<?xml version="1.0" encoding="us-ascii"?><InstanceReport xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema"><Version>2.2.0.25</Version><hasSegments>false</hasSegments><hasScenarios>false</hasScenarios><ReportLongName>1010 - Disclosure - Organization and Basis of Presentation</ReportLongName><DisplayLabelColumn>true</DisplayLabelColumn><ShowElementNames>false</ShowElementNames><RoundingOption /><HasEmbeddedReports>false</HasEmbeddedReports><Columns><Column><Id>1</Id><IsAbstractGroupTitle>false</IsAbstractGroupTitle><LabelColumn>false</LabelColumn><CurrencyCode>USD</CurrencyCode><FootnoteIndexer /><hasSegments>false</hasSegments><hasScenarios>false</hasScenarios><MCU><KeyName>1/1/2011 - 3/31/2011
USD ($)

USD ($) / shares
</KeyName><CurrencySymbol>$</CurrencySymbol><contextRef><ContextID>D2011Q1</ContextID><EntitySchema>http://www.sec.gov/CIK</EntitySchema><EntityValue>0001166036</EntityValue><PeriodDisplayName /><PeriodType>duration</PeriodType><PeriodStartDate>2011-01-01T00:00:00</PeriodStartDate><PeriodEndDate>2011-03-31T00:00:00</PeriodEndDate><Segments /><Scenarios /></contextRef><UPS><UnitProperty><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></UnitProperty><UnitProperty><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></UnitProperty><UnitProperty><UnitID>USDPerShare</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></UnitProperty></UPS><CurrencyCode>USD</CurrencyCode><OriginalCurrencyCode>USD</OriginalCurrencyCode></MCU><CurrencySymbol>$</CurrencySymbol><Labels><Label Id="1" Label="3 Months Ended" /><Label Id="2" Label="Mar. 31, 2011" /></Labels></Column></Columns><Rows><Row><Id>2</Id><IsAbstractGroupTitle>true</IsAbstractGroupTitle><Level>0</Level><ElementName>mwe_OrganizationAndBasisOfPresentationDisclosureAbstract</ElementName><ElementPrefix>mwe</ElementPrefix><IsBaseElement>false</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><IsEquityPrevioslyReportedAsRow>false</IsEquityPrevioslyReportedAsRow><IsEquityAdjustmentRow>false</IsEquityAdjustmentRow><IsBeginningBalance>false</IsBeginningBalance><IsEndingBalance>false</IsEndingBalance><IsReverseSign>false</IsReverseSign><PreferredLabelRole /><FootnoteIndexer /><Cells><Cell><Id>1</Id><IsNumeric>false</IsNumeric><IsRatio>false</IsRatio><DisplayZeroAsNone>false</DisplayZeroAsNone><NumericAmount>0</NumericAmount><RoundedNumericAmount>0</RoundedNumericAmount><NonNumbericText /><NonNumericTextHeader /><FootnoteIndexer /><CurrencyCode /><CurrencySymbol /><IsIndependantCurrency>false</IsIndependantCurrency><ShowCurrencySymbol>false</ShowCurrencySymbol><DisplayDateInUSFormat>false</DisplayDateInUSFormat><hasSegments>false</hasSegments><hasScenarios>false</hasScenarios></Cell></Cells><OriginalInstanceReportColumns /><Unit>Other</Unit><ElementDataType>xbrli:stringItemType</ElementDataType><SimpleDataType>string</SimpleDataType><ElementDefenition>No definition available.</ElementDefenition><IsTotalLabel>false</IsTotalLabel><IsEPS>false</IsEPS><Label>Organization and Basis of Presentation</Label></Row><Row><Id>3</Id><IsAbstractGroupTitle>false</IsAbstractGroupTitle><Level>0</Level><ElementName>us-gaap_OrganizationConsolidationAndPresentationOfFinancialStatementsDisclosureTextBlock</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><IsEquityPrevioslyReportedAsRow>false</IsEquityPrevioslyReportedAsRow><IsEquityAdjustmentRow>false</IsEquityAdjustmentRow><IsBeginningBalance>false</IsBeginningBalance><IsEndingBalance>false</IsEndingBalance><IsReverseSign>false</IsReverseSign><PreferredLabelRole>terselabel</PreferredLabelRole><FootnoteIndexer /><Cells><Cell><Id>1</Id><IsNumeric>false</IsNumeric><IsRatio>false</IsRatio><DisplayZeroAsNone>false</DisplayZeroAsNone><NumericAmount>0</NumericAmount><RoundedNumericAmount>0</RoundedNumericAmount><NonNumbericText>&lt;table style="font-size:10pt; font-family:'Times New Roman',times,serif;"&gt;
&lt;tr&gt;
&lt;td&gt;
&lt;p style="FONT-FAMILY: times"&gt;&lt;font size="2"&gt;&lt;b&gt;1. Organization and Basis of Presentation &lt;/b&gt;&lt;/font&gt;&lt;/p&gt;
&lt;p style="FONT-FAMILY: times"&gt;&lt;font size="2"&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;MarkWest Energy Partners,&amp;nbsp;L.P. was formed in 2002 as a Delaware limited partnership. The Partnership is engaged in the gathering, transportation and processing of natural gas; the transportation, fractionation, marketing and storage of NGLs; and the gathering and transportation of crude oil. The Partnership has extensive natural gas gathering, processing and transmission operations in the southwest, Gulf Coast, and northeast regions of the United States, including the Marcellus Shale, and is the largest natural gas processor and fractionator in the Appalachian region. &lt;/font&gt;&lt;/p&gt;
&lt;p style="FONT-FAMILY: times"&gt;&lt;font size="2"&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;These unaudited condensed consolidated financial statements have been prepared in accordance with the rules and regulations of the SEC for interim financial reporting. Accordingly, certain information and footnote disclosures normally included in financial statements prepared in accordance with GAAP have been condensed or omitted. These condensed consolidated financial statements should be read in conjunction with the Partnership's consolidated financial statements included in the Partnership's Annual Report on Form&amp;nbsp;10-K for the year ended December&amp;nbsp;31, 2010. In management's opinion, the Partnership has made all adjustments necessary for a fair presentation of its results of operations, financial position and cash flows for the periods shown. These adjustments are of a normal recurring nature. Finally, results for the three months ended March&amp;nbsp;31, 2011 are not necessarily indicative of results for the full year 2011, or any other future period. &lt;/font&gt;&lt;/p&gt;
&lt;p style="FONT-FAMILY: times"&gt;&lt;font size="2"&gt;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;The Partnership's unaudited condensed consolidated financial statements include all majority-owned or majority-controlled subsidiaries. In addition, MarkWest Liberty Midstream&amp;nbsp;&amp;amp; Resources L.L.C. ("MarkWest Liberty Midstream") and MarkWest Pioneer, L.L.C. ("MarkWest Pioneer"), variable interest entities for which the Partnership has been determined to be the primary beneficiary, are included in the condensed consolidated financial statements (see Note&amp;nbsp;4). All significant intercompany investments, accounts and transactions have been eliminated. Investments in which the Partnership exercises significant influence but does not control, and is not the primary beneficiary, are accounted for using the equity method. &lt;/font&gt;&lt;/p&gt;&lt;/td&gt;&lt;/tr&gt;&lt;/table&gt;
</NonNumbericText><NonNumericTextHeader>1. Organization and Basis of Presentation
&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;MarkWest Energy Partners,&amp;nbsp;L.P. was formed in 2002 as a Delaware</NonNumericTextHeader><FootnoteIndexer /><CurrencyCode /><CurrencySymbol /><IsIndependantCurrency>false</IsIndependantCurrency><ShowCurrencySymbol>false</ShowCurrencySymbol><DisplayDateInUSFormat>false</DisplayDateInUSFormat><hasSegments>false</hasSegments><hasScenarios>false</hasScenarios></Cell></Cells><OriginalInstanceReportColumns /><Unit>Other</Unit><ElementDataType>us-types:textBlockItemType</ElementDataType><SimpleDataType>string</SimpleDataType><ElementDefenition>Description containing the entire organization, consolidation and basis of presentation of financial statements disclosure. May be provided in more than one note to the financial statements, as long as users are provided with an understanding of (1) the significant judgments and assumptions made by an enterprise in determining whether it must consolidate a VIE and/or disclose information about its involvement with a VIE, (2) the nature of restrictions on a consolidated VIE's assets reported by an enterprise in its statement of financial position, including the carrying amounts of such assets, (3) the nature of, and changes in, the risks associated with an enterprise's involvement with the VIE, and (4) how an enterprise's involvement with the VIE affects the enterprise's financial position, financial performance, and cash flows.  Describes procedure if disclosures are provided in more than one note to the financial statements.</ElementDefenition><ElementReferences>Reference 1: http://www.xbrl.org/2003/role/presentationRef
 -Publisher FASB
 -Name FASB Staff Position (FSP)
 -Number FAS140-4 and FIN46(R)-8
 -Paragraph 8, C1, C7

Reference 2: http://www.xbrl.org/2003/role/presentationRef
 -Publisher AICPA
 -Name Accounting Research Bulletin (ARB)
 -Number 51
 -Paragraph 2-6

Reference 3: http://www.xbrl.org/2003/role/presentationRef
 -Publisher AICPA
 -Name Statement of Position (SOP)
 -Number 94-6
 -Paragraph 10

Reference 4: http://www.xbrl.org/2003/role/presentationRef
 -Publisher FASB
 -Name FASB Interpretation (FIN)
 -Number 46R
 -Paragraph 4, 14, 15

</ElementReferences><IsTotalLabel>false</IsTotalLabel><IsEPS>false</IsEPS><Label>Organization and Basis of Presentation</Label></Row></Rows><Footnotes /><NumberOfCols>1</NumberOfCols><NumberOfRows>2</NumberOfRows><ReportName>Organization and Basis of Presentation</ReportName><MonetaryRoundingLevel>UnKnown</MonetaryRoundingLevel><SharesRoundingLevel>UnKnown</SharesRoundingLevel><PerShareRoundingLevel>UnKnown</PerShareRoundingLevel><ExchangeRateRoundingLevel>UnKnown</ExchangeRateRoundingLevel><HasCustomUnits>false</HasCustomUnits><SharesShouldBeRounded>true</SharesShouldBeRounded></InstanceReport>
