**United
                  States Securities and Exchange Commission****Washington,
                  D.C. 20549****Form
                  10-KSB/A**Amendment
                  No. 1 to Form
                  10-KSB(Mark
                  One)**R**
              **ANNUAL
                  REPORT UNDER SECTION 13 OR 15 (d) OF THE****SECURITIES
                  EXCHANGE ACT OF 1934**For
                  the fiscal year ended December 31, 2006o
              **TRANSITION
                  REPORT UNDER SECTION 13 OR 15 (d) OF THE SECURITIES EXCHANGE ACT
                  OF
                  1934**For
                  the transition period from _____ to _____Commission
                  file number 333-105811**ATLAS
                  AMERICA PUBLIC #12-2003 Limited Partnership**(Name
                  of small business issuer in its
                  charter)
 
 **Delaware**
              
              **54-2113989**(State
                  or other jurisdiction of
              
              (I.R.S.
                  EmployerIncorporation
                  or organization)
              
              Identification
                  No)311
                  Rouser Rd.
              
              Zip
                  CodeMoon
                  Township, PA
              
              15108(address
                  of principal executive offices)Issuer's
                  telephone number**(412)
                  262-2830**Securities
                  registered under Section 12(b) of the Exchange Act.Title
                  of each class
              
              Name
                  of each exchange on which registeredNone
              
              NoneSecurities
                  registered under Section 12(g) of the Exchange Act Investor General
                  Partner Units and Limited Partner Units(Title
                  of Class)
 
 Check
        whether the issuer (1) filed all reports required to be filed by Section
        13 or
        15(d) of the Exchange Act during the past 12 months (or for such shorter
        period
        that the registrant was required to file such reports), and (2) has been
        subject
        to such filing requirements for the past 90 days Yes R
 
 Check
        if
        there is no disclosure of delinquent filers in response to Item 405 of
        Regulation S-B contained in this form, and no disclosure will be contained,
        to
        the best of registrant's knowledge, in definitive proxy or information
        statements incorporated by reference in Part III of this Form 10-KSB or any
        amendment to this Form 10-KSB. R
 
 State
        issuer's revenues for its most recent fiscal year $8,561,600
 
 State
        the
        aggregate market value of the voting and non-voting common equity held by
        non-affiliates computed by reference to the price at which the common equity
        was
        sold, or the average bid and asked price of such common equity, as of a
        specified date within the past 60 days. (See definition of affiliate in Rule
        12b-2 of the Exchange Act.)
 
 Indicate
        by check mark whether the registrant is a shell company (as defined in Rule
        12b-2 of the Exchange Act).
 Yes o No R
 
 Transitional
        Small Business Disclosure Format (check one): Yes o No R
 
 .
  Explanatory
        Note
  We
        are
        filing this Amendment No.1 to our Annual Report on Form 10-KSB (“Amendment
        No.1”) for the year ended December 31, 2006. The Annual Report on Form 10-KSB
        was originally filed on April 2, 2007 (the “Original Filing”). Amendment No. 1
        is being filed to recognize a signature date change due to a clerical error
        from
        March 30, 2006 to March 30, 2007 on the auditor’s report. Amendment No. 1 amends
        Item 7 Financial Statements, the auditor’s report, of the Original Filing to
        reflect the date change and for the convenience of the reader, sets forth
        the
        remainder of Item 7 and Exhibits in their entirety.
  Except
        as
        described above, no other information in Amendment No. 1 is amended hereby.
        Amendment No. 1 does not reflect events occurring after the date of the Original
        Filing or modify or update those disclosures affected by subsequent events.
        Accordingly, Amendment No. 1 should be read in conjunction with our other
        filings made with the SEC subsequent to the date of the Original
        Filing.
 
  2
  
 
 
 **ITEM
        7.  FINANCIAL
        STATEMENTS**
 
 
 
 **REPORT
        OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM**
 
 
 To
        the
        Partners of
 Atlas
          America Public #12-2003 Limited Partnership
 
 We
          have
          audited the accompanying balance sheets of Atlas America Public #12-2003
          Limited
          Partnership (a Delaware Limited Partnership) as of December 31, 2006 and
          2005,
          and the related statements of operations, comprehensive income, changes
          in
          partners’ capital, and cash flows for the years then ended. These financial
          statements are the responsibility of the Partnership’s management. Our
          responsibility is to express an opinion
          on these financial statements based on our audits.
 
 We
          conducted our audits in accordance with the standards of the Public Company
          Accounting Oversight Board (United States). ** Those
          standards require that we plan and perform the audit
          to
          obtain reasonable assurance about whether the financial statements are
          free of
          material misstatement.**The
          Partnership is not required to have, nor were we engaged to perform an audit
          of
          its internal control over financial reporting.**Our audit
          included consideration of internal control over financial reporting as
          a basis
          for designing audit
          procedures that are appropriate in the circumstances, but not for the purpose
          of
          expressing an opinion
          on the effectiveness of the Partnership’s internal control over financial
          reporting.**Accordingly,
          we express no such opinion.**An audit
          also includes examining, on a test basis, evidence supporting the amounts
          and
          disclosures in the financial statements, assessing the accounting principles
          used and significant estimates made by management, as well as evaluating
          the
          overall financial statement presentation.**We
          believe that our audits provide a reasonable basis for our opinion.
 
 In
          our
          opinion, the financial statements referred to above present fairly, in
          all
          material respects, the financial position of Atlas America Public #12-2003
          Limited Partnership as of December 31, 2006 and 2005, and the results of
          its
          operations and its cash flows for the years then ended in conformity with
          accounting principles generally accepted in the United States of
          America.
 
 /s/
          GRANT
          THORNTON LLP
  Cleveland,
          Ohio
 March
          30,
          2007
 3
 
 **ATLAS
        AMERICA PUBLIC #12-2003 LIMITED PARTNERSHIP**
 **BALANCE
        SHEETS**
 **DECEMBER
        31,**
 
 
 **2006**
              
              **2005****ASSETS**Current
                  assets:Cash
                  and cash equivalents
              
              $
              1,041,200
              
              $
              1,938,700Accounts
                  receivable affiliate
              
              
              1,319,600
              
              
              3,249,700Hedge
                  receivable short-term-affiliate
              
              
              1,176,900
              
              
              161,900Total
                  current assets
              
              
              3,537,700
              
              
              5,350,300Oil
                  and gas properties, net
              
              
              33,479,600
              
              
              41,014,300Hedge
                  receivable long-term-affiliate
              
              
              1,016,100
              
              
              ―34,495,700
              
              
              41,014,300$
              38,033,400
              
              $
              46,364,600**LIABILITIES
                  AND PARTNERS' CAPITAL**Current
                  liabilities:Accrued
                  liabilities
              
              $
              18,000
              
              $
              33,000Hedge
                  liability short-term-affiliate
              
              
              7,300
              
              
              15,800Total
                  current liabilities
              
              
              25,300
              
              
              48,800Asset
                  retirement obligation
              
              
              1,949,500
              
              
              1,894,900Hedge
                  liability long-term-affiliate
              
              
              163,500
              
              
              708,400Partners'
                  capital:Managing
                  general partner
              
              
              10,158,200
              
              
              11,997,500Limited
                  partners (4,024 units)
              
              
              23,908,300
              
              
              32,277,300Accumulated
                  other comprehensive earnings (loss)
              
              
              1,828,600
              
              
              (562,300
              )35,895,100
              
              
              43,712,500$
              38,033,400
              
              $
              46,364,600
 
 
 
 
 The
        accompanying notes are an integral part of these financial
        statements.
  4
  
 **ATLAS
        AMERICA PUBLIC #12-2003 LIMITED PARTNERSHIP**
 **STATEMENTS
        OF OPERATIONS**
 **YEARS
        ENDED DECEMBER 31, 2006 AND 2005**
 
 **2006**
                
                **2005****REVENUES**Natural
                    gas and oil
                
                $
                8,510,100
                
                $
                13,047,500Interest
                    income
                
                
                51,500
                
                
                34,600Total
                    revenues
                
                
                8,561,600
                
                
                13,082,100**COSTS
                    AND EXPENSES**Production
                
                
                1,780,800
                
                
                1,512,100Depletion
                
                
                3,830,400
                
                
                7,056,100Impairment
                    of oil and gas properties
                
                
                3,466,200
                
                
                ─Accretion
                    of asset retirement obligation
                
                
                113,800
                
                
                71,100General
                    and administrative
                
                
                226,000
                
                
                228,400Total
                    expenses
                
                
                9,417,200
                
                
                8,867,700**Net
                    (loss) earnings**
                
                $
                (855,600
                )
                $
                4,214,400**Allocation
                    of net (loss) earnings:**Managing
                    general partner
                
                $
                1,429,100
                
                $
                2,957,200Limited
                    partners
                
                $
                (2,284,700
                )
                $
                1,257,200Net
                    (loss) earnings per limited partnership unit
                
                $
                (568
                )
                $
                312
 
 
 The
        accompanying notes are an integral part of these financial
        statements
  5
  
 **ATLAS
        AMERICA PUBLIC #12-2003 LIMITED PARTNERSHIP**
 **STATEMENTS
        OF COMPREHENSIVE INCOME (LOSS)**
 **YEARS
        ENDED DECEMBER 31, 2006 AND 2005**
 
 
 **December
                  31,****2006**
              
              **2005**Net
                  (loss) earnings
              
              $
              (855,600
              )
              $
              4,214,400Other
                  comprehensive income (loss):Unrealized
                  holding gain (loss) on hedging contracts
              
              
              3,370,400
              
              
              (502,900
              )Less:
                  reclassification adjustment for gains realized in net
                  earnings
              
              
              (979,500
              )
              
              (59,400
              )Total
                  other comprehensive income (loss)
              
              
              2,390,900
              
              
              (562,300
              )Comprehensive
                  income
              
              $
              1,535,300
              
              $
              3,652,100
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 The
        accompanying notes are an integral part of these financial
        statements
 
  6
  
 **ATLAS
        AMERICA PUBLIC #12-2003 LIMITED PARTNERSHIP**
 **STATEMENTS
        OF CHANGES IN PARTNERS' CAPITAL ACCOUNTS**
 **YEARS
        ENDED DECEMBER 31, 2006 AND 2005**
 
 **Managing**
              
              
              
              **Accumulated****General**
              
              **Limited**
              
              **Other
                  Comprehensive****Partner**
              
              **Partners**
              
              **(Loss)
                  Income**
              
              **Total****Balance
                  at December 31, 2004**
              
              $
              11,945,500
              
              $
              38,772,000
              
              $
              ―
              
              $
              50,717,500Participation
                  in revenue and expenses:Net
                  production revenues
              
              
              4,037,400
              
              
              7,498,000
              
              
              ―
              
              
              11,535,400Interest
                  income
              
              
              12,100
              
              
              22,500
              
              
              ―
              
              
              34,600Depletion
              
              
              (987,600
              )
              
              (6,068,500
              )
              
              ―
              
              
              (7,056,100
              )Accretion
                  of asset retirement obligation
              
              
              (24,900
              )
              
              (46,200
              )
              
              ―
              
              
              (71,100
              )General
                  and administrative
              
              
              (79,800
              )
              
              (148,600
              )
              
              ―
              
              
              (228,400
              )Net
                  earnings
              
              
              2,957,200
              
              
              1,257,200
              
              
              ―
              
              
              4,214,400Managing
                  general partner adjusted asset contribution
              
              
              1,149,500
              
              
              ―
              
              
              ―
              
              
              1,149,500Other
                  comprehensive loss
              
              
              ―
              
              
              ―
              
              
              (562,300
              )
              
              (562,300
              )Distributions
                  to partners
              
              
              (4,054,700
              )
              
              (7,751,900
              )
              
              ―
              
              
              (11,806,600
              )**Balance
                  at December 31, 2005**
              
              $
              11,997,500
              
              $
              32,277,300
              
              $
              (562,300
              )
              $
              43,712,500Participation
                  in revenue and expenses:Net
                  production revenues
              
              
              2,355,300
              
              
              4,374,000
              
              
              ─
              
              
              6,729,300Interest
                  income
              
              
              18,000
              
              
              33,500
              
              
              ─
              
              
              51,500Impairment
                  of oil and gas properties
              
              
              (392,000
              )
              
              (3,074,200
              )
              
              ─
              
              
              (3,466,200
              )Depletion
              
              
              (433,300
              )
              
              (3,397,100
              )
              
              ─
              
              
              (3,830,400
              )Accretion
                  of asset retirement obligation
              
              
              (39,800
              )
              
              (74,000
              )
              
              ─
              
              
              (113,800
              )General
                  and administrative
              
              
              (79,100
              )
              
              (146,900
              )
              
              ─
              
              
              (226,000
              )Net
                  earnings (loss)
              
              
              1,429,100
              
              
              (2,284,700
              )
              
              ─
              
              
              (855,600
              )Other
                  comprehensive income
              
              
              ─
              
              
              ─
              
              
              2,390,900
              
              
              2,390,900Distributions
                  to partners
              
              
              (3,268,400
              )
              
              (6,084,300
              )
              
              ─
              
              
              (9,352,700
              )**Balance
                  at December 31, 2006**
              
              $
              10,158,200
              
              $
              23,908,300
              
              $
              1,828,600
              
              $
              35,895,100
 
 
 The
        accompanying notes are an integral part of these financial
        statements.
  7
  
 
 **ATLAS
        AMERICA PUBLIC #12-2003 LIMITED PARTNERSHIP**
 **STATEMENTS
        OF CASH FLOWS**
 **YEARS
        ENDED DECEMBER 31, 2006 AND 2005**
 
 **2006**
              
              **2005****Cash
                  flows from operating activities:**Net
                  (loss) earnings
              
              $
              (855,600
              )
              $
              4,214,400Adjustments
                  to reconcile net (loss) earnings to net cash provided by operating
                  activities:Depletion
              
              
              3,830,400
              
              
              7,056,100Impairment
                  of oil and gas properties
              
              
              3,466,200
              
              
              ─Accretion
                  of asset retirement obligation
              
              
              113,800
              
              
              71,100Decrease
                  in accounts receivable - affiliate
              
              
              1,930,100
              
              
              1,366,900(Decrease)
                  increase in accrued liabilities
              
              
              (15,000
              )
              
              12,600Net
                  cash provided by operating activities
              
              
              8,469,900
              
              
              12,721,100**Cash
                  flows from investing activities:**Sale
                  of tangible equipment
              
              
              1,200
              
              
              4,000Purchase
                  of tangible equipment
              
              
              (15,900
              )
              
              (4,300
              )Net
                  cash used in investing activities
              
              
              (14,700
              )
              
              (300
              )**Cash
                  flows from financing activities:**Distributions
                  to partners
              
              
              (9,352,700
              )
              
              (11,806,600
              )Net
                  cash used in financing activities
              
              
              (9,352,700
              )
              
              (11,806,600
              )Net
                  (decrease) increase in cash and cash equivalents
              
              
              (897,500
              )
              
              914,200Cash
                  and cash equivalents at beginning of period
              
              
              1,938,700
              
              
              1,024,500Cash
                  and cash equivalents end of period
              
              $
              1,041,200
              
              $
              1,938,700**Supplemental
                  Schedule of non-cash investing and financing
                  activities:**Managing
                  General Partner adjusted asset contributions:Tangible
                  equipment costs included in oil and gas properties
              
              $
              ─
              
              $
              229,100Intangible
                  drilling costs included in oil and gas properties
              
              
              ─
              
              
              920,400$
              ─
              
              $
              1,149,500Asset
                  retirement obligation
              
              $
              (59,200
              )
              $
              638,400$
              (59,200
              )
              $
              638,400
 
 The
        accompanying notes are an integral part of these financial
        statements.
  8
  
 
 **ATLAS
        AMERICA PUBLIC #12-2003 LIMITED PARTNERSHIP**
 **NOTES
        TO FINANCIAL STATEMENTS**
 **DECEMBER
        31, 2006**
 
 **NOTE
        1 - DESCRIPTION OF BUSINESS**
 
 Atlas
        America Public #12-2003 Limited Partnership (the “Partnership”) is a Delaware
        Limited Partnership which includes Atlas Resources, LLC of Pittsburgh,
        Pennsylvania, as Managing General Partner (“MGP”) and Operator, and 1,121
        Limited Partners. The Partnership was formed on October 17, 2003 to drill
        and
        operate gas wells located primarily in western Pennsylvania. At December
        31,
        2006, the Partnership had various working interests in 227 gross
        wells.
  In
          March
          2006, Atlas Resources, Inc., the Partnership's MGP was merged into a
          newly-formed limited liability company, Atlas Resources, LLC, which became
          an
          indirect subsidiary of Atlas Energy Resources, LLC, a newly-formed subsidiary
          of
          Atlas America, Inc. Atlas Resources, LLC, now serves as the Partnership’s MGP.
          In December 2006, Atlas America, Inc. contributed substantially all of
          its
          natural gas and oil exploration and production assets into Atlas Energy
          Resources, LLC.
  **NOTE
        2 - SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES**
 
 A
        summary
        of significant accounting policies applied in the preparation of the
        accompanying financial statements follows:
 
 **Basis
        of Accounting**
 
 The
        financial statements are prepared in accordance with accounting principles
        generally accepted in the United States of America.
 
 **Use
        of Estimates**
 
 Preparation
        of financial statements in conformity with accounting principles generally
        accepted in the United States of America requires management to make estimates
        and assumptions that affect the reported amounts of assets and liabilities
        and
        the disclosure of contingent assets and liabilities as of the date of the
        financial statements and the reported amounts of revenues, costs and expenses
        during the reporting period. Actual results could differ from these
        estimates.
 
 **Reclassifications**
 
 Certain
        reclassifications have been made to the 2005 financial statements to conform
        to
        the 2006 presentation.
 
 **Receivables**
 
 In
        evaluating the need for an allowance for possible losses, the MGP performs
        ongoing credit evaluations of its customers and adjusts credit limits based
        upon
        payment history and the customer's current creditworthiness, as determined
        by
        review of its customers' credit information. Credit is extended on an unsecured
        basis to many of its energy customers. At December 31, 2006 and 2005 the
        Partnership's MGP's credit evaluation indicated that the Partnership has
        no need
        for an allowance for possible losses.
  9
  
 **ATLAS
        AMERICA PUBLIC #12-2003 LIMITED PARTNERSHIP**
 **NOTES
        TO FINANCIAL STATEMENTS - (Continued)**
 **DECEMBER
        31, 2006**
 
 **NOTE
        2 - SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES (Continued)**
 
 **Revenue
        Recognition**
 
 Revenues
        from sales of natural gas and oil are recognized by the Partnership when
        the gas
        and oil have been delivered to the purchaser. The Partnership's natural gas
        is
        sold under various contracts entered into by its MGP. Virtually all of our
        MGP's
        contract pricing provisions are tied to a market index, with certain adjustments
        based on, among other factors, whether a well delivers to a gathering or
        transmission line, quality of natural gas and prevailing supply and demand
        conditions, so that the price the Partnership receives from the sale of its
        natural gas fluctuates to remain competitive with natural gas supplies generally
        available in the market.
 
 Because
        there are timing differences between the delivery the Partnership's natural
        gas
        and oil and its receipt of a delivery statement, the Partnership has unbilled
        revenues. These revenues are accrued based on volumetric data from its records
        and its estimates of the related transportation and compression fees which
        are,
        in turn, based upon applicable product prices. The Partnership had unbilled
        trade receivables of $918,400 at December 31, 2006 and $2,015,800 at December
        31, 2005, which are included in accounts receivable - affiliate on the
        Partnership's balance sheets.
 
 **Fair
        Value of Financial Instruments**
 
 For
        cash,
        receivables and payables, the carrying amounts approximate fair values because
        of the short maturities of these instruments.
 
 For
        derivatives the carrying value approximates fair value because they have
        been
        marked to market.
 
 **Supplemental
        Cash Flow Information**
 
 The
        Partnership considers temporary investments with a maturity at the date of
        acquisition of 90 days or less to be cash equivalents. No cash was paid by
        the
        Partnership for interest or income taxes for the years ended December 31,
        2006
        and 2005.
 
 **Concentration
        of Credit Risk**
 
 Financial
        instruments, which potentially subject the Partnership to concentrations
        of
        credit risk, consist principally of periodic temporary investments of cash
        and
        cash equivalents. The Partnership places its temporary cash investments in
        deposits with high-quality financial institutions. At December 31, 2006,
        the
        Partnership had $1,070,900 in deposits at one bank of which $970,900 was
        over
        the insurance limit of the Federal Deposit Insurance Corporation and at December
        31, 2005 the Partnership had $1,988,300 in deposits at one bank of which
        $1,888,300 was over the insurance limit of the Federal Deposit Insurance
        Corporation. No losses have been experienced on such investments.
 
 **Comprehensive
        Income**
 
 Comprehensive
        income includes net income and all other changes in equity of a business
        during
        a period from non-owner sources that, under accounting principles generally
        accepted in the United States of America, have not been recognized in the
        calculation of net income. For the Partnership this includes only changes
        in the
        fair value of unrealized hedging gains and losses.
  10
  
 **ATLAS
        AMERICA PUBLIC #12-2003 LIMITED PARTNERSHIP**
 **NOTES
        TO FINANCIAL STATEMENTS - (Continued)**
 **DECEMBER
        31, 2006**
 
 **NOTE
        2 - SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES (Continued)**
 
 **Property
        and Equipment**
 
 Property
        and equipment are stated at cost. Depletion is based on cost less estimated
        salvage value primarily using the unit-of-production method over the assets'
        estimated useful lives. Maintenance and repairs are expensed as incurred.
        Major
        renewals and improvements that extend the useful lives of property are
        capitalized. Oil and gas properties consist of the following at the dates
        indicated:
 
 **December
                  31,****2006**
              
              **2005**Mineral
                  interest in properties:Proved
                  properties
              
              $
              1,169,700
              
              $
              1,169,700Wells
                  and related equipment
              
              
              49,132,700
              
              
              52,837,00050,302,400
              
              
              54,006,700Accumulated
                  depletion of oil and gas properties
              
              
              (16,822,800
              )
              
              (12,992,400
              )$
              33,479,600
              
              $
              41,014,300
 
 **Oil
        and Gas Properties**
 
 The
        Partnership uses the successful efforts method of accounting for oil and
        gas
        producing activities. Costs to acquire mineral interests in oil and gas
        properties and to drill and equip wells are capitalized. Oil is converted
        to gas
        equivalent basis (“mcfe”) at the rate of one barrel equals 6 mcf.
 
 The
        Partnership's long-lived assets are reviewed for impairment at least annually
        or
        whenever events or changes in circumstances indicate that the carrying amount
        of
        an asset may not be recoverable. Long-lived assets are reviewed for potential
        impairments at the lowest levels for which there are identifiable cash flows.
        The review is done by determining if the historical cost of proved properties
        less the applicable accumulated depreciation, depletion and amortization
        and
        asset retirement obligation is less than the estimated expected undiscounted
        future cash flows. The expected future cash flows are estimated based on
        the
        Partnership's plans to continue to produce and develop proved reserves. The
        estimated future level of production is based on assumptions surrounding
        future
        levels of prices and costs, field decline rates, market demand and supply,
        and
        the economic and regulatory climates. If the carrying value exceeds such
        undisounted cash flows, an impairment loss is recognized for the difference
        between the estimated fair market value and the carrying value of the
        assets.  The fair market value is determined as the present value of future
        net revenues from the production of proved reserves discounted using as annual
        discount rate of 10% and the 12 month NYMEX forward looking strip
        price for natural gas.  As a result of this assessment an impairment loss
        of $3,466,200, net of an offsetting gain in other comprehensive income of
        $193,600 was recognized in 2006.
 
 Upon
        the
        sale or retirement of a complete or partial unit of a proved property, the
        cost
        is eliminated from the property accounts, and the resultant gain or loss
        is
        reclassified to accumulated depletion. Upon the sale of an entire interest
        where
        the property had been assessed for impairment a gain or loss is recognized
        in
        the statements of operations.
  11
  
 **ATLAS
        AMERICA PUBLIC #12-2003 LIMITED PARTNERSHIP**
 **NOTES
        TO FINANCIAL STATEMENTS - (Continued)**
 **DECEMBER
        31, 2006**
 
 **NOTE
        2 - SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES (Continued)**
 
 **Asset
        Retirement Obligation**
 
 The
        fair
        values of asset retirement obligations are recognized in the period they
        are
        incurred if a reasonable estimate of fair value can be made. Asset retirement
        obligations primarily relate to the abandonment of oil and gas producing
        properties and include costs to dismantle and relocate or dispose of production
        equipment, gathering systems, wells and related structures. Estimates are
        based
        on historical experience in plugging and abandoning wells, estimated remaining
        lives of those wells based on reserve estimates, external estimates as to
        the
        cost to plug and abandon the wells in the future and federal and state
        regulatory requirements. The Partnership does not provide for a market risk
        premium associated with asset retirement obligation because a reliable estimate
        cannot be determined, see Note 3.
 
 **Environmental
        Matters**
 
 The
        Partnership is subject to various federal, state and local laws and regulations
        relating to the protection of the environment. The Partnership has established
        procedures for the ongoing evaluation of its operations, to identify potential
        environmental exposures and to comply with regulatory policies and
        procedures.
 
 The
        Partnership accounts for environmental contingencies in accordance with SFAS
        No.
        5 *Accounting
        for*  *Contingencies* .
        Environmental expenditures that relate to current operations are expensed
        or
        capitalized as appropriate. Expenditures that relate to an existing condition
        caused by past operations, and do not contribute to current or future revenue
        generation, are expensed. Liabilities are recorded when environmental
        assessments and/or clean-ups are probable, and the costs can be reasonably
        estimated. Atlas Energy maintains insurance that may cover in whole or in
        part
        certain environmental expenditures. From inception through December 31, 2006,
        the Partnership had no environmental matters requiring specific disclosure
        or
        the recording of a liability.
 
 **Major
        Customers**
 
 The
        Partnership's natural gas is sold under contract to various purchasers. For
        the
        year ended December 31, 2006, sales to UGI Energy Services, Inc., Hess
        Corporation, Exelon Energy Company and Colonial Energy Inc. accounted for
        44%,
        14%, 13% and 11%, respectively, of total revenues. For the year ended December
        31, 2005 sales to UGI Energy Services, Inc. and Hess Corporation accounted
        for
        58% and 15%, respectively, of total revenues. No other customers accounted
        for
        10% or more of total revenues for the years ended December 31, 2006 and
        2005.
 
 **Income
        Taxes**
 
 The
        Partnership is not treated as a taxable entity for federal income tax purposes.
        Any item of income, gain, loss, deduction or credit flows through to the
        partners as though each partner had incurred such item directly. As a result,
        each partner must take into account his pro rata share of all items of
        partnership income and deductions in computing his federal income tax
        liability.
 
 **Derivative
        Instruments**
 
 The
        Partnership applies the provisions of SFAS No. 133, *Accounting
        for Derivative Instruments and Hedging*  *Activity* (“SFAS
        No. 133”) and its various interpretations. SFAS No. 133 requires each derivative
        instrument to be recorded in the balance sheet as either an asset or liability
        measured at fair value. Changes in a derivative instrument's fair value are
        recognized currently in earnings unless specific hedge accounting criteria
        are
        met.
  12
  
 **ATLAS
        AMERICA PUBLIC #12-2003 LIMITED PARTNERSHIP**
 **NOTES
        TO FINANCIAL STATEMENTS - (Continued)**
 **DECEMBER
        31, 2006**
 
 **NOTE
        2 - SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES (Continued)**
 
 **Recently
        Issued Financial Accounting Standards**
 
 In
        February 2007, the FASB issued Statement of Financial Accounting Standards
        No.
        159, *The
        Fair Value Option for Financial Assets and Financial
        Liabilities* ,
        (“SFAS
        159”). SFAS 159 permits entities to choose to measure eligible financial
        instruments and certain other items at fair value. The objective is to improve
        financial reporting by providing entities with the opportunity to mitigate
        volatility in reported earnings caused by measuring related assets and
        liabilities differently without having to apply complex hedge accounting
        provisions. The Statement will be effective as of the beginning of an entity's
        first fiscal year beginning after November 15, 2007. The Statement offers
        various options in electing to apply the provisions of this statement and
        at
        this time the Partnership has not made any decisions on its application to
        the
        Partnership's financial position or results of operations. The Partnership
        is
        currently evaluating the impact of the adoption of SFAS 159 on its financial
        position and results of operations.
 
 In
        September 2006, the SEC staff issued Staff Accounting bulletin No. 108, *Considering
        the Effects of Prior year*  *Misstatements
        When Quantifying Misstatements in Current Year Financial
        Statement,* (“SAB
        108”). SAB 108 was issued to provide consistency in how registrants quantify
        financial statement misstatements. The Partnership initially applied SAB
        108 in
        connection with the preparation of its annual financial statements for the
        year
        ended December 31, 2006. The application of SAB 108 did not have a material
        effect on the Partnership's financial position or results of
        operations.
 
 In
        September 2006, the Financial Accounting Standards Board, or FASB, issued
        Statement of Financial Accounting Standards No. 157, *Fair
        Value Measurement* ,
        (“SFAS
        157”). SFAS 157 addresses the need for increased consistency in fair value
        measurements, defining fair value as the price that would be received to
        sell an
        asset or paid to transfer a liability in an orderly transaction between market
        participants at the measurement date. It also establishes a framework for
        measuring fair value and expands disclosure requirements. SFAS 157 is effective
        for us beginning January 1, 2008. The Partnership is currently evaluating
        the
        impact of the adoption of SFAS 157 on its financial position and results
        of
        operations.
 
 In
        June
        2006, the FASB issued FASB Interpretation No. 48, *Accounting
        for Uncertainty in Income Taxes and*  *Interpretation
        of FASB Statement No 109* ,
        (“FIN
        48”). FIN 48 clarifies the accounting for uncertainty in income taxes recognized
        in an entity's financial statements and provides guidance on the recognition,
        de-recognition and measurement of benefits related to an entity's uncertain
        tax
        positions. FIN 48 is effective for the Partnership beginning January 1, 2007.
        The Partnership's taxable income or loss will be absorbed by the Partners.
        The
        Partnership is currently evaluating the impact of the adoption of FIN 48
        on its
        financial position and results of operations, but since it is a non-taxable
        entity, does not currently expect the adoption of FIN 48 to have a material
        impact on its financial position or results of operations.
 
 In
        March
        2005, the FASB issued FASB Interpretation No. 47, *Accounting
        for Conditional Asset Retirement Obligations* (“FIN
        47”), which will result in (a) more consistent recognition of liabilities
        relating to asset retirement obligations, (b) more information about expected
        future cash outflows associated with those obligations, and (c) more information
        about investments in long-lived assets because additional asset retirement
        cost
        will be recognized as part of the carrying amounts of the assets. FIN 47
        clarifies that the term conditional asset retirement obligation as used in
        statement No. 143, *Accounting
        for Asset Retirement Obligations* ,
        refers
        to a legal obligation to perform an asset retirement activity in which the
        timing and/or method of settlement. Uncertainty about the timing and/or method
        of settlement of a conditional asset retirement obligation should be factored
        into the measurement of the liability when sufficient information exists.
        FIN 47
        also clarifies when an entity would have sufficient information to reasonably
        estimate the fair value of an asset retirement obligation. The adoption of
        FIN
        47 in the 4 th quarter
        2005, did not have a material effect on the Partnership's financial position
        or
        results of operations.
 
  13
  
 **ATLAS
        AMERICA PUBLIC #12-2003 LIMITED PARTNERSHIP**
 **NOTES
        TO FINANCIAL STATEMENTS - (Continued)**
 **DECEMBER
        31, 2006**
 
 **NOTE
        3 - ASSET RETIREMENT OBLIGATION**
 
 The
        Partnership accounts for its estimated plugging and abandonment costs for
        its
        oil and gas properties in accordance with SFAS 143, *Accounting
        for Asset Retirement Obligations* and FASB
        Interpretation No. 47, *Accounting
        for Conditional Asset Retirement Obligations,* (“FIN
        47”).
 
 A
        reconciliation of the Partnership's liability for plugging and abandonment
        costs
        for the years ended December 31, 2006 and 2005 is as follows:
 
 **2006**
              
              **2005**Asset
                  retirement obligation, at beginning of year
              
              $
              1,894,900
              
              $
              1,185,400Revisions
                  in estimates
              
              
              (59,200
              )
              
              638,400Accretion
                  expense
              
              
              113,800
              
              
              71,100Asset
                  retirement obligation, at end of year
              
              $
              1,949,500
              
              $
              1,894,900
 
 **NOTE
        4 - PARTICIPATION IN REVENUES AND COSTS**
 
 The
        MGP
        and the Limited Partners generally participate in revenues and costs in the
        following manner:
 
 **Managing****General**
              
              **Limited****Partner**
              
              **Partners**Organization
                  and offering costs
              
              
              100
              %
              
              0
              %Lease
                  costs
              
              
              100
              %
              
              0
              %Revenues(1)
              
              
              35
              %
              
              65
              %Operating
                  costs, administrative costs, direct and all other costs(2)
              
              
              35
              %
              
              65
              %Intangible
                  drilling costs
              
              
              0
              %
              
              100
              %Tangible
                  equipment costs
              
              
              69.55
              %
              
              30.45
              %
  
 (1)
            Subject
                to the Managing General Partner's subordination obligation, substantially
                all partnership revenues will be credited as follows: before net
                of tax
                savings payout and partnership payout (as defined in the partnership
                agreement), partnership revenues will be shared in the same percentage
                as
                capital contributions are to the total partnership capital contributions,
                After net of tax savings payout, the Managing General Partner will
                receive
                an additional 7% of the partnership revenues, which may not exceed
                35%. (2)
            These
                costs will be charged to the partners in the same ratio as the related
                production revenues are credited. 
 **NOTE
        5 - CERTAIN RELAITONSHIPS AND RELATED PARTY TRANSACTIONS**
 
 The
        Partnership has entered into the following significant transactions with
        its
        MGP, and its affiliates as provided under the Partnership
        agreement:
 
 ·
            Administrative
                costs which are included in general and administrative expenses in
                the
                Partnership's Statements of Operations are at $75 per well per month.
                Administrative costs incurred in 2006 and 2005 were $183,900 and
                $182,100,
                respectively.  14
  
 **ATLAS
        AMERICA PUBLIC #12-2003 LIMITED PARTNERSHIP**
 **NOTES
        TO FINANCIAL STATEMENTS - (Continued)**
 **DECEMBER
        31, 2006**
 
 **NOTE
        5 - CERTAIN RELAITONSHIPS AND RELATED PARTY TRANSACTIONS
        (Continued)**
 
 ·
            Monthly
                well supervision fees which are included in production expenses in
                the
                Partnership's Statements of Operations are payable at $289 per well
                per
                month for operating and maintaining the wells. Well supervision fees
                incurred in 2006 and 2005 were $708,700 and $673,800,
                respectively. 
 ·
            Transportation
                fees which are included in production expenses in the Partnership's
                Statements of Operations are payable at rates ranging from $ .29-$
                .35 per
                Mcf (one thousand cubic feet) to 10% of the natural gas sales price.
                A
                gathering fee is paid to the MGP at a competitive rate for each Mcf
                of
                natural gas transported. Transportation costs incurred in 2006 and
                2005
                were $758,900 and $491,600, respectively. 
 ·
            The
                managing general partner and its affiliates are reimbursed for all
                direct
                costs expended on the Partnership's behalf. For the years ended December
                31, 2006 and 2005, the managing general partner was reimbursed for
                $355,300 and $393,000, respectively, for direct
                costs. 
 The
        MGP, performs all administrative and management functions for the
        Partnership including billing revenues and paying expenses. Accounts receivable
        - affiliate on the Partnership's Balance Sheet represents the net production
        revenues due from Atlas.
 
 **NOTE
        6 - COMMITMENTS**
 
 Subject
        to certain conditions, investor partners may present their interests beginning
        in 2008 for purchase by Atlas Resources. The purchase price is calculated
        by
        Atlas Resources in accordance with the terms of the Partnership agreement.
        Atlas
        Resource is not obligated to purchase more than 5% of the units in any calendar
        year. In the event that Atlas Resource is unable to obtain the necessary
        funds,
        it may suspend its purchase obligation. At December 31, 2006 Atlas Resources
        had
        purchased less than 1% of investor partner units.
 
 Beginning
        one year after each of the Partnership's wells has been placed into production
        the MGP, as operator, may retain $200 per month to cover the estimated future
        plugging and abandonment costs. As of December 31, 2006 the MGP has not withheld
        any such funds.
 
 **NOTE
        7 - SUBORDINATION OF MGP'S REVENUE SHARE**
 
 Under
        the
        terms of the partnership agreement, the MGP may be required to subordinate
        up to
        50% of its share of production revenues of the Partnership, net of related
        operating costs, administrative costs and well supervision fees to the receipt
        by the limited partners of cash distributions from the Partnership equal
        to at
        least 10% of their agreed subscriptions, determined on a cumulative basis,
        in
        each of the first five years of Partnership operations, commencing with the
        first distribution of revenues to the limited partners (June 2004). During
        the
        subordination period, the MGP can be reimbursed for any subordination advances
        to the extent distributions to limited partners exceed the 10% return. Since
        inception of the program the MGP has not been required to subordinate any
        of its
        net revenues to the limited partners.
  15
  
 **ATLAS
        AMERICA PUBLIC #12-2003 LIMITED PARTNERSHIP**
 **NOTES
        TO FINANCIAL STATEMENTS - (Continued)**
 **DECEMBER
        31, 2006**
 
 **NOTE
        8 - DERIVATIVE INSTRUMENTS**
 
 Atlas
        Energy on behalf of the Partnership from time to time enters into natural
        gas
        futures and option contracts to hedge exposure to changes in natural gas
        prices.
        At any point in time, such contracts may include regulated NYMEX futures,
        options contracts, and non-regulated over-the-counter futures contracts with
        qualified counterparties. NYMEX contracts are generally settled with offsetting
        positions, but may be settled by the delivery of natural gas.
 
 Atlas
        Energy on behalf of the Partnership formally documents all relationships
        between
        hedging instruments and the items being hedged, including the Partnership's
        risk
        management objective and strategy for undertaking the hedging transactions.
        This
        includes matching the natural gas futures and options contracts to the
        forecasted transactions. Atlas Energy assesses, both at the inception of
        the
        hedge and on an ongoing basis, whether the derivatives are highly effective
        in
        offsetting changes in the fair value of hedged items. Historically these
        contracts have qualified and been designated as cash flow hedges and recorded
        at
        their fair values. Derivatives are recorded on the balance sheet as assets
        and
        liabilities at fair value. Gains or losses on future contracts are determined
        as
        the difference between the contract price and a reference price,
        generally prices on NYMEX. Changes in fair value are recognized in Partners'
        Capital as accumulated other comprehensive income (loss) and recognized within
        the Statements of Operations in the month the hedged gas is settled. If it
        is
        determined that a derivative is not highly effective as a hedge or it has
        ceased
        to be a highly effective hedge, due to the loss of correlation between changes
        in gas reference prices under a hedging instrument and actual gas prices,
        Atlas
        Energy will discontinue hedge accounting for the derivative and subsequent
        changes in fair value for the derivative will be recognized immediately into
        earnings.
 
 At
        December 31, 2006, Atlas Energy had allocated open natural gas futures contracts
        to the Partnership related to natural gas sales covering 2,340,900 dekatherms
        (“Dth”) (net to the Partnership) of natural gas, maturing through December 31,
        2010 at an average settlement price of $8.51 per Dth. At December 31, 2006,
        the
        Partnership reflected net hedging assets on its balance sheet of $2,022,200.
        Due
        to the impairment of the Partnership's oil and gas properties, the net
        offsetting unrealized gain of $193,600 was reclassified into earnings from
        accumulated other comprehensive income. Ineffective hedge gains or losses
        are recorded within the Statement of Operations while the hedge contract
        is open
        and may increase or decrease until settlement of the contract. The Partnership
        realized gains of $979,500 and $59,400 for the years ended December 31, 2006
        and
        2005, respectively, within its Statement of Operations related to the settlement
        of qualifying hedge instruments. The Partnership recognized no gains or losses
        during the two years ended December 31, 2006 for hedge ineffectiveness or
        as a
        result of the discontinuance of these cash flow hedges.
  16
  
 **ATLAS
        AMERICA PUBLIC #12-2003 LIMITED PARTNERSHIP**
 **NOTES
        TO FINANCIAL STATEMENTS - (Continued)**
 **DECEMBER
        31, 2006**
 
 **NOTE
        9 - NATURAL GAS AND OIL PRODUCING ACTIVITIES (UNAUDITED)**
 
 As
        of
        December 31, 2006, Atlas Energy had allocated to the Partnership the following
        natural gas hedged volumes:
 
 **Natural
                  Gas Fixed - Price Swaps****Production**
              
              
              
              **Average**
              
              **Net
                  Fair Value****Period**
              
              **Volumes**
              
              **Fixed
                  Price**
              
              **Asset****(2)****Ended
                  December 31,**
              
              **(MMBTU)****(1)**
              
              **(per
                  MMBTU)**
              
              **(in
                  thousands)**2007
              
              
              701,000
              
              $
              8.60
              
              $
              1,1692008
              
              
              739,800
              
              
              8.91
              
              
              5002009
              
              
              669,900
              
              
              8.31
              
              
              3282010
              
              
              230,200
              
              
              7.53
              
              
              25Total
                  asset
              
              
              
              
              
              
              
              $
              2,022
  
 (1)
            MMBTU
                represents million British Thermal Units. (2)
            Fair
                value based on forward NYMEX natural gas prices, as
                applicable. 
 The
        following table sets forth the book and estimated fair values of derivative
        instruments at the dates indicated (in thousands):
  **December
                  31, 2006**
              
              **December
                  31, 2005****Book
                  Value**
              
              **Fair
                  Value**
              
              **Book
                  Value**
              
              **Fair
                  Value**AssetsDerivative
                  instruments
              
              $
              2,193
              
              $
              2,193
              
              $
              162
              
              $
              162$
              2,193
              
              $
              2,193
              
              $
              162
              
              $
              162LiabilitiesDerivative
                  instruments
              
              $
              (171
              )
              $
              (171
              )
              $
              (724
              )
              $
              (724
              )$
              2,022
              
              $
              2,022
              
              $
              (562
              )
              $
              (562
              )
 
 The
        supplementary information summarized below presents the results of natural
        gas
        and oil activities in accordance with Statements of Financial Accounting
        Standards No. 69, *Disclosures
        About Oil and Gas Producing Activities,* (“SFAS
        No, 69”). Annually, reserve value information is provided to the investor
        partners pursuant to the partnership agreement. The partnership agreement
        provides a presentment feature whereby the MGP will buy partnership units,
        subject to annual limitations, based upon a valuation formula price in the
        partnership agreement. Therefore, reserve value information under SFAS No.
        69 is
        not presented.
 
 No
        consideration has been given in the following information to the income tax
        effect of the activities, as the Partnership is not treated as a taxable
        entity
        for income tax purposes.
 
  17
  
 **ATLAS
        AMERICA PUBLIC #12-2003 LIMITED PARTNERSHIP**
 **NOTES
        TO FINANCIAL STATEMENTS - (Continued)**
 **DECEMBER
        31, 2006**
 
 **NOTE
        9 - NATURAL GAS AND OIL PRODUCING ACTIVITIES (UNAUDITED)
        (Continued)**
 
 ***(1)***  ***Capitalized
        Costs Related to Oil and Gas Producing Activities***
 
 The
        following table presents the capitalized costs related to natural gas and
        oil
        producing activities at December 31:
 
 **2006**
              
              **2005**Mineral
                  interests in proved properties
              
              $
              1,169,700
              
              $
              1,169,700Wells
                  and related equipment
              
              
              49,132,700
              
              
              52,837,000Accumulated
                  depletion
              
              
              (16,822,800
              )
              
              (12,992,400
              )**Net
                  capitalized cost**
              
              $
              33,479,600
              
              $
              41,014,300
 
 ***(2)***  ***Results
        of Operations for Oil and Gas Producing Activities***
 
 The
        following table presents the results of operations related to natural gas
        and
        oil production for the years ended December 31:
 
 **2006**
              
              **2005**Natural
                  gas and oil sales
              
              $
              8,510,100
              
              $
              13,047,500Production
                  costs
              
              
              (1,780,800
              )
              
              (1,512,100
              )Accretion
                  of asset retirement obligation
              
              
              (113,800
              )
              
              (71,100
              )Depletion
              
              
              (3,830,400
              )
              
              (7,056,100
              )Impairment
                  of oil and gas properties
              
              
              (3,466,200
              )
              
              ─General
                  and administrative
              
              
              (226,000
              )
              
              (228,400
              )**Results
                  of operations from oil and gas producing
                  activities**
              
              $
              (907,100
              )
              $
              4,179,800
 
 ***(3)***  ***Costs
        Incurred in Oil and Gas Producing Activities***
 
 Costs
        incurred for the years ended December 31, are as follows:
 
 **2006**
              
              **2005**Development
                  costs
              
              $
              (59,200
              )
              $
              638,400
 
 ***(4)***  ***Oil
        and Gas Reserve Information***
 
 The
        information presented below represents estimates of proved natural gas and
        oil
        reserves. The estimates of the Partnership's proved gas and oil reserves
        are
        based upon evaluations made by management and verified by Wright & Company,
        Inc., an independent petroleum-engineering firm, as of December 31, 2006
        and
        2005. All reserves are located within the United States of America. Reserves
        are
        estimated in accordance with guidelines established by the Securities and
        Exchange Commission and the Financial Accounting Standards Board which require
        that reserve estimates be prepared under existing economic and operating
        conditions with no provision for price and cost escalation except by contractual
        arrangements. Proved reserves are estimated quantities of crude oil and natural
        gas which geological and engineering data demonstrate with reasonable certainty
        to be recoverable in future years from known reservoirs under existing economic
        and operating conditions, i.e. prices and costs as of the date the estimate
        is
        made. Prices include consideration of changes in existing prices provided
        only
        by contractual arrangements, but not on escalations based upon future
        conditions .
 
  18
  
 **ATLAS
        AMERICA PUBLIC #12-2003 LIMITED PARTNERSHIP**
 **NOTES
        TO FINANCIAL STATEMENTS - (Continued)**
 **DECEMBER
        31, 2006**
 
 **NOTE
        9 - NATURAL GAS AND OIL PRODUCING ACTIVITIES (UNAUDITED)
        (Continued)**
 
 Proved
        developed reserves are those which are expected to be recovered through existing
        wells with existing equipment and operating methods. Additional oil and gas
        expected to be obtained through the application of fluid injection or other
        improved recovery techniques for supplementing the natural forces and mechanisms
        of primary recovery should be included as “proved developed reserves” only after
        testing by a pilot project or after the operation of an installed program
        has
        confirmed through production response that increased recovery will be achieved.
        All reserves are proved developed reserves and are located in the Appalachian
        Basin area.
 
 There
        are
        numerous uncertainties inherent in estimating quantities of proved reserves
        and
        in projecting future net revenues and the timing of development expenditures.
        The reserve data presented represents estimates only and should not be construed
        as being exact. In addition, the standardized measure of discounted future
        net
        cash flows may not represent the fair market value of the Partnership's oil
        and
        gas reserves or the present value of future cash flows of equivalent reserves,
        due to anticipated future changes in oil and gas prices and in production
        and
        development costs and other factors for which effects have not been
        provided.
 **Natural
                  Gas**
              
              **Oil****(Mcf)**
              
              **(Bbls)**Proved
                  developed reserves:**Balance
                  December 31, 2004**
              
              
              12,524,500
              
              
              61,700Production
              
              
              (1,658,300
              )
              
              (7,200
              )Revisions
                  to previous estimates
              
              
              (2,077,800
              )
              
              (50,100
              )**Balance
                  December 31, 2005**
              
              
              8,788,400
              
              
              4,400Production
              
              
              (918,100
              )
              
              (2,300
              )Revisions
                  to previous estimates
              
              
              (2,069,000
              )
              
              800**Balance
                  December 31, 2006**
              
              
              5,801,300
              
              
              2,900
 
 **ITEM
                  8.**
              **CHANGES
                  IN AND DISAGREEMENTS WITH ACCOUNTANTS ON ACCOUNTING
                  AND****FINANCIAL
                  DISCLOSURE:**
 
 None.
 
 **ITEM
        8A.  CONTROLS AND
        PROCEDURES**
 
 Under
        the
        supervision and with the participation of, our MGP's management, including
        our
        MGP's Chief Executive Officer and Chief Financial Officer, our MGP has evaluated
        the effectiveness of the design and operation of its disclosure controls
        and
        procedures (as defined in Exchange Act Rule 13a-15(e) and Rule 15d-15(e))
        as of
        the end of the period covered by this annual report on Form 10-KSB, and based
        on
        their evaluation, the Chief Executive Officer and Chief Financial Officer
        have
        concluded that these disclosure controls and procedures are effective in
        all
        material respects, including those to ensure that information required to
        be
        disclosed in reports filed or submitted under the Securities Exchange Act
        is
        recorded, processed, summarized, and reported, within the time periods specified
        in the SEC's rules and forms, and is accumulated and communicated to management,
        including our MGP's Chief Executive Officer and Chief Financial Officer,
        as
        appropriate to allow for timely disclosure. There have been no changes during
        our last fiscal quarter that materially affected, or are reasonably likely
        to
        materially affect, our internal control over financial
        reporting.
  19
  
 **ITEM
        8B.  OTHER
        INFORMATION**
 
 None.
 **PART
        III**
 
 **ITEM
                  9.**
              **DIRECTORS,
                  EXECUTIVE OFFICERS AND SIGNIFICANT EMPLOYEES, COMPLIANCE
                  WITH****SECTION
                  16 (A) OF THE EXCHANGE ACT**
 
 Atlas
        America (ATLS) transferred to Atlas Energy Resources, LLC (ATN), a newly-formed,
        limited liability company subsidiary of Atlas America, substantially all
        of its
        natural gas and oil exploration and production assets in December 2006 pursuant
        to the completion of an initial public offering of 7,273,750 of its Class
        B
        limited liability company interest.  As consideration for this
        contribution, on December 18, 2006 Atlas Energy Resources, LLC distributed
        to
        Atlas America $139,944,000 net proceeds of the offering, 29,352,996 of common
        units, 748,456 Class A units, and the management incentive interest. Also
        pursuant to the contribution agreement, Atlas America contributed to its
        subsidiary, Atlas Energy Management, Inc. (“Atlas Management”), the 748,456
        Class A units and the management incentive interest. Atlas America retained
        approximately 81% of the limited liability company interest of Atlas Energy
        Resources, LLC, which will continue to provide Atlas America control over
        Atlas
        Energy Resources, LLC and its assets and business.
 
 Atlas
        America is headquartered at 311 Rouser Road, Moon Township, Pennsylvania
        15108,
        which is also our MGP's primary office.
 
 **Executive
        Officers and Directors.** The
        executive officers and directors of our MGP will serve until their successors
        are elected. The executive officers and directors of our MGP are as
        follows:
 
 **NAME**
              
              **AGE**
              
              **POSITION
                  OR OFFICE**Freddie
                  M. Kotek
              
              51
              
              Chairman
                  of the Board of Directors, Chief Executive Officer and
                  PresidentFrank
                  P. Carolas
              
              47
              
              Executive
                  Vice President - Land and Geology and a DirectorJeffrey
                  C. Simmons
              
              48
              
              Executive
                  Vice President - Operations and a DirectorJack
                  L. Hollander
              
              50
              
              Senior
                  Vice President - Direct Participation ProgramsNancy
                  J. McGurk
              
              51
              
              Senior
                  Vice President - Chief Accounting OfficerMichael
                  L. Staines
              
              57
              
              Senior
                  Vice President, Secretary and a DirectorMatthew
                  A. Jones
              
              45
              
              Chief
                  Financial Officer
 
 With
        respect to the biographical information set forth below:
 
 ·
            The
                approximate amount of an individual's professional time devoted to
                the
                business and affairs of our managing general partner and Atlas America
                have been aggregated because there is no reasonable method for them
                to
                distinguish their activities between the two companies;
                and ·
            For
                those individuals who also hold senior positions with other affiliates
                of
                our managing general partner, if it is stated that they devote
                approximately 100% of their professional time to our managing general
                partner and Atlas America, it is because either the other affiliates
                are
                not currently active in drilling new wells, such as Viking Resources
                or
                Resource Energy, and the individuals are not required to devote a
                material
                amount of their professional time to the affiliates, or there is
                no
                reasonable method to distinguish their activities between our managing
                general partner and Atlas America as compared with the other affiliates
                of
                our managing general partner, such as Viking Resources or Resource
                Energy.  20
  
 **Freddie
        M. Kotek.** President
        and Chief Executive Officer since January 2002 and Chairman of the Board
        of
        Directors since September 2001. Mr. Kotek has been Executive Vice President
        of
        Atlas America since February 2004, and served as a director from September
        2001
        until February 2004 and served as Chief Financial Officer from February 2004
        until March 2005. Mr. Kotek was a Senior Vice President of Resource America
        and
        President of Resource Leasing, Inc. (a wholly-owned subsidiary of Resource
        America) from 1995 until May 2004 when he resigned from Resource America
        and all
        of its subsidiaries which are not subsidiaries of Atlas America. Mr. Kotek
        was
        President of Resource Properties from September 2000 to October 2001 and
        its
        Executive Vice President from 1993 to August 1999. Mr. Kotek received a Bachelor
        of Arts degree from Rutgers College in 1977 with high honors in Economics.
        He
        also received a Master in Business Administration degree from the Harvard
        Graduate School of Business Administration in 1981. Mr. Kotek will devote
        approximately 95% of his professional time to the business and affairs of
        the
        MGP and Atlas America, Atlas Energy Resources, LLC and Atlas Energy Management,
        Inc., and the remainder of his professional time to the business and affairs
        of
        the MGP's other affiliates.
 
 **Frank
        P. Carolas.** Executive
        Vice President-Land and Geology and a Director since January 2001. Mr. Carolas
        has been an Executive Vice President of Atlas America since January 2001
        and
        served as a Director of Atlas America from January 2002 until February 2004.
        Mr.
        Carolas has been a Senior Vice President of Atlas Energy Management, Inc.
        since
        2006. Mr. Carolas was a Vice President of Resource America from April 2001
        until
        May 2004 when he resigned from Resource America. Mr. Carolas served as Vice
        President of Land and Geology for the MGP from July 1999 until December 2000
        and
        for Atlas America from 1998 until December 2000. Before that Mr. Carolas
        served
        as Vice President of Atlas Energy Group, Inc. from 1997 until 1998, which
        was
        the former parent company of the MGP. Mr. Carolas is a certified petroleum
        geologist and has been with the MGP and its affiliates since 1981. He received
        a
        Bachelor of Science degree in Geology from Pennsylvania State University
        in 1981
        and is an active member of the American Association of Petroleum Geologists.
        Mr.
        Carolas devotes approximately 100% of his professional time to the business
        and
        affairs of the MGP, Atlas America, Atlas Energy Resources, LLC and Atlas
        Energy
        Management, Inc.
 
 **Jeffrey
        C. Simmons.** Executive
        Vice President-Operations and a Director since January, 2001. Mr. Simmons
        has
        been an Executive Vice President of Atlas America since January 2001 and
        was a
        Director of Atlas America from January 2002 until February 2004. Mr. Simmons
        has
        been a Senior Vice President of Atlas Energy Management, Inc., since 2006.
        Mr.
        Simmons was a Vice President of Resource America from April 2001 until May
        2004
        when he resigned from Resource America. Mr. Simmons served as Vice President
        of
        Operations for the MGP from July 1999 until December 2000 and for Atlas America
        from 1998 until December 2000. Mr. Simmons joined Resource America in 1986
        as a
        senior petroleum engineer and has served in various executive positions with
        its
        energy subsidiaries since then. Mr. Simmons received his Bachelor of Science
        degree with honors from Marietta College in 1981 and his Masters degree in
        Business Administration from Ashland University in 1992. Mr. Simmons devotes
        approximately 90% of his professional time to the business and affairs of
        the
        MGP, Atlas America, and the remainder of his professional time to the business
        and affairs of the MGP's other affiliates, primarily Viking Resources and
        Resource Energy, Atlas Energy Resources, LLC and Atlas Energy Management,
        Inc.
 
 **Jack
        L. Hollander.** Senior
        Vice President - Direct Participation Programs since January 2002 and before
        that he served as Vice President - Direct Participation Programs from January
        2001 until December 2001. Mr. Hollander also serves as Senior Vice President
        -
        Direct Participation Programs of Atlas America since January 2002. Mr. Hollander
        practiced law with Rattet, Hollander & Pasternak, concentrating in tax
        matters and real estate transactions, from 1990 to January 2001, and served
        as
        in-house counsel for Integrated Resources, Inc. (a diversified financial
        services company) from 1982 to 1990. Mr. Hollander earned a Bachelor of Science
        degree from the University of Rhode Island in 1978, his law degree from Brooklyn
        Law School in 1981, and a Master of Law degree in Taxation from New York
        University School of Law Graduate Division in 1982. Mr. Hollander is a member
        of
        the New York State bar and the Chairman of the Investment Program Association
        which is an industry association, as of March 2005. Mr. Hollander devotes
        approximately 100% of his professional time to the business and affairs of
        the
        MGP, Atlas America, Atlas Energy Resources, LLC and Atlas Energy Management,
        Inc.
  21
  
 **Nancy
        J. McGurk.** Ms.
        McGurk has been Chief Accounting Officer of Atlas Energy Resources, LLC and
        Atlas Energy Management. Senior Vice President since January 2002, Chief
        Accounting Officer since January 2001 and Chief Financial Officer until March
        2006. Ms. McGurk also serves as Senior Vice President since January 2002
        and
        Chief Accounting Officer of Atlas America since January 2001. Ms. McGurk
        served
        as Chief Financial Officer for Atlas America from January 2001 until February
        2004. Ms. McGurk was a Vice President of Resource America from 1992 until
        May
        2004 and its Treasurer and Chief Accounting Officer from 1989 until May 2004
        when she resigned from Resource America. Also, since 1995 Ms. McGurk has
        served
        as Vice President - Finance of Resource Energy, Inc. Ms. McGurk received
        a
        Bachelor of Science degree in Accounting from Ohio State University in 1978,
        and
        has been a Certified Public Accountant since 1982. Ms. McGurk devotes
        approximately 80% of her professional time to the business and affairs of
        the
        MGP, Atlas America, Atlas Energy Resources, LLC and Atlas Energy Management
        and
        the remainder of her professional time to the business and affairs of the
        MGP's
        other affiliates.
 
 **Michael
        L. Staines.** Senior
        Vice President, Secretary, and a Director since 1998. Mr. Staines has been
        an
        Executive Vice President and Secretary of Atlas America since 1998. Mr. Staines
        was a Senior Vice President of Resource America from 1989 until May, 2005
        when
        he resigned from Resource America. Mr. Staines was a director of Resource
        America from 1989 to February 2000 and Secretary from 1989 to October 1998.
        Mr.
        Staines has been President of Atlas Pipeline Partners GP since January 2001
        and
        its Chief Operating Officer and a member of its Managing Board since its
        formation in November 1999. Mr. Staines is a member of the Ohio Oil and Gas
        Association and the Independent Oil and Gas Association of New York. Mr.
        Staines
        received a Bachelor of Science degree from Cornell University in 1971 and
        a
        Master of Business degree from Drexel University in 1977. Mr. Staines devotes
        approximately 5% of his professional time to the business and affairs of
        the MGP
        and Atlas America, and the remainder of his professional time to the business
        and affairs of the MGP's other affiliates, including Atlas Pipeline Partners
        GP.
 
 **Matthew
        A. Jones** Chief
        Financial Officer since March 2006 for Atlas Resources, LLC. Mr. Jones has
        been
        the Chief Financial Officer since January 2006 and a director of Atlas Pipeline
        Holdings since February 2006 and has been Chief Financial Officer of Atlas
        Pipeline Partners GP and Atlas America since March 2005. He has been the
        Chief
        Financial Officer and a director of Atlas Energy Resources and Atlas Energy
        Management since their formation. From 1996 to 2005, Mr. Jones worked in
        the
        Investment Banking Group at Friedman Billings Ramsey, concluding as Managing
        Director. Mr. Jones worked in Friedman Billings Ramsey's Energy Investment
        Banking Group from 1999 to 2005, and in Friedman Billings Ramsey's Specialty
        Finance and Real Estate Group from 1996 to 1999. Mr. Jones is a Chartered
        Financial Analyst.
 
 **Audit
        Committee Financial Expert.** The
        Board of Directors of our MGP acts as the audit committee. The Board of
        Directors has determined that Freddie M. Kotek meets the requirement of an
        “audit committee financial expert”, he is not independent.
 
 **Remuneration
        of Officers and Directors.** No
        officer or director of the MGP will receive any direct remuneration or other
        compensation from the Partnership. These persons will receive compensation
        solely from affiliated companies of the MGP.
 
 **Code
        of Business Conduct and Ethics.** Because
        the Partnership does not directly employ and persons, the MGP has determined
        that the partnership will rely on a Code of business Conduct and Ethics adopted
        by Atlas America, Inc. and/or Atlas Energy Resources, LLC that applies to
        the
        principal executive officer, principal financial officer and principal
        accounting officer of the MGP, as well as to persons performing services
        for the
        managing general partner generally. You may obtain a copy of this Code of
        Business Conduct and Ethics by a request to the MGP at Atlas Resources, LLC,
        311
        Rouser Road, Moon Township, Pennsylvania 15108.
  22
  
 **ITEM
        10.  EXECUTIVE
        COMPENSATION**
 
 We
        have
        no employees and rely on the employees of our MGP and its affiliates for
        all
        services. No officer or director of our MGP will receive any direct remuneration
        or other compensation from us. Those persons will receive compensation solely
        from affiliated companies of our MGP. See Item 12 “Certain Relationships and
        Related Party Transactions” for a discussion of compensation paid by us to our
        MGP.
 
 **ITEM
        11.  SECURITY OWNERSHIP OF
        CERTAIN BENEFICIAL OWNERS AND MANAGEMENT**
 
 As
        of
        December 31, 2006, we had issued and outstanding units of 4,024. No officer
        or
        director of our MGP owns any units. Although, subject to certain conditions,
        investor partners may present their units to us beginning in 2008 for purchase,
        the MGP is not obligated by the Partnership agreement from purchasing more
        than 5% of our total outstanding units in any calendar year.
 
 **Organizational
        and Security Ownership of Beneficial Owners.** Atlas
        America owns approximately 81% of the limited liability company interest
        of
        Atlas Energy Resources, LLC which owns 100% of the limited liability company
        interests of Atlas Energy Operating Company, LLC, which owns 100% of the
        limited
        liability company interests of AIC, LLC, which owns 100% of the limited
        liability company interest of the managing general partner. The officers
        and
        directors of Atlas America and Atlas Energy Resources LLC are set forth below.
        The directors of AIC, LLC are Jonathan Z. Cohen, Michael L. Staines, and
        Jeffrey
        Simmons. The biographies of Messrs, Staines and Simmons are set forth
        above.
 
 **ITEM
        12.  CERTAIN RELATIONSHIPS
        AND RELATED PARTY TRANSACTIONS**
 
 **Oil
        and Gas Revenues.** Our
        MGP
        is allocated 35% of our oil and gas revenues in return for its payment and/or
        contribution of services towards our organization and offering costs equal
        to
        12.8% of our subscriptions, its payment of 69.55% of the tangible costs of
        drilling and completing our wells and its contribution to us of all of our
        oil
        and gas leases. These capital contributions from our MGP totaled $17,222,900.
        During the years ended December 31, 2006 and 2005, our MGP received $2,355,300
        and $4,037,400, respectively, from our net production revenues.
 
 **Leases.** Following the final closing date for the offering of our units to potential
        investors, which was December 22, 2003, our MGP contributed oil and gas leases
        to us covering 227 undeveloped prospects for the wells we would drill, and
        it
        received a credit to its capital account in the amount of
        $1,169,700.
 
 **Administrative
        Costs.** Our MGP
        and its affiliates receive an unaccountable, fixed payment reimbursement
        for the
        administrative costs they incur on our behalf of $75 per well per month,
        which
        is proportionately reduced to the extent we acquired less than 100% of the
        working interest in a well. During the years ended December 31, 2006 and
        2005,
        our MGP received $183,900 and $182,100, respectively, for administrative
        costs.
 
 **Direct
        Costs.** Our MGP
        (including other serving as operator) and its affiliates are reimbursed by
        us
        for all direct costs expended by them on our behalf. During the years ended
        December 31, 2006 and 2005, we reimbursed our MGP $355,300 and $393,000,
        respectively, for direct costs.
  23
  
 **Well
        Charges.** Our MGP,
        as operator is reimbursed at actual cost for all direct expenses incurred
        on our behalf and receives well supervision fees for operating and maintaining
        the wells during producing operations in the amount of $289 per well per
        month
        subject to an annual adjustment for inflation. The well supervision fees
        were
        proportionately reduced to the extent we acquired less than 100% of the working
        interest in a well. For the years ended December 31, 2006 and 2005, our MGP
        received $708,700 and $673,800, respectively, for well supervision
        fees.
 
 **Transportation
        Fees.** We pay a
        gathering fee to our MGP at a competitive rate for each mcf of our natural
        gas
        transported. Transportation rates range from $.29-$.35 per Mcf (one thousand
        cubic feet) to 10% of the natural gas sales price. For the years ended December
        31, 2006 and 2005, $758,900 and $491,600, respectively, was paid to our MGP
        for
        gathering fees. In turn, our MGP paid 100% of these amounts to Atlas Pipeline
        Partners, L.P. for the use of its gathering system in transporting a majority
        of
        our natural gas production.
 
 **Other
        Compensation** .
        For the
        years ended December 31, 2006 and 2005, our MGP did not advance any funds
        to us,
        nor did it provide us with any equipment, supplies or other
        services.
 
 **ITEM
        13.  EXHIBITS**
 **EXHIBIT
        INDEX**
 
 **Description**
              
              **Location**4(a)
              
              Certificate
                  of Limited Partnership for Atlas America
              
              Previously
                  filed in our Form S-1 onPublic
                  #12-2003 Limited Partnership
              
              June
                  3, 2003.4(b)
              
              Amended
                  and Restated Certificate and Agreement
              
              Previously
                  filed in our Form S-1 onof
                  Limited Partnership for Atlas America
              
              June
                  3, 2003Public
                  #12-2003 Limited Partnership4(c)
              
              Drilling
                  and Operating Agreement for Atlas America
              
              Previously
                  filed in our Form S-1 onPublic
                  #12-2003 Limited Partnership
              
              June
                  3, 200331.1
              
              Certification
                  Pursuant to Rule 13a-14(a)/15(d) - 14(a) Certification.31.2
              
              Certification
                  Pursuant to Rule 13a-14(a)/15(d) - 14(a) Certification.32.1
              
              Section
                  1350 Certification.32.2
              
              Section
                  1350 Certification.
 
 **ITEM
        14.  PRINCIPAL ACCOUNTANT
        FEES AND SERVICES**
 
 **Audit
        Fees.** The
        aggregate fees billed by our independent auditors, Grant Thornton LLP, for
        professional services rendered for the audit of our annual financial statements
        for the years ended December 31, 2006 and 2005, and for the reviews of the
        financial statements included in our Quarterly Reports on Form 10-QSB during
        such years, were $20,700 and $28,000, respectively.
 
 **Procedures
        for Audit Committee Pre-Approval of Audit and Permissible Non-Audit Services
        of
        Independent Auditor.** Pursuant
        to its charter, the Audit Committee of our MGP is responsible for reviewing
        and
        approving, in advance, any audit and any permissible non-audit engagement
        or
        relationship between us and our independent auditors. We do not have a separate
        audit committee.
  24
 
 **SIGNATURES**
 
 In
                  accordance with Section 13 or 15(d) of the Exchange Act, the registrant
                  caused this report to be signed on itsbehalf
                  by the undersigned, thereunto duly authorized.Atlas
                  America Public #12-2003 Limited PartnershipAtlas
                  Resources, LLC, Managing General PartnerDate:
                  June 1, 2007
              
              By:/s/
                  Freddie M. KotekFreddie
                  M. Kotek, Chairman of the Board of Directors, Chief Executive
                  Officerand
                  President
 
 In
                  accordance with the Exchange Act, this report has been signed by
                  the
                  following persons on behalf of theregistrant
                  and in the capacities and on the dates indicated.Date:
                  June 1, 2007
              
              By:/s/
                  Freddie M. KotekFreddie
                  M. Kotek, Chairman of the Board of Directors, Chief Executive
                  Officerand
                  PresidentDate:
                  June 1, 2007
              
              By:/s/
                  Frank P. CarolasFrank
                  P. Carolas, Executive Vice President - Land and GeologyDate:
                  June 1, 2007
              
              By:/s/
                  Jeffrey C. SimmonsJeffrey
                  C. Simmons, Executive Vice President - OperationsDate:
                  June 1, 2007
              
              By:/s/
                  Nancy J. McGurkNancy
                  J. McGurk, Vice President, and Chief Accounting OfficerDate:
                  June 1, 2007
              
              By:/s/
                  Matthew A. JonesMatthew
                  A. Jones, Chief Financial Officer
 
 **Supplemental
        information to be furnished with reports filed pursuant to Section 15(d)
        of
        the**
 **Exchange
        Act by Non-reporting Issuers**
 
 An
        annual
        report will be furnished to security holders subsequent to the filing of
        this
        report.
 
 25