
          <value>14.6575</value>
      </conversionOrExercisePrice>
      <exerciseDate>
          <value>1997-10-17</value>
      </exerciseDate>
      <expirationDate>
          <value>2004-10-15</value>
      </expirationDate>
      <underlyingSecurity>
          <underlyingSecurityTitle>
              <value>Common Stock</value>
          </underlyingSecurityTitle>
          <underlyingSecurityShares>
              <value>16000.00</value>
          </underlyingSecurityShares>
      </underlyingSecurity>
      <ownershipNature>
          <directOrIndirectOwnership>
              <value>D</value>
          </directOrIndirectOwnership>
      </ownershipNature>
   </derivativeHolding>
   <derivativeHolding>
      <securityTitle>
          <value>Employee stock option (right to buy)</value>
      </securityTitle>
      <conversionOrExercisePrice>
          <value>23.4075</value>
      </conversionOrExercisePrice>
      <exerciseDate>
          <value>1998-10-16</value>
      </exerciseDate>
      <expirationDate>
          <value>2005-10-14</value>
      </expirationDate>
      <underlyingSecurity>
          <underlyingSecurityTitle>
              <value>Common Stock</value>
          </underlyingSecurityTitle>
          <underlyingSecurityShares>
              <value>27728.00</value>
          </underlyingSecurityShares>
      </underlyingSecurity>
      <ownershipNature>
          <directOrIndirectOwnership>
              <value>D</value>
          </directOrIndirectOwnership>
      </ownershipNature>
   </derivativeHolding>
   <derivativeHolding>
      <securityTitle>
          <value>Employee stock option (right to buy)</value>
      </securityTitle>
      <conversionOrExercisePrice>
          <value>34.595</value>
      </conversionOrExercisePrice>
      <exerciseDate>
          <value>1999-10-21</value>
      </exerciseDate>
      <expirationDate>
          <value>2006-10-20</value>
      </expirationDate>
      <underlyingSecurity>
          <underlyingSecurityTitle>
              <value>Common Stock</value>
          </underlyingSecurityTitle>
          <underlyingSecurityShares>
              <value>13110.00</value>
          </underlyingSecurityShares>
      </underlyingSecurity>
      <ownershipNature>
          <directOrIndirectOwnership>
              <value>D</value>
          </directOrIndirectOwnership>
      </ownershipNature>
   </derivativeHolding>
   <derivativeHolding>
      <securityTitle>
          <value>Employee stock option (right to buy)</value>
      </securityTitle>
      <conversionOrExercisePrice>
          <value>64.06</value>
      </conversionOrExercisePrice>
      <exerciseDate>
          <value>2000-10-20</value>
      </exerciseDate>
      <expirationDate>
          <value>2007-10-19</value>
      </expirationDate>
      <underlyingSecurity>
          <underlyingSecurityTitle>
              <value>Common Stock</value>
          </underlyingSecurityTitle>
          <underlyingSecurityShares>
              <value>20000.00</value>
          </underlyingSecurityShares>
      </underlyingSecurity>
      <ownershipNature>
          <directOrIndirectOwnership>
              <value>D</value>
          </directOrIndirectOwnership>
      </ownershipNature>
   </derivativeHolding>
   <derivativeHolding>
      <securityTitle>
          <value>Employee stock option (right to buy)</value>
      </securityTitle>
      <conversionOrExercisePrice>
          <value>74.2813</value>
      </conversionOrExercisePrice>
      <exerciseDate>
          <value>1998-10-19</value>
      </exerciseDate>
      <expirationDate>
          <value>2008-10-17</value>
      </expirationDate>
      <underlyingSecurity>
          <underlyingSecurityTitle>
              <value>Common Stock</value>
          </underlyingSecurityTitle>
          <underlyingSecurityShares>
              <value>25000.00</value>
          </underlyingSecurityShares>
      </underlyingSecurity>
      <ownershipNature>
          <directOrIndirectOwnership>
              <value>D</value>
          </directOrIndirectOwnership>
      </ownershipNature>
   </derivativeHolding>
   <derivativeHolding>
      <securityTitle>
          <value>Employee Stock Option (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>46000.00</value>
          </underlyingSecurityShares>
      </underlyingSecurity>
      <ownershipNature>
          <directOrIndirectOwnership>
              <value>D</value>
          </directOrIndirectOwnership>
      </ownershipNature>
   </derivativeHolding>
   <derivativeHolding>
      <securityTitle>
          <value>Employee stock option (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>50600.00</value>
          </underlyingSecurityShares>
      </underlyingSecurity>
      <ownershipNature>
          <directOrIndirectOwnership>
              <value>D</value>
          </directOrIndirectOwnership>
      </ownershipNature>
   </derivativeHolding>
   <derivativeHolding>
      <securityTitle>
          <value>Employee stock option (right to buy)</value>
      </securityTitle>
      <conversionOrExercisePrice>
          <value>79.28</value>
      </conversionOrExercisePrice>
      <exerciseDate>
          <value>2004-10-05</value>
      </exerciseDate>
      <expirationDate>
          <value>2011-10-04</value>
      </expirationDate>
      <underlyingSecurity>
          <underlyingSecurityTitle>
              <value>Common Stock</value>
          </underlyingSecurityTitle>
          <underlyingSecurityShares>
              <value>23000.00</value>
          </underlyingSecurityShares>
      </underlyingSecurity>
      <ownershipNature>
          <directOrIndirectOwnership>
              <value>D</value>
          </directOrIndirectOwnership>
      </ownershipNature>
   </derivativeHolding>
   <derivativeHolding>
      <securityTitle>
          <value>Employee stock option (right to buy)</value>
      </securityTitle>
      <conversionOrExercisePrice>
          <value>75.92</value>
      </conversionOrExercisePrice>
      <exerciseDate>
          <value>2005-02-19</value>
      </exerciseDate>
      <expirationDate>
          <value>2012-02-17</value>
      </expirationDate>
      <underlyingSecurity>
          <underlyingSecurityTitle>
              <value>Common Stock</value>
          </underlyingSecurityTitle>
          <underlyingSecurityShares>
              <value>46000.00</value>
          </underlyingSecurityShares>
      </underlyingSecurity>
      <ownershipNature>
          <directOrIndirectOwnership>
              <value>D</value>
          </directOrIndirectOwnership>
      </ownershipNature>
   </derivativeHolding>
   <derivativeHolding>
      <securityTitle>
          <value>Employee stock option (right to buy)</value>
      </securityTitle>
      <conversionOrExercisePrice>
          <value>57.85</value>
      </conversionOrExercisePrice>
      <exerciseDate>
          <value>2006-02-17</value>
      </exerciseDate>
      <expirationDate>
          <value>2013-02-15</value>
      </expirationDate>
      <underlyingSecurity>
          <underlyingSecurityTitle>
              <value>Common Stock</value>
          </underlyingSecurityTitle>
          <underlyingSecurityShares>
              <value>50000.00</value>
          </underlyingSecurityShares>
      </underlyingSecurity>
      <ownershipNature>
          <directOrIndirectOwnership>
              <value>D</value>
          </directOrIndirectOwnership>
      </ownershipNature>
   </derivativeHolding>
  </derivativeTable>
<footnotes>
   <footnote id="F1">Reporting person disclaims beneficial ownership of these shares.</footnote>
</footnotes>
<remarks></remarks>    <ownerSignature>
       <signatureName>Gino   Santini</signatureName>
       <signatureDate>2004-01-12</signatureDate>
    </ownerSignature>
</ownershipDocument>

