<?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>2112100 - Disclosure - Commitments and Contingencies</ReportLongName><DisplayLabelColumn>true</DisplayLabelColumn><ShowElementNames>false</ShowElementNames><RoundingOption /><HasEmbeddedReports>false</HasEmbeddedReports><Columns><Column FlagID="0"><Id>1</Id><IsAbstractGroupTitle>false</IsAbstractGroupTitle><LabelSeparator>

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</LabelSeparator><Level>1</Level><ElementName>us-gaap_CommitmentsAndContingenciesDisclosureAbstract</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><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>Commitments and Contingencies Disclosure [Abstract]</Label></Row><Row FlagID="0"><Id>2</Id><IsAbstractGroupTitle>false</IsAbstractGroupTitle><LabelSeparator>

</LabelSeparator><Level>2</Level><ElementName>us-gaap_CommitmentsAndContingenciesDisclosureTextBlock</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:120%;padding-top:18px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;font-weight:bold;"&gt;Commitments and Contingencies&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;padding-top:6px;text-align:left;text-indent:32px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;In the normal course of business, the Company has made certain guarantees and indemnities, under which it may be required to make payments to a guaranteed or indemnified party, in relation to certain transactions. The Company indemnifies other parties, including customers, lessors, and parties to other transactions with the Company, with respect to certain matters. The Company has agreed to hold the other party harmless against losses arising from certain events as defined within the particular contract, which may include, for example, litigation or claims arising from a breach of representations or covenants. In addition, the Company has entered into indemnification agreements with its executive officers and directors and the Company's bylaws contain similar indemnification obligations. Under these arrangements, the Company is obligated to indemnify, to the fullest extent permitted under applicable law, its current or former officers and directors for various amounts incurred with respect to actions, suits or proceedings in which they were made, or threatened to be made, a party as a result of acting as an officer or director.&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;padding-top:12px;text-indent:32px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;It is not possible to determine the maximum potential amount under these indemnification agreements due to the limited history of prior indemnification claims and the unique facts and circumstances involved in each particular agreement.&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;padding-top:12px;text-indent:32px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;Historically, payments made related to these indemnifications have been immaterial. At June 30, 2013, the Company has determined that &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;no&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt; liability is necessary related to these guarantees and indemnities.&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;padding-top:12px;text-align:left;text-indent:32px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;In connection with our acquisition of Medical Outsourcing Services,&amp;#160;LLC (&amp;#8220;MOS&amp;#8221;) in the third quarter of 2008, we subsequently identified a Medicare billing practice related to a portion of MOS's retail billing operations that raised compliance issues under Medicare reimbursement guidelines. The practice was in place before the acquisition and was discontinued when we became aware of it. In accordance with our corporate compliance program, we entered into discussions with representatives of the federal government to advise them of the issue and seek guidance on appropriate next steps. &lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;font-size:8pt;"&gt;&lt;font style="font-family:inherit;font-size:8pt;"&gt;&amp;#160;&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;text-indent:32px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;In June 2010, the Company commenced arbitration proceedings against the former owners of MOS related to the Medicare billing matter, in addition to certain other indemnification issues. In the arbitration, the Company asserted claims of fraud and breach of representations and warranties.&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;padding-top:12px;text-indent:32px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;On December&amp;#160;29, 2011, the Company received notice of an award by the arbitration panel, which awarded the Company &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;$2,527&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt; in damages for breach of contract claims, plus prejudgment interest at &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;9%&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt; under New York law from July&amp;#160;29, 2008 (which interest continues to accrue until the award is paid in full); &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;$255&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt; for &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;two&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt; other indemnification claims; &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;$1,453&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt; for attorneys&amp;#8217; fees and expenses; and &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;$110&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt; for arbitration expenses. The award also provides that approximately &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;$1,300&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt; of a remaining indemnification cap created in connection with the acquisition is available for future indemnification claims, including with respect to the potential government claim discussed above, and must be satisfied by the former owners of MOS. On January&amp;#160;25, 2012, one of the former owners of MOS paid &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;$665&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt; to the Company, and on February&amp;#160;17, 2012, the same owner released &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;$592&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt; to the Company from amounts held in an indemnification escrow related to the acquisition. On January&amp;#160;25, 2012, the Company filed an action in the United States District Court for the Northern District of Illinois to confirm the award as a judgment against the other former owner of MOS that has refused to satisfy its obligations under the award. &lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;padding-top:12px;text-align:left;text-indent:32px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;In the first quarter of 2013, the former owners of MOS paid &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;$1,198&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt; which amount represented the remaining amount of the indemnification cap created in connection with the acquisition.&amp;#160; This amount was in addition to &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;$5,300&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt; we already recovered from the former owners of MOS in connection with the arbitration award against them.&amp;#160; With these final payments totaling &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;$1,198&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;, the former owners of MOS have now fully satisfied their obligations to us under the arbitration award.&amp;#160; Following receipt of the final payments from the former owners of MOS, we then entered into a settlement agreement to resolve the government's investigation of the Medicare billing practices engaged in by MOS prior to our acquisition.&amp;#160; Under the terms of the settlement agreement, we paid &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;$2,400&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt; to the government, which amount was paid primarily from the funds recovered in the arbitration from the former owners of MOS.&amp;#160; &lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;padding-top:12px;text-indent:32px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;In June 2012, Pacific Coast Cardiology (&amp;#8220;PCC&amp;#8221;) d/b/a Pacific Coast Imaging, Emanuel Shaoulian, MD, Inc., and Michael&amp;#160;M.&amp;#160;Radin, MD, Inc. filed a lawsuit in California state court against the Company and other defendants. The complaint asserts a number of claims related to the Company&amp;#8217;s decision not to purchase PCC in 2010, and also separately seeks a determination regarding an amount the Company contends is owed to it by PCC pursuant to a previous contractual arrangement. Plaintiffs are seeking monetary and punitive damages. The Company intends to vigorously defend against the claims asserted in this lawsuit. The Company has not recorded an expense related to any potential damages in connection with this matter because any potential loss is not probable or reasonably estimable.&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;padding-top:12px;text-align:left;text-indent:32px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;On November 9, 2012, USR a subsidiary of Alliance Healthcare Services, Inc. (the &amp;#8220;Company&amp;#8221;), received a grand jury subpoena issued by the United States Attorney's Office for the Middle District of Tennessee seeking documents related to USR and its financial relationships with physicians and other healthcare providers.  The Company and USR are cooperating fully with the inquiry.  The Company is currently unable to predict the timing or outcome of this matter, however, it is not unusual for such matters to continue for a considerable period of time.  Responding to this matter will require management's attention and likely result in significant legal expense.  To our knowledge, the federal government has not initiated any proceedings against us at this time.&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;padding-top:12px;text-align:left;text-indent:32px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;On March 27, 2013, Alliance was served with a lawsuit filed in U.S. District Court for the Northern District of Mississippi by Superior MRI Services, Inc.&amp;#160; The plaintiff is an alleged successor in interest to a former local competitor, P&amp;amp;L Contracting, Inc.&amp;#160; Plaintiff alleges Alliance disregarded Mississippi Certificate of Need ("CON") rules and regulations by operating without obtaining the appropriate authority, and is seeking in excess of &lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;color:#000000;text-decoration:none;"&gt;$1,000&lt;/font&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt; in damages as well as requesting injunctive relief.&amp;#160; The Company intends to vigorously defend against the claims asserted in this lawsuit. The Company has not recorded an expense related to any potential damages in connection with this matter because any potential loss is not probable or reasonably estimable.&lt;/font&gt;&lt;/div&gt;&lt;div style="line-height:120%;padding-top:12px;text-indent:32px;font-size:10pt;"&gt;&lt;font style="font-family:inherit;font-size:10pt;"&gt;The Company from time to time is involved in routine litigation and regulatory matters incidental to the conduct of its business. 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