<?xml version="1.0" encoding="us-ascii"?><InstanceReport xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"><Version>2.4.0.8</Version><ReportLongName>2118100 - Disclosure - Collaboration Agreements (Notes)</ReportLongName><DisplayLabelColumn>true</DisplayLabelColumn><ShowElementNames>false</ShowElementNames><RoundingOption /><HasEmbeddedReports>false</HasEmbeddedReports><Columns><Column FlagID="0"><Id>1</Id><IsAbstractGroupTitle>false</IsAbstractGroupTitle><LabelSeparator>

</LabelSeparator><CurrencyCode /><FootnoteIndexer /><hasSegments>false</hasSegments><hasScenarios>false</hasScenarios><MCU><KeyName /><CurrencySymbol /><contextRef><ContextID>D2013Q2YTD</ContextID><EntitySchema>http://www.sec.gov/CIK</EntitySchema><EntityValue>0001113481</EntityValue><PeriodDisplayName /><PeriodType>duration</PeriodType><PeriodStartDate>2013-01-01T00:00:00</PeriodStartDate><PeriodEndDate>2013-06-30T00:00:00</PeriodEndDate><Segments /><Scenarios /></contextRef><UPS /><CurrencyCode /><OriginalCurrencyCode /></MCU><CurrencySymbol /><Labels><Label Key="CalendarSupplement" Id="0" Label="6 Months Ended" /><Label Key="Calendar" Id="1" Label="Jun. 30, 2013" /></Labels></Column></Columns><Rows><Row FlagID="0"><Id>1</Id><IsAbstractGroupTitle>true</IsAbstractGroupTitle><LabelSeparator>

</LabelSeparator><Level>1</Level><ElementName>mdco_CollaborationAgreementsAbstract</ElementName><ElementPrefix>mdco_</ElementPrefix><IsBaseElement>false</IsBaseElement><BalanceType>na</BalanceType><PeriodType>duration</PeriodType><IsReportTitle>false</IsReportTitle><IsSegmentTitle>false</IsSegmentTitle><IsCalendarTitle>false</IsCalendarTitle><IsEquityPrevioslyReportedAsRow>false</IsEquityPrevioslyReportedAsRow><IsEquityAdjustmentRow>false</IsEquityAdjustmentRow><IsBeginningBalance>false</IsBeginningBalance><IsEndingBalance>false</IsEndingBalance><IsReverseSign>false</IsReverseSign><FootnoteIndexer /><Cells><Cell FlagID="0" ContextID="" UnitID=""><Id>1</Id><IsNumeric>false</IsNumeric><IsRatio>false</IsRatio><DisplayZeroAsNone>false</DisplayZeroAsNone><NumericAmount>0</NumericAmount><RoundedNumericAmount>0</RoundedNumericAmount><NonNumbericText /><FootnoteIndexer /><CurrencyCode /><CurrencySymbol /><IsIndependantCurrency>false</IsIndependantCurrency><ShowCurrencySymbol>false</ShowCurrencySymbol><DisplayDateInUSFormat>false</DisplayDateInUSFormat></Cell></Cells><ElementDataType>xbrli:stringItemType</ElementDataType><SimpleDataType>string</SimpleDataType><IsTotalLabel>false</IsTotalLabel><UnitID>0</UnitID><Label>Collaboration Agreements [Abstract]</Label></Row><Row FlagID="0"><Id>2</Id><IsAbstractGroupTitle>false</IsAbstractGroupTitle><LabelSeparator>

</LabelSeparator><Level>2</Level><ElementName>us-gaap_CollaborativeArrangementDisclosureTextBlock</ElementName><ElementPrefix>us-gaap_</ElementPrefix><IsBaseElement>true</IsBaseElement><BalanceType>na</BalanceType><PeriodType>duration</PeriodType><IsReportTitle>false</IsReportTitle><IsSegmentTitle>false</IsSegmentTitle><IsCalendarTitle>false</IsCalendarTitle><IsEquityPrevioslyReportedAsRow>false</IsEquityPrevioslyReportedAsRow><IsEquityAdjustmentRow>false</IsEquityAdjustmentRow><IsBeginningBalance>false</IsBeginningBalance><IsEndingBalance>false</IsEndingBalance><IsReverseSign>false</IsReverseSign><PreferredLabelRole>terseLabel</PreferredLabelRole><FootnoteIndexer /><Cells><Cell FlagID="0" ContextID="D2013Q2YTD" UnitID=""><Id>1</Id><IsNumeric>false</IsNumeric><IsRatio>false</IsRatio><DisplayZeroAsNone>false</DisplayZeroAsNone><NumericAmount>0</NumericAmount><RoundedNumericAmount>0</RoundedNumericAmount><NonNumbericText>&lt;div style="font-family:Times New Roman;font-size:10pt;"&gt;&lt;div style="line-height:174%;text-align:left;text-indent:18px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;font-weight:bold;"&gt;Collaboration Agreements&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:174%;text-align:left;text-indent:18px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;&lt;br clear="none"/&gt;&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:174%;text-align:left;text-indent:18px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;font-style:italic;"&gt;AstraZeneca&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;text-align:left;padding-left:78px;text-indent:30px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;&lt;br clear="none"/&gt;&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;text-align:justify;text-indent:30px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;In April 2012, the Company entered into an agreement with AstraZeneca pursuant to which the Company and AstraZeneca agreed to collaborate globally to develop and commercialize certain acute ischemic heart disease compounds.  Under the terms of the collaboration agreement, a joint development and research committee and a joint commercialization committee have been established to prepare and deliver a global development plan and a country-by-country collaboration and commercialization plan, respectively, related to BRILINTA and Angiomax and cangrelor. Implementation of these plans is subject to agreement between both parties.&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;text-align:justify;text-indent:48px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;&lt;br clear="none"/&gt;&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;text-align:justify;text-indent:30px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;The first joint activity agreed upon by the parties under the collaboration agreement was a &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;four&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;-year co-promotion arrangement for BRILINTA in the United States.  The Company and AstraZeneca have not agreed as to any development and commercialization activities to be performed with respect to Angiomax and cangrelor or as to any terms under which such activities would be performed. &lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;text-align:left;text-indent:48px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;&lt;br clear="none"/&gt;&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;text-align:justify;text-indent:30px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;Pursuant to the co-promotion arrangement, the Company's sales force began supporting promotion activities for BRILINTA in May 2012.  Under the terms of the collaboration agreement, AstraZeneca agreed to pay the Company base consideration fees for conducting BRILINTA co-promotion activities during the specified periods, plus additional consideration fees for the same periods, if specified performance targets are achieved with respect to the number of new prescriptions written during the specified periods.  The Company recognizes as co-promotion revenue both the base consideration fee and the additional consideration related to new prescriptions of BRILINTA as performance requirements are met.  The base consideration fee for a specified time period is recognized ratably as our sales force activities meet the required performance target.  The additional consideration fee for a specified time period related to the number of new prescriptions of BRILINTA written during the time period is recognized when the number of new prescriptions of BRILINTA exceeds the required performance target for such period.  As of June 30, 2013, the Company has recognized a total co-promotion revenue of approximately &lt;/font&gt;&lt;font style="font-family:Times New Roman;font-size:10pt;color:#000000;font-style:normal;font-weight:normal;text-decoration:none;"&gt;$17.8 million&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt; from AstraZeneca under the global collaboration agreement.  &lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;text-align:justify;padding-left:78px;text-indent:30px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;&lt;br clear="none"/&gt;&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;text-align:justify;text-indent:30px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;At the end of the second year of the agreement, AstraZeneca may terminate the agreement if performance targets for the second year are not achieved. Conversely, the Company may terminate the agreement at such time if the performance targets for the second year are achieved. Either party may terminate the agreement at the end of the third year of the agreement. If AstraZeneca elects to terminate the agreement at the end of the third year and the performance targets for the third year have been achieved, AstraZeneca must pay the Company a termination fee of &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;$5 million&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;.&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;text-align:left;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;&lt;br clear="none"/&gt;&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:174%;text-align:left;text-indent:18px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;font-style:italic;"&gt;Alnylam Pharmaceuticals, Inc.&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:174%;text-align:left;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;&lt;br clear="none"/&gt;&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;text-align:justify;text-indent:18px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;In February 2013, the Company entered into a license and collaboration agreement with Alnylam Pharmaceuticals, Inc. (Alnylam) to develop, manufacture and commercialize therapeutic products targeting the proprotein convertase subtilisin/kexin type 9 (PCSK9) gene, based on certain of Alnylam's RNA interference (RNAi) technology. Under the terms of the agreement, the Company obtained the exclusive, worldwide right under Alnylam's technology to develop, manufacture and commercialize PCSK-9 products for the treatment, palliation and/or prevention of all human diseases.  Alnylam is responsible for the development costs of the products, subject to an agreed upon limit, until the completion of Phase 1 clinical studies.  The Company is responsible for completing and funding the development costs of the products through commercialization, if successful. The Company paid Alnylam &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;$25 million&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt; in an initial license payment, which the Company recorded as research and development expense. The Company has also agreed to pay up to an aggregate of &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;$180 million&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt; in success-based development and commercialization milestones. In addition, the Company has agreed to pay specified royalties on net sales of these products. Royalties to Alnylam are payable by the Company on a product-by-product and country-by-country basis until the last to occur of the expiration of patent rights in the applicable country that cover the applicable product, the expiration of non-patent regulatory exclusivities for such product in such country, and the twelfth anniversary of the first commercial sale of the product in such country, subject to reduction in specified circumstances. The Company is also responsible for paying royalties, and in some cases, milestone payments, owed by Alnylam to its licensors with respect to intellectual property covering these products.  As of June 30, 2013, other than the initial &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;$25 million&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt; license payment, the Company has not made any payments to Alnylam under the agreement.&lt;/font&gt;&lt;/div&gt;&lt;/div&gt;</NonNumbericText><FootnoteIndexer /><CurrencyCode /><CurrencySymbol /><IsIndependantCurrency>false</IsIndependantCurrency><ShowCurrencySymbol>false</ShowCurrencySymbol><DisplayDateInUSFormat>false</DisplayDateInUSFormat></Cell></Cells><ElementDataType>nonnum:textBlockItemType</ElementDataType><SimpleDataType>na</SimpleDataType><ElementDefenition>The entire disclosure for collaborative arrangements in which the entity is a participant, including a) information about the nature and purpose of such arrangements; b) its rights and obligations thereunder; c) the accounting policy for collaborative arrangements; and d) the income statement classification and amounts attributable to transactions arising from the collaborative arrangement between participants.</ElementDefenition><ElementReferences>Reference 1: http://www.xbrl.org/2003/role/presentationRef

 -Publisher FASB

 -Name Accounting Standards Codification

 -Topic 808

 -SubTopic 10

 -Section 50

 -Paragraph 1

 -URI http://asc.fasb.org/extlink&amp;oid=6931272&amp;loc=SL5834143-161434



</ElementReferences><IsTotalLabel>false</IsTotalLabel><UnitID>0</UnitID><Label>Collaboration Agreements</Label></Row></Rows><Footnotes /><IsEquityReport>false</IsEquityReport><ReportName>Collaboration Agreements (Notes)</ReportName><MonetaryRoundingLevel>UnKnown</MonetaryRoundingLevel><SharesRoundingLevel>UnKnown</SharesRoundingLevel><PerShareRoundingLevel>UnKnown</PerShareRoundingLevel><ExchangeRateRoundingLevel>UnKnown</ExchangeRateRoundingLevel><HasCustomUnits>true</HasCustomUnits><IsEmbedReport>false</IsEmbedReport><IsMultiCurrency>false</IsMultiCurrency><ReportType>Notes</ReportType><RoleURI>http://www.themedicinescompany.com/role/CollaborationAgreementsNotes</RoleURI><NumberOfCols>1</NumberOfCols><NumberOfRows>2</NumberOfRows></InstanceReport>
