|                                                                                                                                                                                                                                                                                                                                                                       | United      States                                                                                  |
|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------|
|                                                                                                                                                                                                                                                                                                                                                                       |                                                                                                |
|                                                                                                                                                                                                                                                                                                                                                                       | Securities      and Exchange Commission                                                             |
|                                                                                                                                                                                                                                                                                                                                                                       |                                                                                                |
|                                                                                                                                                                                                                                                                                                                                                                       | Washington,      D.C. 20549                                                                         |
|                                                                                                                                                                                                                                                                                                                                                                       |                                                                                                |
|                                                                                                                                                                                                                                                                                                                                                                       | Form      10-Q                                                                                      |
|                                                                                                                                                                                                                                                                                                                                                                       |                                                                                                |
| (Mark      One)                                                                                                                                                                                                                                                                                                                                                            |
|                                                                                                                                                                                                                                                                                                                                                                       |                                                                                                |
| R                                                                                                                                                                                                                                                                                                                                                                          | QUARTERLY      REPORT PURSUANT TO SECTION 13 OR 15 (d) OF THE SECURITIES EXCHANGE ACT OF      1934  |
|                                                                                                                                                                                                                                                                                                                                                                       |                                                                                                |
|                                                                                                                                                                                                                                                                                                                                                                       | For      the quarterly period ended September 30, 2009                                              |
|                                                                                                                                                                                                                                                                                                                                                                       |                                                                                                |
| o                                                                                                                                                                                                                                                                                                                                                                          | TRANSITION      REPORT PURSUANT TO 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 ofincorporation      or organization)                                                                                                                                                                                                                                                                                                    | (I.R.S.      EmployerIdentification      No.)                                                       |
|                                                                                                                                                                                                                                                                                                                                                                       |                                                                                                |
| Westpointe      Corporate Center One                                                                                                                                                                                                                                                                                                                                       |                                                                                                |
| 1550      Coraopolis Heights Rd. 2nd Floor                                                                                                                                                                                                                                                                                                                                 |                                                                                                |
| Moon      Township, PA                                                                                                                                                                                                                                                                                                                                                     | 15108                                                                                               |
| (Address      of principal executive offices)                                                                                                                                                                                                                                                                                                                              | (zip      code)                                                                                     |
|                                                                                                                                                                                                                                                                                                                                                                       |                                                                                                |
| Issuer’s      telephone number, including area code: (412)      262-2830                                                                                                                                                                                                                                                                                             |
|                                                                                                                                                                                                                                                                                                                                                                       |
| Indicate      by check mark whether the registrant (1) has filed all reports required to      be filed by Section 13 or 15 (d) of the Securities  Exchange                                                                                                                                                                                                                 |
| Act      of 1934 during the preceding 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      No o                                                                                                                                                                                                                                                                  |
|                                                                                                                                                                                                                                                                                                                                                                       |
| Indicate      by check mark whether the registrant has submitted electronically and      posted on its corporate Web site, if any, every  Interactive                                                                                                                                                                                                                      |
| Data      File required to be submitted and posted pursuant to Rule 405 of      Regulation S-T (§232.405 of this chapter) during the preceding      12                                                                                                                                                                                                                |
| months      (or for such shorter period that the registrant was required to submit and      post such files). Yes o No R                                                                                                                                                                                                                                                   |
|                                                                                                                                                                                                                                                                                                                                                                       |
| Indicate      by check mark whether the registrant is a large accelerated filer, an      accelerated filer, a non-accelerated filer or a smaller      reporting                                                                                                                                                                                                            |
| company.      See the definitions of “large accelerated filer”, “accelerated filer”,      ”non-accelerated filer” and “smaller reporting company” in Rule 12b-2 of      the Exchange Act (Check One) Large accelerated filer  ̈ Accelerated filer       ̈      Non-accelerated filer  ̈ Smaller      reporting |
| company      R                                                                                                                                                                                                                                                                                                                                                             |
|                                                                                                                                                                                                                                                                                                                                                                       |
| 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                                                                                                                                                                                                                                                                                                 |

| PART      I.   |   | FINANCIAL      INFORMATION                                                                                | PAGE   |
|----------------|--------|-----------------------------------------------------------------------------------------------------------|--------|
|           |   |                                                                                                      |   |
| Item      1:   |   | Financial      Statements                                                                                 |   |
|           |   |                                                                                                      |   |
|           |   | Balance      Sheets as of September 30, 2009 and December 31, 2008                                        | 3      |
|           |   |                                                                                                      |   |
|           |   | Statements      of Operations for the Three Months and Nine Months Ended September 30,      2009 and 2008 | 4      |
|           |   |                                                                                                      |   |
|           |   | Statement      of Changes in Partners’ Capital for the Nine Months ended September 30,      2009    | 5      |
|           |   |                                                                                                      |   |
|           |   | Statements      of Cash Flows for the Nine Months ended September 30, 2009 and      2008                  | 6      |
|           |   |                                                                                                      |   |
|           |   | Notes      to Financial Statements                                                                        | 7-18   |
|           |   |                                                                                                      |   |
| Item      2:   |   | Management’s      Discussion and Analysis of Financial Condition or Plan of      Operations         | 18-23  |
|           |   |                                                                                                      |   |
| Item      4:   |   | Controls      and Procedures                                                                              | 23     |
|           |   |                                                                                                      |   |
| PART      II.  |   | OTHER      INFORMATION                                                                                    |   |
|           |   |                                                                                                      |   |
| Item      6:   |   | Exhibits                                                                                                  | 24     |
|           |   |                                                                                                      |   |
|           |   |                                                                                                      |   |
| SIGNATURES     | 25     |
|           |   |                                                                                                      |   |
| CERTIFICATIONS | 26-29  |

|                                                |   | September      30, |       |   | December      31, |   |
|-----------------------------------------------------|--------|--------------------|------------|--------|-------------------|--------|
|                                                |   | 2009               |       |   | 2008              |   |
|                                                |   | (Unaudited)        |       |   |              |   |
| ASSETS                                              |   |               |       |   |              |   |
| Current      assets:                                |   |               |       |   |              |   |
| Cash      and cash equivalents                      |   | $                  | 270,200    |   |              | $      | 574,000 |   |
| Accounts      receivable-affiliate                  |   |               | 613,400    |   |              |   | 1,003,000 |   |
| Short-term      hedge receivable due from affiliate |   |               | 482,900    |   |              |   | 1,071,500 |   |
| Total      current assets                           |   |               | 1,366,500  |   |              |   | 2,648,500 |   |
|                                                |   |               |       |   |              |   |   |   |
| Oil      and gas properties, net                    |   |               | 25,953,700 |   |              |   | 27,285,200 |   |
| Long-term      hedge receivable due from affiliate  |   |               | 335,000    |   |              |   | 666,900 |   |
|                                                |   | $                  | 27,655,200 |   |              | $      | 30,600,600 |   |
|                                                |   |               |       |   |              |   |   |   |
| LIABILITIES      AND PARTNERS’ CAPITAL        |   |               |       |   |              |   |   |   |
| Current      liabilities:                           |   |               |       |   |              |   |   |   |
| Accrued      liabilities                            |   | $                  | 28,500     |   |              | $      | 22,200 |   |
| Short-term      hedge liability due to affiliate    |   |               | 7,300      |   |              |   | 95,700 |   |
| Total      current liabilities                      |   |               | 35,800     |   |              |   | 117,900 |   |
|                                                |   |               |       |   |              |   |   |   |
| Asset      retirement obligation                    |   |               | 2,192,300  |   |              |   | 2,097,900 |   |
| Long-term      hedge liability due to affiliate     |   |               | 86,600     |   |              |   | 86,100 |   |
|                                                |   |               |       |   |              |   |   |   |
| Partners’      capital:                       |   |               |       |   |              |   |   |   |
| Managing      general partner                       |   |               | 8,526,300  |   |              |   | 8,999,800 |   |
| Limited      partners (4,024 units)                 |   |               | 16,099,400 |   |              |   | 17,776,000 |   |
| Accumulated      other comprehensive income         |   |               | 714,800    |   |              |   | 1,522,900 |   |
| Total      partners' capital                        |   |               | 25,340,500 |   |              |   | 28,298,700 |   |
|                                                |   | $                  | 27,655,200 |   |              | $      | 30,600,600 |   |

|                                                  |   | Three      Months Ended |     |   | Nine      Months Ended |   |
|-------------------------------------------------------|--------|-------------------------|----------|--------|------------------------|--------|
|                                                  |   | September      30,      |     |   | September      30,     |   |
|                                                  |   | 2009                    |     |   | 2008                   |   |   | 2009 |   |   | 2008 |   |
| REVENUES                                              |   |                    |     |   |                   |   |   |   |   |   |   |   |
| Natural      gas and oil                              |   | $                       | 771,200  |   |                   | $      | 1,550,400 |   |   | $ | 2,552,600 |   |   | $ | 4,795,500 |   |
| Interest      income                                  |   |                    | 200      |   |                   |   | 1,400 |   |   |   | 800 |   |   |   | 6,400 |   |
| Total      revenues                                   |   |                    | 771,400  |   |                   |   | 1,551,800 |   |   |   | 2,553,400 |   |   |   | 4,801,900 |   |
|                                                  |   |                    |     |   |                   |   |   |   |   |   |   |   |   |   |   |   |
| COSTS      AND EXPENSES                               |   |                    |     |   |                   |   |   |   |   |   |   |   |   |   |   |   |
| Production                                            |   |                    | 349,300  |   |                   |   | 422,500 |   |   |   | 1,076,600 |   |   |   | 1,341,900 |   |
| Depletion                                             |   |                    | 407,000  |   |                   |   | 618,100 |   |   |   | 1,331,500 |   |   |   | 2,201,000 |   |
| Accretion      of asset retirement obligation         |   |                    | 31,500   |   |                   |   | 29,600 |   |   |   | 94,400 |   |   |   | 88,900 |   |
| General      and administrative                       |   |                    | 61,300   |   |                   |   | 56,700 |   |   |   | 171,300 |   |   |   | 177,800 |   |
| Total      expenses                                   |   |                    | 849,100  |   |                   |   | 1,126,900 |   |   |   | 2,673,800 |   |   |   | 3,809,600 |   |
| Net      (loss) earnings                              |   | $                       | (77,700  | )      |                   | $      | 424,900 |   |   | $ | (120,400 | ) |   | $ | 992,300 |   |
|                                                  |   |                    |     |   |                   |   |   |   |   |   |   |   |   |   |   |   |
| Allocation      of net (loss) earnings :              |   |                    |     |   |                   |   |   |   |   |   |   |   |   |   |   |   |
| Managing      general partner                         |   | $                       | 58,100   |   |                   | $      | 298,000 |   |   | $ | 236,900 |   |   | $ | 878,600 |   |
| Limited      partners                                 |   | $                       | (135,800 | )      |                   | $      | 126,900 |   |   | $ | (357,300 | ) |   | $ | 113,700 |   |
| Net      (loss) earnings per limited partnership unit |   | $                       | (34      | )      |                   | $      | 31 |   |   | $ | (89 | ) |   | $ | 28 |   |

|                                          |   |     |      |   |     |   |       | Accumulated        |   |   |      |   |
|-----------------------------------------------|--------|----------|-----------|--------|----------|--------|------------|--------------------|--------|--------|-----------|--------|
|                                          |   | Managing |      |   |     |   |       | Other              |   |   |      |   |
|                                          |   | General  |      |   | Limited  |   |       | Comprehensive      |   |   |      |   |
|                                          |   | Partner  |      |   | Partners |   |       | Income      (Loss) |   |   | Total     |   |
|                                          |   |     |      |   |     |   |       |               |   |   |      |   |
| Balance      at January 1, 2009               |   | $        | 8,999,800 |   |     | $      | 17,776,000 |               |   | $      | 1,522,900 |   |   | $ | 28,298,700 |   |
|                                          |   |     |      |   |     |   |       |               |   |   |      |   |   |   |   |   |
| Participation      in revenues and expenses:  |   |     |      |   |     |   |       |               |   |   |      |   |   |   |   |   |
| Net      production revenues                  |   |     | 516,600   |   |     |   | 959,400    |               |   |   | —   |   |   |   | 1,476,000 |   |
| Interest      income                          |   |     | 300       |   |     |   | 500        |               |   |   | —   |   |   |   | 800 |   |
| Depletion                                     |   |     | (187,000  | )      |     |   | (1,144,500 | )                  |   |   | —   |   |   |   | (1,331,500 | ) |
| Accretion      of asset retirement obligation |   |     | (33,000   | )      |     |   | (61,400    | )                  |   |   | —   |   |   |   | (94,400 | ) |
| General      and administrative               |   |     | (60,000   | )      |     |   | (111,300   | )                  |   |   | —   |   |   |   | (171,300 | ) |
| Net      (loss) earnings                      |   |     | 236,900   |   |     |   | (357,300   | )                  |   |   | —   |   |   |   | (120,400 | ) |
|                                          |   |     |      |   |     |   |       |               |   |   |      |   |   |   |   |   |
| Other      comprehensive loss                 |   |     | —   |   |     |   | —    |               |   |   | (808,100  | )      |   |   | (808,100 | ) |
|                                          |   |     |      |   |     |   |       |               |   |   |      |   |   |   |   |   |
| Distributions      to partners                |   |     | (710,400  | )      |     |   | (1,319,300 | )                  |   |   | —   |   |   |   | (2,029,700 | ) |
|                                          |   |     |      |   |     |   |       |               |   |   |      |   |   |   |   |   |
| Balance      at September 30, 2009            |   | $        | 8,526,300 |   |     | $      | 16,099,400 |               |   | $      | 714,800   |   |   | $ | 25,340,500 |   |

|                                                                                          |   | Nine      Months Ended |       |
|-----------------------------------------------------------------------------------------------|--------|------------------------|------------|
|                                                                                          |   | September      30,     |       |
|                                                                                          |   | 2009                   |       |   | 2008 |   |
| Cash      flows from operating activities:                                                    |   |                   |       |   |   |   |
| Net      (loss) earnings                                                                      |   | $                      | (120,400   | ) |   | $ | 992,300 |   |
| Adjustments      to reconcile net earnings to net cash provided by operating      activities: |   |                   |       |   |   |   |   |   |
| Depletion                                                                                     |   |                   | 1,331,500  |   |   |   | 2,201,000 |   |
| Non-cash      loss on derivative value                                                        |   |                   | 24,500     |   |   |   | 39,100 |   |
| Accretion      of asset retirement obligation                                                 |   |                   | 94,400     |   |   |   | 88,900 |   |
| Decrease      (increase) in accounts receivable – affiliate                             |   |                   | 389,600    |   |   |   | (108,100 | ) |
| Increase      in accrued liabilities                                                          |   |                   | 6,300      |   |   |   | 4,900 |   |
| Net      cash provided by operating activities                                                |   |                   | 1,725,900  |   |   |   | 3,218,100 |   |
|                                                                                          |   |                   |       |   |   |   |   |   |
| Cash      flows from financing activities:                                                    |   |                   |       |   |   |   |   |   |
| Distributions      to partners                                                                |   |                   | (2,029,700 | ) |   |   | (3,106,200 | ) |
| Net      cash used in financing activities                                                    |   |                   | (2,029,700 | ) |   |   | (3,106,200 | ) |
|                                                                                          |   |                   |       |   |   |   |   |   |
| Net      (decrease) increase in cash and cash equivalents                                     |   |                   | (303,800   | ) |   |   | 111,900 |   |
| Cash      and cash equivalents at beginning of period                                         |   |                   | 574,000    |   |   |   | 750,100 |   |
| Cash      and cash equivalents at end of period                                               |   | $                      | 270,200    |   |   | $ | 862,000 |   |

| Oil      and gas properties consist of the following at the dates      indicated: |   | September      30, |        |   | December      31, |   |
|-----------------------------------------------------------------------------------|--------|--------------------|-------------|--------|-------------------|--------|
|                                                                              |   | 2009               |        |   | 2008              |   |
| Natural      gas and oil properties:                                              |   |               |        |   |              |   |
| Proved      properties:                                                           |   |               |        |   |              |   |
| Leasehold      interests                                                          |   | $                  | 1,137,100   |   |              | $      | 1,137,100 |   |
| Wells      and related equipment                                                  |   |               | 51,580,600  |   |              |   | 51,580,600 |   |
|                                                                              |   |               | 52,717,700  |   |              |   | 52,717,700 |   |
|                                                                              |   |               |        |   |              |   |   |   |
| Accumulated      depletion                                                        |   |               | (26,764,000 | )      |              |   | (25,432,500 | ) |
|                                                                              |   | $                  | 25,953,700  |   |              | $      | 27,285,200 |   |

| ·   | Introduce      a new definition of oil and gas producing activities. This new definition      allows companies to include in their reserve base volumes from      unconventional resources. Such unconventional resources include bitumen      extracted from oil sands and oil and gas extracted from coal beds and      shale formations. |
|--------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| ·   | Report      oil and gas reserves using an unweighted average price using the prior      12-month period, based on the closing prices on the first day of each      month, rather than year-end pricing. This should maximize the      comparability of reserve estimates among companies and mitigate the      distortion of the estimates that arises when using a single pricing      date. |
|--------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| ·   | Permit      companies to disclose their probable and possible reserves on a voluntary      basis. Current rules limit disclosure to only proved    reserves. |
|--------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------|

| ·   | Update      and revise reserve definitions to reflect changes in the oil and gas      industry and new technologies. New updated definitions include “by      geographic area” and “reasonablecertainty.” |
|--------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| ·   | Permit      the use of new technologies to determine proved reserves if those      technologies have been demonstrated empirically to lead to reliable      conclusions about reserves volumes. |
|--------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| ·   | Require      additional disclosures regarding the qualifications of the chief technical      person who oversees the Partnership’s overall reserve estimation process.      Additionally, disclosures are required related to internal controls over      reserve estimation, as well as a report addressing the independence and      qualifications of a Partnership’s  reserves preparer or auditor      based on Society of Petroleum Engineers  criteria. |
|--------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| ·   | Administrative      costs which are included in general and administrative expenses in the      Partnership’s Statements of Operations are payable at $75 per well per      month. Administrative costs incurred for the three months and nine months      ended September 30, 2009 were $36,300 and $126,100, respectively.      Administrative costs incurred for the three months and nine months ended      September 30, 2008 were $45,300 and $135,700,  respectively. |
|--------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| ·   | Monthly      well supervision fees which are included in production expenses in the      Partnership’s Statements of Operations are payable at $313 per well per      month in 2009 and 2008, respectively, for operating and maintaining the      wells. Well supervision fees incurred for the three months and nine months      ended September 30, 2009 were $151,600 and $526,800, respectively. Well      supervision fees incurred for the three months and nine months ended      September 30, 2008 were $189,200 and $566,900,    respectively. |
|--------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| ·   | Transportation      fees which are included in production expenses in the Partnership’s      Statements of Operations are generally payable at 13% of the natural gas      sales price. Transportation fees incurred for the three months and nine      months ended September 30, 2009 were $86,200 and $286,000, respectively.      Transportation fees incurred for the three months and nine months ended      September 30, 2008 were $161,400 and $543,000,    respectively. |
|--------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

|                                                                                    |   | Three      Months Ended |     | Nine      Months Ended |   |
|-----------------------------------------------------------------------------------------|--------|-------------------------|----------|------------------------|--------|
|                                                                                    |   | September      30,      |     | September      30,     |   |
|                                                                                    |   | 2009                    |     | 2008                   |   | 2009 |   | 2008 |   |
|                                                                                    |   |                    |     |                   |   |   |   |   |   |
| Net      (loss) earnings                                                                |   | $                       | (77,700  | )                      | $      | 424,900 |   | $ | (120,400 | ) | $ | 992,300 |   |
| Other      comprehensive income (loss):                                                 |   |                    |     |                   |   |   |   |   |   |   |   |   |   |
| Unrealized      holding gain (loss) on hedging contracts                                |   |                    | 900      |                   |   | 3,680,800 |   |   | 27,100 |   |   | (83,300 | ) |
| Less:      reclassification adjustment for (gains) losses realized in net      earnings |   |                    | (310,900 | )                      |   | 356,000 |   |   | (835,200 | ) |   | 245,500 |   |
| Total      other comprehensive income (loss)                                            |   |                    | (310,000 | )                      |   | 4,036,800 |   |   | (808,100 | ) |   | 162,200 |   |
| Comprehensive      income (loss)                                                        |   | $                       | (387,700 | )                      | $      | 4,461,700 |   | $ | (928,500 | ) | $ | 1,154,500 |   |

| Fair      Value of Derivative Instruments: |   |
|--------------------------------------------|--------|
|                                       |   | Asset      Derivatives |   | Liability      Derivatives |   |
| Derivatives      in                        |   |   |   | Fair      Value |   |   |   | Fair      Value |   |
| Cash      Flow Hedging                     |   | Balance      Sheet |   | September      30, |   |   | December      31, |   | Balance      Sheet |   | September      30, |   |   | December      31, |   |
| Relationships                              |   | Location |   | 2009 |   |   | 2008 |   | Location |   | 2009 |   |   | 2008 |   |
|                                       |   |   |   |   |   |   |   |   |   |
| Commodity      contracts:                  |   | Current      assets |   | $ | 482,900 |   |   | $ | 1,071,500 |   | Current      liabilities |   | $ | (7,300 | ) |   | $ | (95,700 | ) |
|                                       |   | Long-term      assets |   |   | 335,000 |   |   |   | 666,900 |   | Long-term      liabilities |   |   | (86,600 | ) |   |   | (86,100 | ) |
|                                       |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
| Total      derivatives                     |   | $ | 817,900 |   |   | $ | 1,738,400 |   |   |   | $ | (93,900 | ) |   | $ | (181,800 | ) |

| Derivatives      in       |   | GainRecognized      in OCI on Derivative(Effective      Portion)Three      Months Ended |   | Location      of Gain/(Loss)Reclassified      from Accumulated |               | Gain/(Loss)Reclassified      from OCI into Income(Effective      Portion)Three      Months Ended |                     |
|---------------------------|--------|-----------------------------------------------------------------------------------------|--------|----------------------------------------------------------------|--------------------|--------------------------------------------------------------------------------------------------|--------------------------|
| Cash      Flow            |   | September      30,                                                                      |   |                                                           | September      30, |                                                                                             | OCI      into Income     |   | September      30, |   |   | September      30, |   |
| Hedging      Relationship |   | 2009                                                                                    |   |                                                           | 2008               |                                                                                             | (Effective      Portion) |   | 2009 |   |   | 2008 |   |
|                      |   |                                                                                    |   |                                                           |               |                                                                                             |                     |
| Commodity      contracts  |   | $                                                                                       | 900    |                                                           |               | $                                                                                                | 3,680,800                |   | Natural      gas and oil revenue |   | $ | 310,900 |   |   | $ | (356,000 | ) |

| Derivatives      in       |   | Gain/(Loss)Recognized      in OCI on Derivative(Effective      Portion)Nine      Months Ended |   | Location      of Gain/(Loss)Reclassified      from Accumulated |               | Gain/(Loss)Reclassified      from OCI into Income(Effective      Portion)Nine      Months Ended |                     |
|---------------------------|--------|-----------------------------------------------------------------------------------------------|--------|----------------------------------------------------------------|--------------------|-------------------------------------------------------------------------------------------------|--------------------------|
| Cash      Flow            |   | September      30,                                                                            |   |                                                           | September      30, |                                                                                            | OCI      into Income     |   | September      30, |   |   | September      30, |   |
| Hedging      Relationship |   | 2009                                                                                          |   |                                                           | 2008               |                                                                                            | (Effective      Portion) |   | 2009 |   |   | 2008 |   |
|                      |   |                                                                                          |   |                                                           |               |                                                                                            |                     |
| Commodity      contracts  |   | $                                                                                             | 27,100 |                                                           |               | $                                                                                               | (83,300                  | ) | Natural      gas and oil revenue |   | $ | 835,200 |   |   | $ | (245,500 | ) |

|               |   |             |    |   |                 |   |   |            |   |
|--------------------|--------|------------------|---------|--------|----------------------|--------|--------|-----------------|--------|
| Production         |   |             |    |   | Average              |   |   |            |   |
| Period      Ending |   | Volumes          |    |   | Fixed      Price     |   |   | Fair      Value |   |
| December      31,  |   | (MMbtu)      (1) |    |   | (per      MMbtu) (1) |   |   | Asset      (2)  |   |
|               |   |             |    |   |                 |   |   |            |   |
| 2009               |   |             | 61,100  |   |                 | $      | 8.24   |            |   | $ | 213,700 |   |
| 2010               |   |             | 179,900 |   |                 |   | 7.71   |            |   |   | 270,700 |   |
| 2011               |   |             | 109,700 |   |                 |   | 7.04   |            |   |   | 90,800 |   |
| 2012               |   |             | 100,600 |   |                 |   | 7.22   |            |   |   | 68,400 |   |
| 2013               |   |             | 58,700  |   |                 |   | 7.08   |            |   |   | 8,500 |   |
|               |   |             |    |   |                 |   |   |            |   | $ | 652,100 |   |

|               |   |                |   |             |   |   |                 |   |   |                 |   |
|--------------------|--------|---------------------|--------|------------------|--------|--------|----------------------|--------|--------|----------------------|--------|
| Production         |   |                |   |             |   |   | Average              |   |   | Fair      Value      |   |
| Period      Ending |   | Option              |   | Volumes          |   |   | Floor      & Cap |   |   | Asset                |   |
| December      31,  |   | Type                |   | (MMbtu)      (1) |   |   | (per      MMbtu) (1) |   |   | (Liability)      (2) |   |
|               |   |                |   |             |   |   |                 |   |   |                 |   |
| 2009               |   | Puts      purchased |   |             | 300    |   |                 | $      | 11.00  |                 |   |   | 2,200 |   |
| 2009               |   | Calls      sold     |   |             | 300    |   |                 |   | 15.35  |                 |   |   | — |   |
| 2010               |   | Puts      purchased |   |             | 18,700 |   |                 |   | 7.84   |                 |   |   | 34,100 |   |
| 2010               |   | Calls      sold     |   |             | 18,700 |   |                 |   | 9.01   |                 |   |   | — |   |
| 2011               |   | Puts      purchased |   |             | 49,600 |   |                 |   | 6.52   |                 |   |   | 32,200 |   |
| 2011               |   | Calls      sold     |   |             | 49,600 |   |                 |   | 7.67   |                 |   |   | — |   |
| 2012               |   | Puts      purchased |   |             | 18,900 |   |                 |   | 6.51   |                 |   |   | 200 |   |
| 2012               |   | Calls      sold     |   |             | 18,900 |   |                 |   | 7.72   |                 |   |   | — |   |
| 2013               |   | Puts      purchased |   |             | 23,500 |   |                 |   | 6.52   |                 |   |   | — |   |
| 2013               |   | Calls      sold     |   |             | 23,500 |   |                 |   | 7.81   |                 |   |   | (2,400 | ) |
|               |   |                |   |             |   |   |                 |   |   |                 |   | $ | 66,300 |   |

|               |   |           |   |   |               |   |   |            |   |
|--------------------|--------|----------------|--------|--------|--------------------|--------|--------|-----------------|--------|
| Production         |   |           |   |   | Average            |   |   |            |   |
| Period      Ending |   | Volumes        |   |   | Fixed      Price   |   |   | Fair      Value |   |
| December      31,  |   | (Bbl)      (1) |   |   | (per      Bbl) (1) |   |   | Asset      (3)  |   |
|               |   |           |   |   |               |   |   |            |   |
| 2009               |   |           | 20     |   |               | $      | 99.32  |            |   | $ | 600 |   |
| 2010               |   |           | 70     |   |               |   | 97.40  |            |   |   | 1,500 |   |
| 2011               |   |           | 60     |   |               |   | 77.46  |            |   |   | 1,000 |   |
| 2012               |   |           | 40     |   |               |   | 76.86  |            |   |   | 600 |   |
| 2013               |   |           | 10     |   |               |   | 77.36  |            |   |   | 200 |   |
|               |   |           |   |   |               |   |   |            |   | $ | 3,900 |   |

|               |   |                |   |           |   |   |                 |                 |   |            |   |
|--------------------|--------|---------------------|--------|----------------|--------|--------|----------------------|----------------------|--------|-----------------|--------|
| Production         |   |                |   |           |   |   | Average              |                 |   |            |   |
| Period      Ending |   | Option              |   | Volumes        |   |   | Floor      & Cap |                 |   | Fair      Value |   |
| December      31,  |   | Type                |   | (Bbl)      (1) |   |   | (per      Bbl) (1)   |                 |   | Asset      (3)  |   |
|               |   |                |   |           |   |   |                 |                 |   |            |   |
| 2009               |   | Puts      purchased |   |           | 10     |   |                 | $                    | 85.00  |            |   | $ | 200 |   |
| 2009               |   | Calls      sold     |   |           | 10     |   |                 |                 | 116.56 |            |   |   | — |   |
| 2010               |   | Puts      purchased |   |           | 35     |   |                 |                 | 85.00  |            |   |   | 600 |   |
| 2010               |   | Calls      sold     |   |           | 35     |   |                 |                 | 112.92 |            |   |   | — |   |
| 2011               |   | Puts      purchased |   |           | 30     |   |                 |                 | 67.22  |            |   |   | 500 |   |
| 2011               |   | Calls      sold     |   |           | 30     |   |                 |                 | 89.44  |            |   |   | — |   |
| 2012               |   | Puts      purchased |   |           | 20     |   |                 |                 | 65.51  |            |   |   | 300 |   |
| 2012               |   | Calls      sold     |   |           | 20     |   |                 |                 | 91.45  |            |   |   | — |   |
| 2013               |   | Puts      purchased |   |           | 5      |   |                 |                 | 65.36  |            |   |   | 100 |   |
| 2013               |   | Calls      sold     |   |           | 5      |   |                 |                 | 93.44  |            |   |   | — |   |
|               |   |                |   |           |   |   |                 |                 |   |            |   | $ | 1,700 |   |
|               |   |                |   |           |   |   |                 |                 |   |            |   |   |   |   |
|               |   |                |   |           |   |   |                 | Total      Net Asset |   |            | $      | 724,000 |   |

| (1)   | MMBTU      represents million British Thermal Units. Bbl represents      barrels. |
|-----------------|-----------------------------------------------------------------------------------|

| (2)   | Fair      value based on forward NYMEX natural gasprices. |
|-----------------|-----------------------------------------------------------|

| (3)   | Fair      value based on forward WTI crude oilprices. |
|-----------------|-------------------------------------------------------|

|                                                                                                                                                                                                                                                                          |   | September      30, 2009 |    |   | December      31, 2008 |   |
|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|--------|-------------------------|---------|--------|------------------------|--------|
|                                                                                                                                                                                                                                                                          |   | Level      2            |    |   | Total                  |   |   | Level      2 |   |   | Total |   |
|                                                                                                                                                                                                                                                                          |   |                    |    |   |                   |   |   |   |   |   |   |   |
| Commodity-based      derivatives                                                                                                                                                                                                                                              |   | $                       | 724,000 |   |                   | $      | 724,000 |   |   | $ | 1,556,600 |   |   | $ | 1,556,600 |   |
| Total                                             |   | $                       | 724,000 |   |                   | $      | 724,000 |   |   | $ | 1,556,600 |   |   | $ | 1,556,600 |   |

|                                                    |   | Three      Months Ended |      |   | Nine      Months Ended |   |
|---------------------------------------------------------|--------|-------------------------|-----------|--------|------------------------|--------|
|                                                    |   | September      30,      |      |   | September      30,     |   |
|                                                    |   | 2009                    |      |   | 2008                   |   |   | 2009 |   |   | 2008 |   |
|                                                    |   |                    |      |   |                   |   |   |   |   |   |   |   |
| Asset      retirement obligation at beginning of period |   | $                       | 2,160,800 |   |                   | $      | 2,035,300 |   |   | $ | 2,097,900 |   |   | $ | 1,976,000 |   |
| Accretion      expense                                  |   |                    | 31,500    |   |                   |   | 29,600 |   |   |   | 94,400 |   |   |   | 88,900 |   |
| Asset      retirement obligation at end of period       |   | $                       | 2,192,300 |   |                   | $      | 2,064,900 |   |   | $ | 2,192,300 |   |   | $ | 2,064,900 |   |

| ITEM      2. | MANAGEMENT'S      DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION OR PLAN OF OPERATIONS      (UNAUDITED) |
|--------------|---------------------------------------------------------------------------------------------------------|

|                                     |   | Three      Months Ended |   |   | Nine      Months Ended |   |
|------------------------------------------|--------|-------------------------|--------|--------|------------------------|--------|
|                                     |   | September      30,      |   |   | September      30,     |   |
|                                     |   | 2009                    |   |   | 2008                   |   |   | 2009 |   |   | 2008 |   |
|                                     |   |                    |   |   |                   |   |   |   |   |   |   |   |
| Production      revenues (in thousands): |   |                    |   |   |                   |   |   |   |   |   |   |   |
| Gas                                      |   | $                       | 719    |   |                   | $      | 1,448 |   |   | $ | 2,466 |   |   | $ | 4,602 |   |
| Oil                                      |   |                    | 52     |   |                   |   | 102 |   |   |   | 87 |   |   |   | 193 |   |
| Total                                    |   | $                       | 771    |   |                   | $      | 1,550 |   |   | $ | 2,553 |   |   | $ | 4,795 |   |
|                                     |   |                    |   |   |                   |   |   |   |   |   |   |   |   |   |   |   |
| Production      volumes:                 |   |                    |   |   |                   |   |   |   |   |   |   |   |   |   |   |   |
| Gas      (mcf/day) (1)                   |   |                    | 968    |   |                   |   | 1,434 |   |   |   | 1,088 |   |   |   | 1,743 |   |
| Oil      (bbls/day) (1)                  |   |                    | 8      |   |                   |   | 9 |   |   |   | 5 |   |   |   | 6 |   |
| Total      (mcfe/day) (1)                |   |                    | 1,016  |   |                   |   | 1,488 |   |   |   | 1,118 |   |   |   | 1,779 |   |
|                                     |   |                    |   |   |                   |   |   |   |   |   |   |   |   |   |   |   |
| Average      sales prices: (2)           |   |                    |   |   |                   |   |   |   |   |   |   |   |   |   |   |   |
| Gas      (per mcf) (1)      (3)          |   | $                       | 8.24   |   |                   | $      | 11.12 |   |   | $ | 8.39 |   |   | $ | 9.72 |   |
| Oil      (per bbl) (1)                   |   | $                       | 73.22  |   |                   | $      | 126.22 |   |   | $ | 61.97 |   |   | $ | 111.96 |   |
|                                     |   |                    |   |   |                   |   |   |   |   |   |   |   |   |   |   |   |
| Average      production costs:           |   |                    |   |   |                   |   |   |   |   |   |   |   |   |   |   |   |
| As      a percent of revenues            |   |                    | 45     | %      |                   |   | 27 | % |   |   | 42 | % |   |   | 28 | % |
| Per      mcfe (1)                        |   | $                       | 3.74   |   |                   | $      | 3.09 |   |   | $ | 3.53 |   |   | $ | 2.75 |   |
|                                     |   |                    |   |   |                   |   |   |   |   |   |   |   |   |   |   |   |
| Depletion      per mcfe                  |   | $                       | 4.36   |   |                   | $      | 4.52 |   |   | $ | 4.36 |   |   | $ | 4.51 |   |

| (1)   | “Mcf”      means thousand cubic feet, “mcfe” means thousand cubic feet equivalent and      “bbls” means barrels. Bbls are converted to mcfe using the ratio of six      mcfs to one bbl. |
|-----------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| (2)   | Average      sales prices represent accrual basis pricing after reversing the effect of      previously recognized gains resulting from prior period impairment      charges. |
|-----------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| (3)   | Average      gas prices are calculated by including in total revenue derivative gains      previously recognized into income and dividing by the total volume for the      period. Previously recognized derivative gains were $14,500 and $24,500      for the three months and nine months ended September 30, 2009. Previously      recognized derivative gains were $18,400 and $39,100 for the three months      and nine months ended September 30, 2008. The derivative gains are      included in other comprehensive income and resulted from prior period      impairment charges. |
|-----------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| ·   | Introduce      a new definition of oil and gas producing activities. This new definition      allows companies to include in their reserve base volumes from      unconventional resources. Such unconventional resources include bitumen      extracted from oil sands and oil and gas extracted from coal beds and      shale formations. |
|--------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| ·   | Report      oil and gas reserves using an unweighted average price using the prior      12-month period, based on the closing prices on the first day of each      month, rather than year-end pricing. This should maximize the      comparability of reserve estimates among companies and mitigate the      distortion of the estimates that arises when using a single pricing      date. |
|--------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| ·   | Permit      companies to disclose their probable and possible reserves on a voluntary      basis. Current rules limit disclosure to only proved    reserves. |
|--------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------|

| ·   | Update      and revise reserve definitions to reflect changes in the oil and gas      industry and new technologies. New updated definitions include “by      geographic area” and “reasonablecertainty.” |
|--------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| ·   | Permit      the use of new technologies to determine proved reserves if those      technologies have been demonstrated empirically to lead to reliable      conclusions about reserves volumes. |
|--------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| ·   | Require      additional disclosures regarding the qualifications of the chief technical      person who oversees the Partnership’s overall reserve estimation process.      Additionally, disclosures are required related to internal controls over      reserve estimation, as well as a report addressing the independence and      qualifications of a Partnership’s reserves preparer or auditor based on      Society of Petroleum Engineerscriteria. |
|--------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| Exhibit      No. |   | Description                                                                                                          |
|------------------|--------|----------------------------------------------------------------------------------------------------------------------|
|             |   |                                                                                                                 |
| 4.0              |   | Amended      and Restated Certificate and Agreement of Limited Partnership for Public      #12-2003 Limited          |
|             |   | Partnership      (1)                                                                                                 |
| 10.1             |   | Drilling      and Operating Agreement for Atlas America Public #12-2003 Limited      Partnership (1)                 |
| 31.1             |   | Certification      Pursuant to Rule 13a-14/15(d)-14                                                                  |
| 31.2             |   | Certification      Pursuant to Rule 13a-14/15(d)-14                                                                  |
| 32.1             |   | Certification      Pursuant to 18 U.S.C. Section 1350, as Adopted Pursuant to Section 906 of      the Sarbanes-Oxley |
|             |   | Act      of 2002                                                                                                     |
| 32.2             |   | Certification      Pursuant to 18 U.S.C. Section 1350, as Adopted Pursuant to Section 906 of      the Sarbanes-Oxley |
|             |   | Act      of 2002                                                                                                     |

| (1) |   | Filed      on September 3, 2003 in the Form S-1 Registration Statement dated      September 3, 2003, File No.333-105811 |
|-----|--------|-------------------------------------------------------------------------------------------------------------------------|

| Pursuant      to the requirements of the Securities of the Exchange Act of 1934, the      registrant has duly caused this report to be signed on its behalf by the      undersigned, thereunto duly authorized. |
|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
|                                                                                                                                                                                                            |
|                                                                                                                                                                                                            |   |   |
|                                                                                                                                                                                                            |   |   |
| Atlas      America Public #12-2003 Limited Partnership                                                                                                                                                          |
|                                                                                                                                                                                                            |   |   |
|                                                                                                                                                                                                            |   | Atlas      Resources, LLC, Managing General Partner |
|                                                                                                                                                                                                            |   |   |
| Date:  November      16, 2009                                                                                                                                                                         |   | By:/s/ Freddie M.      Kotek |
|                                                                                                                                                                                                            |   | Freddie      M. Kotek, Chairman of the Board of Directors, Chief Executive      Officer |
|                                                                                                                                                                                                            |   | and      President |
|                                                                                                                                                                                                            |   |   |
|                                                                                                                                                                                                            |   |   |
| In      accordance with the Exchange Act, this report has been signed by the      following persons on behalf of the registrant and in the capacities and on      the dates indicated.                          |
|                                                                                                                                                                                                            |
|                                                                                                                                                                                                            |   |   |
|                                                                                                                                                                                                            |   |   |
| Date:  November      16, 2009                                                                                                                                                                         |   | By:/s/ Freddie M.      Kotek |
|                                                                                                                                                                                                            |   | Freddie      M. Kotek, Chairman of the Board of Directors, Chief    Executive |
|                                                                                                                                                                                                            |   | Officer      and President |
|                                                                                                                                                                                                            |   |   |
|                                                                                                                                                                                                            |   |   |
| Date:  November      16, 2009                                                                                                                                                                         |   | By:/s/ Matthew A.      Jones |
|                                                                                                                                                                                                            |   | Matthew      A. Jones, Chief Financial Officer |
|                                                                                                                                                                                                            |   |   |
|                                                                                                                                                                                                            |   |   |
| Date:  November      16, 2009                                                                                                                                                                         |   | By:/s/ Sean P.      McGrath |
|                                                                                                                                                                                                            |   | Sean      P. McGrath, Chief Accounting Officer |
|                                                                                                                                                                                                            |   |   |
|                                                                                                                                                                                                            |   |   |
|                                                                                                                                                                                                            |   |   |
|                                                                                                                                                                                                            |   |   |
|                                                                                                                                                                                                            |   |   |