|                                                                                                                                                            | 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 March 31, 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", 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 March 31, 2009 and December 31, 2008                                      | 3      |
|           |   |                                                                                                |   |
|           |   | Statements      of Net Earnings for the Three Months Ended March 31, 2009 and      2008             | 4      |
|           |   |                                                                                                |   |
|           |   | Statement      of Changes in Partners’ Capital for the Three Months ended March 31,      2009 | 5      |
|           |   |                                                                                                |   |
|           |   | Statements      of Cash Flows for the Three Months ended March 31, 2009 and      2008               | 6      |
|           |   |                                                                                                |   |
|           |   | Notes      to Financial Statements                                                                  | 7-15   |
|           |   |                                                                                                |   |
| Item      2:   |   | Management’s      Discussion and Analysis of Financial Condition or Plan of      Operations   | 15-18  |
|           |   |                                                                                                |   |
| Item      4:   |   | Controls      and Procedures                                                                        | 18-19  |
|           |   |                                                                                                |   |
| PART      II.  |   | OTHER      INFORMATION                                                                              |   |
|           |   |                                                                                                |   |
| Item      1:   |   | Legal      Proceedings                                                                              | 19     |
|           |   |                                                                                                |   |
| Item      6:   |   | Exhibits                                                                                            | 19     |
|           |   |                                                                                                |   |
|           |   |                                                                                                |   |
| SIGNATURES     | 20     |
|           |   |                                                                                                |   |
| CERTIFICATIONS | 21-24  |

|                                                |   | March      31, |       |   | December      31, |   |
|-----------------------------------------------------|--------|----------------|------------|--------|-------------------|--------|
|                                                |   | 2009           |       |   | 2008              |   |
|                                                |   | (Unaudited)    |       |   |              |   |
| ASSETS                                              |   |           |       |   |              |   |
| Current      assets:                                |   |           |       |   |              |   |
| Cash      and cash equivalents                      |   | $              | 552,700    |   |              | $      | 574,000 |   |
| Accounts      receivable-affiliate                  |   |           | 774,800    |   |              |   | 1,003,000 |   |
| Short-term      hedge receivable due from affiliate |   |           | 871,500    |   |              |   | 1,071,500 |   |
| Total      current assets                           |   |           | 2,199,000  |   |              |   | 2,648,500 |   |
|                                                |   |           |       |   |              |   |   |   |
| Oil      and gas properties, net                    |   |           | 26,801,800 |   |              |   | 27,285,200 |   |
| Long-term      hedge receivable due from affiliate  |   |           | 547,000    |   |              |   | 666,900 |   |
|                                                |   | $              | 29,547,800 |   |              | $      | 30,600,600 |   |
|                                                |   |           |       |   |              |   |   |   |
| LIABILITIES      AND PARTNERS’ CAPITAL        |   |           |       |   |              |   |   |   |
| Current      liabilities:                           |   |           |       |   |              |   |   |   |
| Accrued      liabilities                            |   | $              | 10,000     |   |              | $      | 22,200 |   |
| Short-term      hedge liability due to affiliate    |   |           | 2,000      |   |              |   | 95,700 |   |
| Total      current liabilities                      |   |           | 12,000     |   |              |   | 117,900 |   |
|                                                |   |           |       |   |              |   |   |   |
| Asset      retirement obligation                    |   |           | 2,129,400  |   |              |   | 2,097,900 |   |
| Long-term      hedge liability due to affiliate     |   |           | 200        |   |              |   | 86,100 |   |
|                                                |   |           |       |   |              |   |   |   |
| Partners’      capital:                       |   |           |       |   |              |   |   |   |
| Managing      general partner                       |   |           | 8,839,800  |   |              |   | 8,999,800 |   |
| Limited      partners (4,024 units)                 |   |           | 17,189,400 |   |              |   | 17,776,000 |   |
| Accumulated      other comprehensive income         |   |           | 1,377,000  |   |              |   | 1,522,900 |   |
| Total      partners' capital                        |   |           | 27,406,200 |   |              |   | 28,298,700 |   |
|                                                |   | $              | 29,547,800 |   |              | $      | 30,600,600 |   |

|                                          |   | Three      Months Ended |      |
|-----------------------------------------------|--------|-------------------------|-----------|
|                                          |   | March      31,          |      |
|                                          |   | 2009                    |      |   | 2008 |   |
| REVENUES                                      |   |                    |      |   |   |   |
| Natural      gas and oil                      |   | $                       | 1,016,300 |   |   | $ | 1,507,000 |   |
| Interest      income                          |   |                    | 400       |   |   |   | 3,400 |   |
| Total      revenues                           |   |                    | 1,016,700 |   |   |   | 1,510,400 |   |
|                                          |   |                    |      |   |   |   |   |   |
| COSTS      AND EXPENSES                       |   |                    |      |   |   |   |   |   |
| Production                                    |   |                    | 360,300   |   |   |   | 429,400 |   |
| Depletion                                     |   |                    | 483,400   |   |   |   | 754,200 |   |
| Accretion      of asset retirement obligation |   |                    | 31,500    |   |   |   | 29,600 |   |
| General      and administrative               |   |                    | 53,100    |   |   |   | 54,200 |   |
| Total      expenses                           |   |                    | 928,300   |   |   |   | 1,267,400 |   |
| Net      earnings                             |   | $                       | 88,400    |   |   | $ | 243,000 |   |
|                                          |   |                    |      |   |   |   |   |   |
| Allocation      of net (loss) earnings:       |   |                    |      |   |   |   |   |   |
| Managing      general partner                 |   | $                       | 132,200   |   |   | $ | 267,100 |   |
| Limited      partners                         |   | $                       | (43,800   | ) |   | $ | (24,100 | ) |
| Net      loss per limited partnership unit    |   | $                       | (11       | ) |   | $ | (6 | ) |

|                                          |   |     |      |   |     |   |       | 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                  |   |     | 229,600   |   |     |   | 426,400    |               |   |   | —   |   |   |   | 656,000 |   |
| Interest      income                          |   |     | 100       |   |     |   | 300        |               |   |   | —   |   |   |   | 400 |   |
| Depletion                                     |   |     | (67,900   | )      |     |   | (415,500   | )                  |   |   | —   |   |   |   | (483,400 | ) |
| Accretion      of asset retirement obligation |   |     | (11,000   | )      |     |   | (20,500    | )                  |   |   | —   |   |   |   | (31,500 | ) |
| General      and administrative               |   |     | (18,600   | )      |     |   | (34,500    | )                  |   |   | —   |   |   |   | (53,100 | ) |
| Net      earnings                             |   |     | 132,200   |   |     |   | (43,800    | )                  |   |   | —   |   |   |   | 88,400 |   |
|                                          |   |     |      |   |     |   |       |               |   |   |      |   |   |   |   |   |
| Other      comprehensive loss                 |   |     | —   |   |     |   | —    |               |   |   | (145,900  | )      |   |   | (145,900 | ) |
|                                          |   |     |      |   |     |   |       |               |   |   |      |   |   |   |   |   |
| Distributions      to partners                |   |     | (292,200  | )      |     |   | (542,800   | )                  |   |   | —   |   |   |   | (835,000 | ) |
|                                          |   |     |      |   |     |   |       |               |   |   |      |   |   |   |   |   |
| Balance      at March 31, 2009                |   | $        | 8,839,800 |   |     | $      | 17,189,400 |               |   | $      | 1,377,000 |   |   | $ | 27,406,200 |   |

|                                                                                          |   | Three      Months Ended |     |
|-----------------------------------------------------------------------------------------------|--------|-------------------------|----------|
|                                                                                          |   | March      31,          |     |
|                                                                                          |   | 2009                    |     |   | 2008 |   |
| Cash      flows from operating activities:                                                    |   |                    |     |   |   |   |
| Net      earnings                                                                             |   | $                       | 88,400   |   |   | $ | 243,000 |   |
| Adjustments      to reconcile net earnings to net cash provided by operating      activities: |   |                    |     |   |   |   |   |   |
| Depletion                                                                                     |   |                    | 483,400  |   |   |   | 754,200 |   |
| Non-cash      gain on derivative value                                                        |   |                    | (5,600   | ) |   |   | (400 | ) |
| Accretion      of asset retirement obligation                                                 |   |                    | 31,500   |   |   |   | 29,600 |   |
| Decrease      in accounts receivable – affiliate                                        |   |                    | 228,200  |   |   |   | 74,300 |   |
| Decrease      in accrued liabilities                                                          |   |                    | (12,200  | ) |   |   | (7,500 | ) |
| Net      cash provided by operating activities                                                |   |                    | 813,700  |   |   |   | 1,093,200 |   |
|                                                                                          |   |                    |     |   |   |   |   |   |
| Cash      flows from financing activities:                                                    |   |                    |     |   |   |   |   |   |
| Distributions      to partners                                                                |   |                    | (835,000 | ) |   |   | (892,200 | ) |
| Net      cash used in financing activities                                                    |   |                    | (835,000 | ) |   |   | (892,200 | ) |
|                                                                                          |   |                    |     |   |   |   |   |   |
| Net      (decrease) increase in cash and cash equivalents                                     |   |                    | (21,300  | ) |   |   | 201,000 |   |
| Cash      and cash equivalents at beginning of period                                         |   |                    | 574,000  |   |   |   | 750,100 |   |
| Cash      and cash equivalents at end of period                                               |   | $                       | 552,700  |   |   | $ | 951,100 |   |

| Oil      and gas properties consist of the following at the dates      indicated: |   | March      31, |        |   | 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                                                        |   |           | (25,915,900 | )      |              |   | (25,432,500 | ) |
|                                                                              |   | $              | 26,801,800  |   |              | $      | 27,285,200 |   |

| ·   | Administrative      costs which are included in general and administrative expenses in the      Partnership’s Statements of Net Earnings are payable at $75 per well per      month. Administrative costs incurred for both the three months ended March      31, 2009 and 2008 were $45,100. |
|--------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| ·   | Monthly      well supervision fees which are included in production expenses in the      Partnership’s Statements of Net Earnings 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 ended March 31,      2009 and 2008 were $188,200 and $188,600,  respectively. |
|--------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| ·   | Transportation      fees which are included in production expenses in the Partnership’s      Statements of Net Earnings are generally payable at 13% of the natural gas      sales price. Transportation fees incurred for the three months ended March      31, 2009 and 2008 were $115,200 and $176,000,  respectively. |
|--------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

|                                                                         |   | Three      Months Ended |     |
|------------------------------------------------------------------------------|--------|-------------------------|----------|
|                                                                         |   | March      31,          |     |
|                                                                         |   | 2009                    |     |   | 2008 |   |
|                                                                         |   |                    |     |   |   |   |
| Net      earnings                                                            |   | $                       | 88,400   |   |   | $ | 243,000 |   |
| Other      comprehensive loss:                                               |   |                    |     |   |   |   |   |   |
| Unrealized      holding gain (loss) on hedging contracts                     |   |                    | 80,200   |   |   |   | (1,440,900 | ) |
| Less:      reclassification adjustment for gains realized in net    earnings |   |                    | (226,100 | ) |   |   | (146,900 | ) |
| Total      other comprehensive loss                                          |   |                    | (145,900 | ) |   |   | (1,587,800 | ) |
| Comprehensive      loss                                                      |   | $                       | (57,500  | ) |   | $ | (1,344,800 | ) |

| Fair      Value of Derivative Instruments: |                   |
|--------------------------------------------|------------------------|
|                                       | Asset      Derivatives |   | Liability      Derivatives |   |
| Derivatives      in                        |                   |   | Fair      Value |   |   |   | Fair      Value |   |
| SFAS      133 Cash Flow                    | Balance      Sheet     |   | March      31, |   |   | December      31, |   | Balance      Sheet |   | March      31, |   |   | December      31, |   |
| Hedging      Relationships                 | Location               |   | 2009 |   |   | 2008 |   | Location |   | 2009 |   |   | 2008 |   |
|                                       |                   |   |   |   |   |   |   |   |
| Commodity      contracts:                  | Current      assets    |   | $ | 871,500 |   |   | $ | 1,071,500 |   | Current      liabilities |   | $ | (2,000 | ) |   | $ | (95,700 | ) |
|                                       | Long-term      assets  |   |   | 547,000 |   |   |   | 666,900 |   | Long-term      liabilities |   |   | (200 | ) |   |   | (86,100 | ) |
|                                       |                   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
| Total      derivatives under SFAS No. 133  |                   | $ | 1,418,500 |   |   | $ | 1,738,400 |   |   |   | $ | (2,200 | ) |   | $ | (181,800 | ) |

| Derivatives      in       |   | Gain/(Loss)Recognized      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 |   |
|---------------------------|--------|------------------------------------------------------------------------------------------------|--------|--------|----------------------------------------------------------------|--------|------------|--------------------------------------------------------------------------------------------------|--------|
| SFAS      133 Cash Flow   |   | March      31,                                                                                 |   |   | March      31,                                                 |   |       | OCI      into Income                                                                             |   |   | March      31, |   |   | March      31, |   |
| Hedging      Relationship |   | 2009                                                                                           |   |   | 2008                                                           |   |       | (Effective      Portion)                                                                         |   |   | 2009 |   |   | 2008 |   |
|                      |   |                                                                                           |   |   |                                                           |   |       |                                                                                             |   |
| Commodity      contracts  |   | $                                                                                              | 80,200 |   |                                                           | $      | (1,440,900 | )                                                                                                |   |   | Natural      gas and oil revenue |   | $ | 226,100 |   |   | $ | 146,900 |   |

|               |   |   |             |    |   |             |   |   |            |   |
|--------------------|--------|--------|------------------|---------|--------|------------------|--------|--------|-----------------|--------|
| Production         |   |   |             |    |   | Average          |   |   |            |   |
| Period      Ending |   |   | Volumes          |    |   | Fixed      Price |   |   | Fair      Value |   |
| December      31,  |   |   | (MMbtu)      (1) |    |   | (per      MMbtu) |   |   | Asset      (2)  |   |
|               |   |   |             |    |   |             |   |   |            |   |
| 2009               |   |   |             | 187,000 |   |             | $      | 8.24   |            |   | $ | 738,800 |   |
| 2010               |   |   |             | 153,400 |   |             |   | 8.11   |            |   |   | 330,900 |   |
| 2011               |   |   |             | 103,300 |   |             |   | 7.84   |            |   |   | 116,200 |   |
| 2012               |   |   |             | 73,200  |   |             |   | 8.06   |            |   |   | 76,100 |   |
| 2013               |   |   |             | 7,800   |   |             |   | 8.73   |            |   |   | 11,500 |   |
|               |   |   |             |    |   |             |   |   |            |   | $ | 1,273,500 |   |

|               |   |                |   |             |   |   |                 |   |   |            |   |
|--------------------|--------|---------------------|--------|------------------|--------|--------|----------------------|--------|--------|-----------------|--------|
| Production         |   |                |   |             |   |   | Average              |   |   |            |   |
| Period      Ending |   | Option              |   | Volumes          |   |   | Floor      & Cap |   |   | Fair      Value |   |
| December      31,  |   | Type                |   | (MMbtu)      (1) |   |   | (per      MMbtu)     |   |   | Asset      (2)  |   |
|               |   |                |   |             |   |   |                 |   |   |            |   |
| 2009               |   | Puts      purchased |   |             | 1,100  |   |                 | $      | 11.00  |            |   | $ | 7,200 |   |
| 2009               |   | Calls      sold     |   |             | 1,100  |   |                 |   | 15.35  |            |   |   | — |   |
| 2010               |   | Puts      purchased |   |             | 19,600 |   |                 |   | 7.84   |            |   |   | 41,100 |   |
| 2010               |   | Calls      sold     |   |             | 19,600 |   |                 |   | 9.01   |            |   |   | — |   |
| 2011               |   | Puts      purchased |   |             | 41,500 |   |                 |   | 7.48   |            |   |   | 42,800 |   |
| 2011               |   | Calls      sold     |   |             | 41,500 |   |                 |   | 8.44   |            |   |   | — |   |
| 2012               |   | Puts      purchased |   |             | 5,400  |   |                 |   | 7.00   |            |   |   | 2,200 |   |
| 2012               |   | Calls      sold     |   |             | 5,400  |   |                 |   | 8.32   |            |   |   | — |   |
| 2013               |   | Puts      purchased |   |             | 1,500  |   |                 |   | 7.00   |            |   |   | 300 |   |
| 2013               |   | Calls      sold     |   |             | 1,500  |   |                 |   | 8.25   |            |   |   | — |   |
|               |   |                |   |             |   |   |                 |   |   |            |   | $ | 93,600 |   |

|               |   |   |    |   |   |             |   |   |            |   |
|--------------------|--------|--------|---------|--------|--------|------------------|--------|--------|-----------------|--------|
| Production         |   |   |    |   |   | Average          |   |   |            |   |
| Period      Ending |   |   | Volumes |   |   | Fixed      Price |   |   | Fair      Value |   |
| December      31,  |   |   | (Bbl)   |   |   | (per      Bbl)   |   |   | Asset      (3)  |   |
|               |   |   |    |   |   |             |   |   |            |   |
| 2009               |   |   |    | 300    |   |             | $      | 99.73  |            |   | $ | 12,800 |   |
| 2010               |   |   |    | 300    |   |             |   | 97.40  |            |   |   | 9,400 |   |
| 2011               |   |   |    | 200    |   |             |   | 96.44  |            |   |   | 6,300 |   |
| 2012               |   |   |    | 100    |   |             |   | 96.00  |            |   |   | 4,100 |   |
| 2013               |   |   |    | 100    |   |             |   | 96.06  |            |   |   | 1,100 |   |
|               |   |   |    |   |   |             |   |   |            |   | $ | 33,700 |   |

|               |   |                |   |    |   |   |                 |                 |   |            |   |
|--------------------|--------|---------------------|--------|---------|--------|--------|----------------------|----------------------|--------|-----------------|--------|
| Production         |   |                |   |    |   |   | Average              |                 |   |            |   |
| Period      Ending |   | Option              |   | Volumes |   |   | Floor      & Cap |                 |   | Fair      Value |   |
| December      31,  |   | Type                |   | (Bbl)   |   |   | (per      Bbl)       |                 |   | Asset      (3)  |   |
|               |   |                |   |    |   |   |                 |                 |   |            |   |
| 2009               |   | Puts      purchased |   |    | 200    |   |                 | $                    | 85.00  |            |   | $ | 5,500 |   |
| 2009               |   | Calls      sold     |   |    | 200    |   |                 |                 | 117.48 |            |   |   | — |   |
| 2010               |   | Puts      purchased |   |    | 200    |   |                 |                 | 85.00  |            |   |   | 4,400 |   |
| 2010               |   | Calls      sold     |   |    | 200    |   |                 |                 | 112.92 |            |   |   | — |   |
| 2011               |   | Puts      purchased |   |    | 100    |   |                 |                 | 85.00  |            |   |   | 3,100 |   |
| 2011               |   | Calls      sold     |   |    | 100    |   |                 |                 | 110.81 |            |   |   | — |   |
| 2012               |   | Puts      purchased |   |    | 50     |   |                 |                 | 85.00  |            |   |   | 2,000 |   |
| 2012               |   | Calls      sold     |   |    | 50     |   |                 |                 | 110.06 |            |   |   | — |   |
| 2013               |   | Puts      purchased |   |    | 50     |   |                 |                 | 85.00  |            |   |   | 500 |   |
| 2013               |   | Calls      sold     |   |    | 50     |   |                 |                 | 110.09 |            |   |   | — |   |
|               |   |                |   |    |   |   |                 |                 |   |            |   | $ | 15,500 |   |
|               |   |                |   |    |   |   |                 |                 |   |            |   |   |   |   |
|               |   |                |   |    |   |   |                 | Total      Net Asset |   |            | $      | 1,416,300 |   |

| (1)   | MMBTU      represents million British ThermalUnits. |
|-----------------|-----------------------------------------------------|

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

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

|                                                                                                                                                                                                                                                                                                                                |   | Fair      Value Measurements at March 31, 2009 Using |    |
|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|--------|------------------------------------------------------|---------|
|                                                                                                                                                                                                                                                                                                                                |   | Quoted      prices                                   |    |   | Significant      other |   |   | Significant |   |
|                                                                                                                                                                                                                                                                                                                                |   | in      active                                       |    |   | observable |   |   | unobservable |   |
|                                                                                                                                                                                                                                                                                                                                |   | markets                                              |    |   | inputs |   |   | inputs |   |
|                                                                                                                                                                                                                                                                                                                                |   | (Level      1)                                       |    |   | (Level      2) |   |   | (Level      3) |   |
|                                                                                                                                                                                                                                                                                                                                |   |                                                 |    |   |   |   |   |   |   |
| Commodity-based      derivatives                                                                                                                                                                                                                                                                                                    |   | $                                                    | — |   |   | $ | 1,416,300 |   |   | $ | — |   |
|                                                                                                                                                                                                                                                                                                                                |   |                                                 |    |   |   |   |   |   |   |   |   |   |
| Total                                                      |   | $                                                    | — |   |   | $ | 1,416,300 |   |   | $ | — |   |

|                                                    |   | Three      Months Ended |      |
|---------------------------------------------------------|--------|-------------------------|-----------|
|                                                    |   | March      31,          |      |
|                                                    |   | 2009                    |      |   | 2008 |   |
|                                                    |   |                    |      |   |   |   |
| Asset      retirement obligation at beginning of period |   | $                       | 2,097,900 |   |   | $ | 1,976,000 |   |
| Accretion      expense                                  |   |                    | 31,500    |   |   |   | 29,600 |   |
| Asset      retirement obligation at end of period       |   | $                       | 2,129,400 |   |   | $ | 2,005,600 |   |

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

|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |   | Three      Months Ended |   |
|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|--------|-------------------------|--------|
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |   | March      31,          |   |
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |   | 2009                    |   |   | 2008 |   |
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |   |                    |   |   |   |   |
| Production      revenues (in thousands):                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |   |                    |   |   |   |   |
| Gas                                                                                                                                           |   | $                       | 989    |   |   | $ | 1,456 |   |
| Oil                                                                                                                                           |   |                    | 27     |   |   |   | 51 |   |
| Total                                                                                                                                         |   | $                       | 1,016  |   |   | $ | 1,507 |   |
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |   |                    |   |   |   |   |   |   |
| Production      volumes:                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |   |                    |   |   |   |   |   |   |
| Gas      (mcf/day) (1)                                                                                                                        |   |                    | 1,197  |   |   |   | 1,804 |   |
| Oil      (bbls/day) (1)                                                                                                                       |   |                    | 6      |   |   |   | 6 |   |
| Total      (mcfe/day) (1)                                                                                                                     |   |                    | 1,233  |   |   |   | 1,840 |   |
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |   |                    |   |   |   |   |   |   |
| Average      sales prices:                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   |   |                    |   |   |   |   |   |   |
| Gas      (per mcf) (1)                                                                                                                        |   | $                       | 9.18   |   |   | $ | 8.87 |   |
| Oil      (per bbl) (1)                                                                                                                        |   | $                       | 53.21  |   |   | $ | 92.48 |   |
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |   |                    |   |   |   |   |   |   |
| Average      production costs:                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |   |                    |   |   |   |   |   |   |
| As      a percent of      revenues                                                                                                            |   |                    | 35     | % |   |   | 28 | % |
| Per      mcfe (1)                                                                                                                             |   | $                       | 3.25   |   |   | $ | 2.56 |   |
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |   |                    |   |   |   |   |   |   |
| Depletion      per      mcfe                                                                                         |   | $                       | 4.36   |   |   | $ | 4.50 |   |

| (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. |
|-----------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| 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:  May      14, 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:  May      14, 2009                                                                                                                                                                              |   | By:/s/ Freddie M.      Kotek |
|                                                                                                                                                                                                            |   | Freddie      M. Kotek, Chairman of the Board of Directors, Chief    Executive |
|                                                                                                                                                                                                            |   | Officer      and President |
|                                                                                                                                                                                                            |   |   |
|                                                                                                                                                                                                            |   |   |
| Date:  May      14, 2009                                                                                                                                                                              |   | By:/s/ Matthew A.      Jones |
|                                                                                                                                                                                                            |   | Matthew      A. Jones, Chief Financial Officer |
|                                                                                                                                                                                                            |   |   |
|                                                                                                                                                                                                            |   |   |
| Date:  May      14, 2009                                                                                                                                                                              |   | By:/s/ Sean P.      McGrath |
|                                                                                                                                                                                                            |   | Sean      P. McGrath, Chief Accounting Officer |
|                                                                                                                                                                                                            |   |   |
|                                                                                                                                                                                                            |   |   |
|                                                                                                                                                                                                            |   |   |
|                                                                                                                                                                                                            |   |   |
|                                                                                                                                                                                                            |   |   |