﻿<?xml version="1.0" encoding="utf-8"?>
<InstanceReport xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema">
  <Version>2.2.0.7</Version>
  <hasSegments>false</hasSegments>
  <ReportName>Contingencies</ReportName>
  <ReportLongName>0215 - Disclosure - Contingencies</ReportLongName>
  <DisplayLabelColumn>true</DisplayLabelColumn>
  <ShowElementNames>false</ShowElementNames>
  <RoundingOption />
  <HasEmbeddedReports>false</HasEmbeddedReports>
  <Columns>
    <Column>
      <LabelColumn>false</LabelColumn>
      <Id>1</Id>
      <Labels>
        <Label Id="1" Label="6 Months Ended" />
        <Label Id="2" Label="Jun. 30, 2010" />
      </Labels>
      <CurrencyCode>USD</CurrencyCode>
      <FootnoteIndexer />
      <hasSegments>false</hasSegments>
      <hasScenarios>false</hasScenarios>
      <Segments />
      <Scenarios />
      <Units>
        <Unit>
          <UnitID>USD</UnitID>
          <UnitType>Standard</UnitType>
          <StandardMeasure>
            <MeasureSchema>http://www.xbrl.org/2003/iso4217</MeasureSchema>
            <MeasureValue>USD</MeasureValue>
            <MeasureNamespace>iso4217</MeasureNamespace>
          </StandardMeasure>
          <Scale>0</Scale>
        </Unit>
        <Unit>
          <UnitID>USDEPS</UnitID>
          <UnitType>Divide</UnitType>
          <NumeratorMeasure>
            <MeasureSchema>http://www.xbrl.org/2003/iso4217</MeasureSchema>
            <MeasureValue>USD</MeasureValue>
            <MeasureNamespace>iso4217</MeasureNamespace>
          </NumeratorMeasure>
          <DenominatorMeasure>
            <MeasureSchema>http://www.xbrl.org/2003/instance</MeasureSchema>
            <MeasureValue>shares</MeasureValue>
            <MeasureNamespace>xbrli</MeasureNamespace>
          </DenominatorMeasure>
          <Scale>0</Scale>
        </Unit>
        <Unit>
          <UnitID>Shares</UnitID>
          <UnitType>Standard</UnitType>
          <StandardMeasure>
            <MeasureSchema>http://www.xbrl.org/2003/instance</MeasureSchema>
            <MeasureValue>shares</MeasureValue>
            <MeasureNamespace>xbrli</MeasureNamespace>
          </StandardMeasure>
          <Scale>0</Scale>
        </Unit>
      </Units>
      <CurrencySymbol>$</CurrencySymbol>
    </Column>
  </Columns>
  <Rows>
    <Row>
      <Id>2</Id>
      <Label>Contingencies [Abstract]</Label>
      <Level>0</Level>
      <ElementName>mdco_ContingenciesAbstract</ElementName>
      <ElementPrefix>mdco</ElementPrefix>
      <IsBaseElement>false</IsBaseElement>
      <BalanceType>na</BalanceType>
      <PeriodType>duration</PeriodType>
      <ShortDefinition>Contingencies.</ShortDefinition>
      <IsReportTitle>false</IsReportTitle>
      <IsSegmentTitle>false</IsSegmentTitle>
      <IsSubReportEnd>false</IsSubReportEnd>
      <IsCalendarTitle>false</IsCalendarTitle>
      <IsTuple>false</IsTuple>
      <IsAbstractGroupTitle>true</IsAbstractGroupTitle>
      <IsEquityPrevioslyReportedAsRow>false</IsEquityPrevioslyReportedAsRow>
      <IsEquityAdjustmentRow>false</IsEquityAdjustmentRow>
      <IsBeginningBalance>false</IsBeginningBalance>
      <IsEndingBalance>false</IsEndingBalance>
      <IsReverseSign>false</IsReverseSign>
      <PreferredLabelRole />
      <IsEPS>false</IsEPS>
      <FootnoteIndexer />
      <Cells>
        <Cell>
          <Id>1</Id>
          <ShowCurrencySymbol>false</ShowCurrencySymbol>
          <IsNumeric>false</IsNumeric>
          <IsRatio>false</IsRatio>
          <DisplayZeroAsNone>false</DisplayZeroAsNone>
          <NumericAmount>0</NumericAmount>
          <RoundedNumericAmount>0</RoundedNumericAmount>
          <NonNumbericText />
          <NonNumericTextHeader />
          <FootnoteIndexer />
          <hasSegments>false</hasSegments>
          <hasScenarios>false</hasScenarios>
          <DisplayDateInUSFormat>false</DisplayDateInUSFormat>
        </Cell>
      </Cells>
      <OriginalInstanceReportColumns />
      <ElementDataType>xbrli:stringItemType</ElementDataType>
      <SimpleDataType>string</SimpleDataType>
      <ElementDefenition>Contingencies.</ElementDefenition>
      <IsTotalLabel>false</IsTotalLabel>
    </Row>
    <Row>
      <Id>3</Id>
      <Label>Contingencies</Label>
      <Level>1</Level>
      <ElementName>us-gaap_CommitmentsAndContingenciesDisclosureTextBlock</ElementName>
      <ElementPrefix>us-gaap</ElementPrefix>
      <IsBaseElement>true</IsBaseElement>
      <BalanceType>na</BalanceType>
      <PeriodType>duration</PeriodType>
      <ShortDefinition>No definition available.</ShortDefinition>
      <IsReportTitle>false</IsReportTitle>
      <IsSegmentTitle>false</IsSegmentTitle>
      <IsSubReportEnd>false</IsSubReportEnd>
      <IsCalendarTitle>false</IsCalendarTitle>
      <IsTuple>false</IsTuple>
      <IsAbstractGroupTitle>false</IsAbstractGroupTitle>
      <IsEquityPrevioslyReportedAsRow>false</IsEquityPrevioslyReportedAsRow>
      <IsEquityAdjustmentRow>false</IsEquityAdjustmentRow>
      <IsBeginningBalance>false</IsBeginningBalance>
      <IsEndingBalance>false</IsEndingBalance>
      <IsReverseSign>false</IsReverseSign>
      <PreferredLabelRole>verboselabel</PreferredLabelRole>
      <IsEPS>false</IsEPS>
      <FootnoteIndexer />
      <Cells>
        <Cell>
          <Id>1</Id>
          <ShowCurrencySymbol>false</ShowCurrencySymbol>
          <IsNumeric>false</IsNumeric>
          <IsRatio>false</IsRatio>
          <DisplayZeroAsNone>false</DisplayZeroAsNone>
          <NumericAmount>0</NumericAmount>
          <RoundedNumericAmount>0</RoundedNumericAmount>
          <NonNumbericText>&lt;!--DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd" --&gt;
   &lt;!-- Begin Block Tagged Note 15 - us-gaap:CommitmentsAndContingenciesDisclosureTextBlock--&gt;
   &lt;div style="font-family: 'Times New Roman',Times,serif"&gt;
   &lt;div align="left" style="font-size: 10pt; margin-top: 12pt"&gt;&lt;b&gt;15. Contingencies&lt;/b&gt;
   &lt;/div&gt;
   &lt;div align="left" style="font-size: 10pt; margin-top: 6pt"&gt;&amp;#160;&amp;#160;&amp;#160;&amp;#160;&amp;#160;The Company may be, from time to time, a party to various disputes and claims arising from
   normal business activities. The Company accrues for loss contingencies when information available
   indicates that it is probable that a liability has been incurred and the amount of such loss can be
   reasonably estimated. The Company believes that the ultimate resolution of these matters will not
   have a material adverse effect on the Company&amp;#8217;s financial condition or liquidity. However,
   adjustments, if any, to the Company&amp;#8217;s estimates could be material to operating results for the
   periods in which adjustments to the liability are recorded.
   &lt;/div&gt;
   &lt;div align="left" style="font-size: 10pt; margin-top: 6pt"&gt;&amp;#160;&amp;#160;&amp;#160;&amp;#160;&amp;#160;The U.S. Patent and Trademark Office (PTO)&amp;#160;rejected the Company&amp;#8217;s application under the
   Hatch-Waxman Act for an extension of the term of U.S. Patent No.&amp;#160;5,196,404, the principal U.S.
   patent that covers Angiomax (the patent extension filing), because in the PTO&amp;#8217;s view the
   application was not timely filed. The Company has entered into agreements with the law firms
   involved in the patent extension filing that suspend the statute of limitations on any claims
   against them for failing to make a timely filing. The Company has entered into a similar agreement
   with Biogen Idec, one of its licensors for Angiomax, relating to any claims, including claims for
   damages and/or license termination, that Biogen Idec may bring relating to the patent extension
   filing. Such claims by Biogen Idec could have a material adverse effect on the Company&amp;#8217;s financial
   condition, results of operations, liquidity or business. The Company is currently in discussions
   with the law firms involved in the patent extension filing and with Biogen Idec and Health Research
   Inc. with respect to the possible resolution of potential claims among the parties.
   &lt;/div&gt;
   &lt;/div&gt;
</NonNumbericText>
          <NonNumericTextHeader>&lt;!--DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd" --&gt;
   &lt;!-- Begin Block Tagged Note</NonNumericTextHeader>
          <FootnoteIndexer />
          <hasSegments>false</hasSegments>
          <hasScenarios>false</hasScenarios>
          <DisplayDateInUSFormat>false</DisplayDateInUSFormat>
        </Cell>
      </Cells>
      <OriginalInstanceReportColumns />
      <ElementDataType>us-types:textBlockItemType</ElementDataType>
      <SimpleDataType>textblock</SimpleDataType>
      <ElementDefenition>Includes disclosure of commitments and contingencies. This element may be used as a single block of text to encapsulate the entire disclosure including data and tables.</ElementDefenition>
      <ElementReferences>Reference 1: http://www.xbrl.org/2003/role/presentationRef
 -Publisher FASB
 -Name FASB Interpretation (FIN)
 -Number 14
 -Paragraph 3

Reference 2: http://www.xbrl.org/2003/role/presentationRef
 -Publisher FASB
 -Name Statement of Financial Accounting Standard (FAS)
 -Number 5
 -Paragraph 9, 10, 11, 12

</ElementReferences>
      <IsTotalLabel>false</IsTotalLabel>
    </Row>
  </Rows>
  <Footnotes />
  <NumberOfCols>1</NumberOfCols>
  <NumberOfRows>2</NumberOfRows>
  <HasScenarios>false</HasScenarios>
  <MonetaryRoundingLevel>UnKnown</MonetaryRoundingLevel>
  <SharesRoundingLevel>UnKnown</SharesRoundingLevel>
  <PerShareRoundingLevel>UnKnown</PerShareRoundingLevel>
  <HasPureData>false</HasPureData>
  <SharesShouldBeRounded>true</SharesShouldBeRounded>
</InstanceReport>
