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&lt;p style="TEXT-INDENT: -1in; MARGIN: 0in 0in 0pt 1in;"&gt;&lt;b&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt; FONT-WEIGHT: bold;" size="2"&gt;8. Commitments and Contingencies&lt;/font&gt;&lt;/b&gt;&lt;/p&gt;
&lt;p style="TEXT-INDENT: -1in; MARGIN: 0in 0in 0pt 1in;"&gt;&amp;#160;&lt;/p&gt;
&lt;p style="TEXT-INDENT: -1in; MARGIN: 0in 0in 0pt 1in;"&gt;&lt;b&gt;&lt;i&gt;&lt;font style="FONT-STYLE: italic; FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt; FONT-WEIGHT: bold;" size="2"&gt;Operating Leases&lt;/font&gt;&lt;/i&gt;&lt;/b&gt;&lt;/p&gt;
&lt;p style="TEXT-INDENT: -1in; MARGIN: 0in 0in 0pt 1in;"&gt;&amp;#160;&lt;/p&gt;
&lt;p style="TEXT-INDENT: 0.25in; MARGIN: 0in 0in 0pt;"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;The Company leases office space and equipment under various operating lease agreements.&lt;/font&gt;&lt;/p&gt;
&lt;p style="TEXT-INDENT: 0.25in; MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;
&lt;p style="TEXT-INDENT: 0.25in; MARGIN: 0in 0in 0pt;"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;In September&amp;#160;2004, the Company entered into an agreement with Vertex Pharmaceuticals to lease 53,323 square feet of office and laboratory space located on the fourth and fifth floors at 675 West Kendall Street, Cambridge, Massachusetts, for an initial term of 80 months, or the West Kendall Sublease. In November&amp;#160;2005, the Company amended the West Kendall Sublease to lease an additional 25,131 square feet through April&amp;#160;2011. In April&amp;#160;2010, the Company exercised its right to extend the West Kendall Sublease for one additional term of 48 months, ending April&amp;#160;2015, or on such other earlier date as provided in accordance with the West Kendall Sublease. During the extension term, which commenced on May&amp;#160;1, 2011, annual rental payments increased by approximately $1.2 million over the previous annual rental rate.&lt;/font&gt;&lt;/p&gt;
&lt;p style="TEXT-INDENT: 0.25in; MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;
&lt;p style="TEXT-INDENT: 0.25in; MARGIN: 0in 0in 0pt;"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;In December&amp;#160;2011, the Company entered into an agreement to lease 68,575 square feet of office and laboratory space located on the first and second floors at 320 Bent Street, Cambridge, Massachusetts, for a term of approximately 18 months, or the First Bent Street Sublease. The Company gained access to the subleased space in December&amp;#160;2011 and, consequently, the Company commenced expensing the applicable rent on a straight-line basis beginning in December&amp;#160;2011. Annual rental payments due under the First Bent Street Sublease are approximately $2.3 million.&lt;/font&gt;&lt;/p&gt;
&lt;p style="TEXT-INDENT: 0.25in; MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;
&lt;p style="TEXT-INDENT: 0.25in; MARGIN: 0in 0in 0pt;"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;On February&amp;#160;5, 2013, the Company and BMR-Rogers Street LLC, or BMR, entered into a lease agreement, or the Second Bent Street Lease, pursuant to which the Company will lease 104,678 square feet of office and laboratory space located in the basement and first and second floors at 320 Bent Street, Cambridge, Massachusetts, or the Premises, beginning on September&amp;#160;1, 2013 and ending on August&amp;#160;31, 2016. Annual rental payments due under the Second Bent Street Lease will be approximately $6.1 million during the first lease year, $6.2 million during the second lease year and $6.3 million during the third lease year. The Company will be required to provide a security deposit in cash or in the form of a letter of credit in the amount of $0.7 million.&lt;/font&gt;&lt;/p&gt;
&lt;p style="TEXT-INDENT: 0.25in; MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;
&lt;p style="TEXT-INDENT: 0.25in; MARGIN: 0in 0in 0pt;"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;BMR has agreed to pay the Company a tenant improvement allowance of $0.7 million for certain improvements that the Company will construct to the Premises.&lt;/font&gt;&lt;/p&gt;
&lt;p style="TEXT-INDENT: 0.25in; MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;
&lt;p style="TEXT-INDENT: 0.25in; MARGIN: 0in 0in 0pt;"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;The Company has two consecutive options to extend the term of the Second Bent Street Lease for the Premises for one year each at the then-current fair market value. In addition, the Company has two additional consecutive options to extend the term of the Second Bent Street Lease for five years each for the office and laboratory space located in the basement portion of the Premises at the then-current fair market value.&lt;/font&gt;&lt;/p&gt;
&lt;p style="TEXT-INDENT: 0.25in; MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;
&lt;p style="TEXT-INDENT: 0.25in; MARGIN: 0in 0in 0pt;"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;Total operating lease commitments as of June&amp;#160;30, 2013 are as follows (in thousands):&lt;/font&gt;&lt;/p&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;
&lt;table style="text-align:left;TEXT-ALIGN: left; WIDTH: 73.34%; BORDER-COLLAPSE: collapse; MARGIN-LEFT: 1in;" border="0" cellspacing="0" cellpadding="0" width="73%"&gt;

&lt;tr style="padding:0;PADDING-BOTTOM: 0px; PADDING-LEFT: 0px; PADDING-RIGHT: 0px; PADDING-TOP: 0px;"&gt;
&lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 78.88%; PADDING-RIGHT: 0in; PADDING-TOP: 0in;" valign="bottom" width="78%"&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;&lt;/td&gt;
&lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 3.4%; PADDING-RIGHT: 0in; PADDING-TOP: 0in;" valign="bottom" width="3%"&gt;
&lt;p style="TEXT-ALIGN: center; MARGIN: 0in 0in 0pt;" align="center"&gt;&amp;#160;&lt;/p&gt;&lt;/td&gt;
&lt;td style="BORDER-BOTTOM: windowtext 1pt solid; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 16.36%; PADDING-RIGHT: 0in; BORDER-TOP: medium none; BORDER-RIGHT: medium none; PADDING-TOP: 0in;" valign="bottom" width="16%" colspan="2"&gt;
&lt;p style="TEXT-ALIGN: center; MARGIN: 0in 0in 0pt;" align="center"&gt;&lt;b&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 8pt; FONT-WEIGHT: bold;" size="1"&gt;Operating&lt;br /&gt;
Leases&lt;/font&gt;&lt;/b&gt;&lt;/p&gt;&lt;/td&gt;
&lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 1.36%; PADDING-RIGHT: 0in; PADDING-TOP: 0in;" valign="bottom" width="1%"&gt;
&lt;p style="TEXT-ALIGN: center; MARGIN: 0in 0in 0pt;" align="center"&gt;&amp;#160;&lt;/p&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr style="padding:0;PADDING-BOTTOM: 0px; PADDING-LEFT: 0px; PADDING-RIGHT: 0px; PADDING-TOP: 0px;"&gt;
&lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 78.88%; PADDING-RIGHT: 0in; BACKGROUND: #cceeff; PADDING-TOP: 0in;" bgcolor="#CCEEFF" valign="bottom" width="78%"&gt;
&lt;p style="TEXT-INDENT: -10pt; MARGIN: 0in 0in 0pt 10pt;"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;July&amp;#160;1, 2013 &amp;#8212; December&amp;#160;31, 2013&lt;/font&gt;&lt;/p&gt;&lt;/td&gt;
&lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 3.4%; PADDING-RIGHT: 0in; BACKGROUND: #cceeff; PADDING-TOP: 0in;" bgcolor="#CCEEFF" valign="bottom" width="3%"&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;&lt;/td&gt;
&lt;td style="BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 1.3%; PADDING-RIGHT: 0in; BACKGROUND: #cceeff; BORDER-TOP: medium none; BORDER-RIGHT: medium none; PADDING-TOP: 0in;" bgcolor="#CCEEFF" valign="bottom" width="1%"&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;$&lt;/font&gt;&lt;/p&gt;&lt;/td&gt;
&lt;td style="BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 15.06%; PADDING-RIGHT: 0in; BACKGROUND: #cceeff; BORDER-TOP: windowtext 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 0in;" bgcolor="#CCEEFF" valign="bottom" width="15%"&gt;
&lt;p style="TEXT-ALIGN: right; MARGIN: 0in 0in 0pt;" align="right"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;5,047&lt;/font&gt;&lt;/p&gt;&lt;/td&gt;
&lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 1.36%; PADDING-RIGHT: 0in; BACKGROUND: #cceeff; PADDING-TOP: 0in;" bgcolor="#CCEEFF" valign="bottom" width="1%"&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr style="padding:0;PADDING-BOTTOM: 0px; PADDING-LEFT: 0px; PADDING-RIGHT: 0px; PADDING-TOP: 0px;"&gt;
&lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 78.88%; PADDING-RIGHT: 0in; PADDING-TOP: 0in;" valign="bottom" width="78%"&gt;
&lt;p style="TEXT-INDENT: -10pt; MARGIN: 0in 0in 0pt 10pt;"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;2014&lt;/font&gt;&lt;/p&gt;&lt;/td&gt;
&lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 3.4%; PADDING-RIGHT: 0in; PADDING-TOP: 0in;" valign="bottom" width="3%"&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;&lt;/td&gt;
&lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 16.36%; PADDING-RIGHT: 0in; PADDING-TOP: 0in;" valign="bottom" width="16%" colspan="2"&gt;
&lt;p style="TEXT-ALIGN: right; MARGIN: 0in 0in 0pt;" align="right"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;10,937&lt;/font&gt;&lt;/p&gt;&lt;/td&gt;
&lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 1.36%; PADDING-RIGHT: 0in; PADDING-TOP: 0in;" valign="bottom" width="1%"&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr style="padding:0;PADDING-BOTTOM: 0px; PADDING-LEFT: 0px; PADDING-RIGHT: 0px; PADDING-TOP: 0px;"&gt;
&lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 78.88%; PADDING-RIGHT: 0in; BACKGROUND: #cceeff; PADDING-TOP: 0in;" bgcolor="#CCEEFF" valign="bottom" width="78%"&gt;
&lt;p style="TEXT-INDENT: -10pt; MARGIN: 0in 0in 0pt 10pt;"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;2015&lt;/font&gt;&lt;/p&gt;&lt;/td&gt;
&lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 3.4%; PADDING-RIGHT: 0in; BACKGROUND: #cceeff; PADDING-TOP: 0in;" bgcolor="#CCEEFF" valign="bottom" width="3%"&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;&lt;/td&gt;
&lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 16.36%; PADDING-RIGHT: 0in; BACKGROUND: #cceeff; PADDING-TOP: 0in;" bgcolor="#CCEEFF" valign="bottom" width="16%" colspan="2"&gt;
&lt;p style="TEXT-ALIGN: right; MARGIN: 0in 0in 0pt;" align="right"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;7,870&lt;/font&gt;&lt;/p&gt;&lt;/td&gt;
&lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 1.36%; PADDING-RIGHT: 0in; BACKGROUND: #cceeff; PADDING-TOP: 0in;" bgcolor="#CCEEFF" valign="bottom" width="1%"&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr style="padding:0;PADDING-BOTTOM: 0px; PADDING-LEFT: 0px; PADDING-RIGHT: 0px; PADDING-TOP: 0px;"&gt;
&lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 78.88%; PADDING-RIGHT: 0in; PADDING-TOP: 0in;" valign="bottom" width="78%"&gt;
&lt;p style="TEXT-INDENT: -10pt; MARGIN: 0in 0in 0pt 10pt;"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;2016&lt;/font&gt;&lt;/p&gt;&lt;/td&gt;
&lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 3.4%; PADDING-RIGHT: 0in; PADDING-TOP: 0in;" valign="bottom" width="3%"&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;&lt;/td&gt;
&lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 16.36%; PADDING-RIGHT: 0in; PADDING-TOP: 0in;" valign="bottom" width="16%" colspan="2"&gt;
&lt;p style="TEXT-ALIGN: right; MARGIN: 0in 0in 0pt;" align="right"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;4,273&lt;/font&gt;&lt;/p&gt;&lt;/td&gt;
&lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 1.36%; PADDING-RIGHT: 0in; PADDING-TOP: 0in;" valign="bottom" width="1%"&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr style="padding:0;PADDING-BOTTOM: 0px; PADDING-LEFT: 0px; PADDING-RIGHT: 0px; PADDING-TOP: 0px;"&gt;
&lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 78.88%; PADDING-RIGHT: 0in; BACKGROUND: #cceeff; PADDING-TOP: 0in;" bgcolor="#CCEEFF" valign="bottom" width="78%"&gt;
&lt;p style="TEXT-INDENT: -10pt; MARGIN: 0in 0in 0pt 10pt;"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;2017&lt;/font&gt;&lt;/p&gt;&lt;/td&gt;
&lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 3.4%; PADDING-RIGHT: 0in; BACKGROUND: #cceeff; PADDING-TOP: 0in;" bgcolor="#CCEEFF" valign="bottom" width="3%"&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;&lt;/td&gt;
&lt;td style="BORDER-BOTTOM: windowtext 1pt solid; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 16.36%; PADDING-RIGHT: 0in; BACKGROUND: #cceeff; BORDER-TOP: medium none; BORDER-RIGHT: medium none; PADDING-TOP: 0in;" bgcolor="#CCEEFF" valign="bottom" width="16%" colspan="2"&gt;
&lt;p style="TEXT-ALIGN: right; MARGIN: 0in 0in 0pt;" align="right"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;62&lt;/font&gt;&lt;/p&gt;&lt;/td&gt;
&lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 1.36%; PADDING-RIGHT: 0in; BACKGROUND: #cceeff; PADDING-TOP: 0in;" bgcolor="#CCEEFF" valign="bottom" width="1%"&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr style="padding:0;PADDING-BOTTOM: 0px; PADDING-LEFT: 0px; PADDING-RIGHT: 0px; PADDING-TOP: 0px;"&gt;
&lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 78.88%; PADDING-RIGHT: 0in; PADDING-TOP: 0in;" valign="bottom" width="78%"&gt;
&lt;p style="TEXT-INDENT: -10pt; MARGIN: 0in 0in 0pt 10pt;"&gt;&amp;#160;&lt;/p&gt;&lt;/td&gt;
&lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 3.4%; PADDING-RIGHT: 0in; PADDING-TOP: 0in;" valign="bottom" width="3%"&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;&lt;/td&gt;
&lt;td style="BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 16.36%; PADDING-RIGHT: 0in; BORDER-TOP: medium none; BORDER-RIGHT: medium none; PADDING-TOP: 0in;" valign="bottom" width="16%" colspan="2"&gt;
&lt;p style="TEXT-ALIGN: right; MARGIN: 0in 0in 0pt;" align="right"&gt;&amp;#160;&lt;/p&gt;&lt;/td&gt;
&lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 1.36%; PADDING-RIGHT: 0in; PADDING-TOP: 0in;" valign="bottom" width="1%"&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;&lt;/td&gt;&lt;/tr&gt;
&lt;tr style="padding:0;PADDING-BOTTOM: 0px; PADDING-LEFT: 0px; PADDING-RIGHT: 0px; PADDING-TOP: 0px;"&gt;
&lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 78.88%; PADDING-RIGHT: 0in; BACKGROUND: #cceeff; PADDING-TOP: 0in;" bgcolor="#CCEEFF" valign="bottom" width="78%"&gt;
&lt;p style="TEXT-INDENT: -10pt; MARGIN: 0in 0in 0pt 10pt;"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;Total future minimum lease payments&lt;/font&gt;&lt;/p&gt;&lt;/td&gt;
&lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 3.4%; PADDING-RIGHT: 0in; BACKGROUND: #cceeff; PADDING-TOP: 0in;" bgcolor="#CCEEFF" valign="bottom" width="3%"&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;&lt;/td&gt;
&lt;td style="BORDER-BOTTOM: windowtext 2.25pt double; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 1.3%; PADDING-RIGHT: 0in; BACKGROUND: #cceeff; BORDER-TOP: medium none; BORDER-RIGHT: medium none; PADDING-TOP: 0in;" bgcolor="#CCEEFF" valign="bottom" width="1%"&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;$&lt;/font&gt;&lt;/p&gt;&lt;/td&gt;
&lt;td style="BORDER-BOTTOM: windowtext 2.25pt double; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 15.06%; PADDING-RIGHT: 0in; BACKGROUND: #cceeff; BORDER-TOP: medium none; BORDER-RIGHT: medium none; PADDING-TOP: 0in;" bgcolor="#CCEEFF" valign="bottom" width="15%"&gt;
&lt;p style="TEXT-ALIGN: right; MARGIN: 0in 0in 0pt;" align="right"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;28,189&lt;/font&gt;&lt;/p&gt;&lt;/td&gt;
&lt;td style="PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; WIDTH: 1.36%; PADDING-RIGHT: 0in; BACKGROUND: #cceeff; PADDING-TOP: 0in;" bgcolor="#CCEEFF" valign="bottom" width="1%"&gt;
&lt;p style="MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;&lt;/td&gt;&lt;/tr&gt;&lt;/table&gt;
&lt;p style="TEXT-INDENT: -1in; MARGIN: 0in 0in 0pt 1in;"&gt;&amp;#160;&lt;/p&gt;
&lt;p style="TEXT-INDENT: -1in; MARGIN: 0in 0in 0pt 1in;"&gt;&lt;b&gt;&lt;i&gt;&lt;font style="FONT-STYLE: italic; FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt; FONT-WEIGHT: bold;" size="2"&gt;Legal Contingencies&lt;/font&gt;&lt;/i&gt;&lt;/b&gt;&lt;/p&gt;
&lt;p style="TEXT-INDENT: -1in; MARGIN: 0in 0in 0pt 1in;"&gt;&amp;#160;&lt;/p&gt;
&lt;p style="TEXT-INDENT: 0.25in; MARGIN: 0in 0in 0pt;"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;On August&amp;#160;28, 2008, Teva Pharmaceuticals Industries&amp;#160;Ltd. and related entities, or Teva, and Yeda Research and Development Co.,&amp;#160;Ltd., or Yeda, filed suit against the Company and Sandoz in the United States Federal District Court in the Southern District of New York in response to the filing by Sandoz of the ANDA with a Paragraph&amp;#160;IV certification for M356. The suit alleged infringement related to four of the seven Orange Book patents listed for Copaxone and sought declaratory and injunctive relief that would prohibit the launch of the Company&amp;#8217;s product until the last to expire of these patents. The Company and Sandoz asserted various defenses and filed counterclaims for declaratory judgments to have all seven of the Orange Book patents as well as two additional patents in the same patent family adjudicated in the present lawsuit. Another company, Mylan&amp;#160;Inc., or Mylan, also has an ANDA for generic Copaxone under FDA review. In October&amp;#160;2009, Teva sued Mylan for patent infringement related to the Orange Book patents listed for Copaxone, and in October&amp;#160;2010, the court consolidated the Mylan case with the case against the Company and Sandoz. A trial on the issue of inequitable conduct occurred in July&amp;#160;2011 and the trial on the remaining issues occurred in September&amp;#160;2011 in the consolidated case. In June&amp;#160;2012, the Court issued its opinion and found all of the claims in the patents to be valid, enforceable and infringed. In July&amp;#160;2012, the Court issued a final order and permanent injunction prohibiting Sandoz and Mylan from infringing all of the patents in the suit. The Orange Book patents and one non-Orange book patent expire in May&amp;#160;2014 and one non-Orange Book patent expires in September&amp;#160;2015. In addition, the permanent injunction further restricts the FDA, pursuant to 35 U.S.C. section 271(e)(4)(A), from making the effective date of any final approval of the Sandoz or Mylan ANDA prior to the expiration of the Orange Book patents. In July&amp;#160;2012, the Company appealed the decision to the Court of Appeals for the Federal Circuit, or CAFC, and on July&amp;#160;26, 2013, the CAFC issued a written opinion invalidating several of the patents, including the one patent set to expire in 2015.&amp;#160; Several patents expiring in May&amp;#160;2014 remain in force. The CAFC remanded the case to the District Court to modify the injunction in light of the CAFC decision. Teva has announced its intention to seek further appellate review.&lt;/font&gt;&lt;/p&gt;
&lt;p style="TEXT-INDENT: 0.25in; MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;
&lt;p style="TEXT-INDENT: 0.25in; MARGIN: 0in 0in 0pt;"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;On December&amp;#160;10, 2009, in a separate action in the same court, Teva sued Sandoz, Novartis AG and the Company for patent infringement related to certain other non-Orange Book patents seeking declaratory and injunctive relief that would prohibit the launch of the Company&amp;#8217;s product until the last to expire of these patents as well as damages in the event that Sandoz has launched the product. In January&amp;#160;2010, the Company and Sandoz filed a motion to dismiss this second suit on several grounds. On July&amp;#160;16, 2013, the motion to dismiss the suit was granted.&lt;/font&gt;&lt;/p&gt;
&lt;p style="TEXT-INDENT: 0.25in; MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;
&lt;p style="TEXT-INDENT: 0.25in; MARGIN: 0in 0in 0pt;"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;If Teva seeks appellate review and the decision in the first suit is reversed on appeal, or if Teva seeks appellate review of the second suit and is successful in an appeal of the second suit, the final approval and launch of M356 could be significantly delayed until expiration of the relevant patent rights which could impair&amp;#160;the Company's&amp;#160;ability to commercialize M356 and materially harm the Company&amp;#8217;s business. There are no damages being sought in the first suit, and at this time the Company believes a loss is not probable in the second. Litigation involves many risks and uncertainties, and there is no assurance that Novartis AG, Sandoz or the Company will ultimately prevail in either lawsuit.&lt;/font&gt;&lt;/p&gt;
&lt;p style="TEXT-INDENT: 0.25in; MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;
&lt;p style="TEXT-INDENT: 0.25in; MARGIN: 0in 0in 0pt;"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;On September&amp;#160;21, 2011, the Company and Sandoz sued Amphastar, Actavis and International Medical Systems,&amp;#160;Ltd. (a wholly owned subsidiary of Amphastar) in the United States District Court for the District of Massachusetts for infringement of two of the Company&amp;#8217;s patents. Also in September, 2011, the Company filed a request for a temporary restraining order and preliminary injunction to prevent Amphastar, Actavis and International Medical Systems,&amp;#160;Ltd. from selling their enoxaparin product in the United States. In October&amp;#160;2011, the court granted the Company&amp;#8217;s motion for a preliminary injunction and entered an order enjoining Amphastar, Actavis and International Medical Systems,&amp;#160;Ltd. from advertising, offering for sale or selling their enoxaparin product in the United States until the conclusion of a trial on the merits and required the Company and Sandoz to post a security bond of $100 million in connection with the litigation. Amphastar, Actavis and International Medical Systems,&amp;#160;Ltd. appealed the decision and in January&amp;#160;2012, the CAFC stayed the preliminary injunction. In August&amp;#160;2012, the CAFC issued a written opinion vacating the preliminary injunction and remanding the case to the District Court. In September&amp;#160;2012, the Company filed a petition with the CAFC for a rehearing by the full court &lt;i&gt;en banc&lt;/i&gt;, which was denied. In February&amp;#160;2013, the Company filed a petition for a writ of certiorari for review of the CAFC decision by the United States Supreme Court and in June&amp;#160;2013 the Supreme Court denied the request.&lt;/font&gt;&lt;/p&gt;
&lt;p style="TEXT-INDENT: 0.25in; MARGIN: 0in 0in 0pt;"&gt;&amp;#160;&lt;/p&gt;
&lt;p style="TEXT-INDENT: 21pt; MARGIN: 0in 0in 0pt;"&gt;&lt;font style="FONT-FAMILY: Times New Roman; FONT-SIZE: 10pt;" size="2"&gt;In January&amp;#160;2013, Amphastar and Actavis filed a motion for summary judgment in the District Court following the decision from the CAFC. On July&amp;#160;19, 2013, the District Court granted the motion for summary judgment. The Company is evaluating whether to appeal the decision to the CAFC.&amp;#160; The collateral for the security bond posted in the litigation remains outstanding. In the event that the Company is not successful in any appeal, and Amphastar and Actavis are able to prove they suffered damages as a result of the preliminary injunction, the Company could be liable for damages for up to $35&amp;#160;million of the security bond. In June&amp;#160;2012, Amphastar filed a motion to increase the amount of the security bond, which the Company and Sandoz have opposed.&lt;/font&gt;&lt;/p&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>Represents the entire disclosure of capital and operating leases, license agreements and legal contingencies.</ElementDefenition><ElementReferences>No definition available.</ElementReferences><IsTotalLabel>false</IsTotalLabel><UnitID>0</UnitID><Label>Commitments and Contingencies</Label></Row></Rows><Footnotes /><IsEquityReport>false</IsEquityReport><ReportName>Commitments and Contingencies</ReportName><MonetaryRoundingLevel>UnKnown</MonetaryRoundingLevel><SharesRoundingLevel>UnKnown</SharesRoundingLevel><PerShareRoundingLevel>UnKnown</PerShareRoundingLevel><ExchangeRateRoundingLevel>UnKnown</ExchangeRateRoundingLevel><HasCustomUnits>true</HasCustomUnits><IsEmbedReport>false</IsEmbedReport><IsMultiCurrency>false</IsMultiCurrency><ReportType>Sheet</ReportType><RoleURI>http://www.momentapharma.com/role/DisclosureCommitmentsAndContingencies</RoleURI><NumberOfCols>1</NumberOfCols><NumberOfRows>2</NumberOfRows></InstanceReport>
