|                                                                                                                                                         | 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, 2008                                              |
|                                                                                                                                                         |                                                                                                |
| 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) 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 is a large 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 September 30, 2008 and December 31, 2007                                          | 3      |
|           |   |                                                                                                        |   |
|           |   | Statements      of Net Earnings for the Three Months and Nine Months Ended September 30,      2008 and 2007 | 4      |
|           |   |                                                                                                        |   |
|           |   | Statement      of Changes in Partners’ Capital for the Nine Months ended September 30,      2008      | 5      |
|           |   |                                                                                                        |   |
|           |   | Statements      of Cash Flows for the Nine Months ended September 30, 2008 and      2007                    | 6      |
|           |   |                                                                                                        |   |
|           |   | Notes      to Financial Statements                                                                          | 7-14   |
|           |   |                                                                                                        |   |
| Item      2:   |   | Management’s      Discussion and Analysis of Financial Condition and Results of      Operations       | 15-19  |
|           |   |                                                                                                        |   |
| Item      4:   |   | Controls      and Procedures                                                                                | 19     |
|           |   |                                                                                                        |   |
| PART      II.  |   | OTHER      INFORMATION                                                                                      |   |
|           |   |                                                                                                        |   |
| Item      1:   |   | Legal      Proceedings                                                                                      | 20     |
|           |   |                                                                                                        |   |
| Item      6:   |   | Exhibits                                                                                                    | 20     |
|           |   |                                                                                                        |   |
|           |   |                                                                                                        |   |
| SIGNATURES     | 21     |
|           |   |                                                                                                        |   |
| CERTIFICATIONS | 22-25  |

|                                                |   | September      30, |       |   | December      31, |   |
|-----------------------------------------------------|--------|--------------------|------------|--------|-------------------|--------|
|                                                |   | 2008               |       |   | 2007              |   |
|                                                |   | (Unaudited)        |       |   |              |   |
| ASSETS                                              |   |               |       |   |              |   |
| Current      assets:                                |   |               |       |   |              |   |
| Cash      and cash equivalents                      |   | $                  | 862,000    |   |              | $      | 750,100 |   |
| Accounts      receivable-affiliate                  |   |               | 1,233,500  |   |              |   | 1,125,400 |   |
| Short-term      hedge receivable due from affiliate |   |               | 333,500    |   |              |   | 409,300 |   |
| Total      current assets                           |   |               | 2,429,000  |   |              |   | 2,284,800 |   |
|                                                |   |               |       |   |              |   |   |   |
| Oil      and gas properties, net                    |   |               | 27,835,600 |   |              |   | 30,036,600 |   |
| Long-term      hedge receivable due from affiliate  |   |               | 106,100    |   |              |   | 61,200 |   |
|                                                |   | $                  | 30,370,700 |   |              | $      | 32,382,600 |   |
|                                                |   |               |       |   |              |   |   |   |
| LIABILITIES      AND PARTNERS’ CAPITAL        |   |               |       |   |              |   |   |   |
| Current      liabilities:                           |   |               |       |   |              |   |   |   |
| Accrued      liabilities                            |   | $                  | 23,200     |   |              | $      | 18,300 |   |
| Short-term      hedge liability due to affiliate    |   |               | 26,800     |   |              |   | 9,700 |   |
| Total      current liabilities                      |   |               | 50,000     |   |              |   | 28,000 |   |
|                                                |   |               |       |   |              |   |   |   |
| Asset      retirement obligation                    |   |               | 2,064,900  |   |              |   | 1,976,000 |   |
| Long-term      hedge liability due to affiliate     |   |               | 443,800    |   |              |   | 614,900 |   |
|                                                |   |               |       |   |              |   |   |   |
| Partners’      capital:                       |   |               |       |   |              |   |   |   |
| Managing      general partner                       |   |               | 9,339,900  |   |              |   | 9,548,500 |   |
| Limited      partners (4,024 units)                 |   |               | 18,545,600 |   |              |   | 20,450,900 |   |
| Accumulated      other comprehensive loss           |   |               | (73,500    | )      |              |   | (235,700 | ) |
| Total      partners' capital                        |   |               | 27,812,000 |   |              |   | 29,763,700 |   |
|                                                |   | $                  | 30,370,700 |   |              | $      | 32,382,600 |   |

|                                                  |   | Three      Months Ended |      |   | Nine      Months Ended |   |
|-------------------------------------------------------|--------|-------------------------|-----------|--------|------------------------|--------|
|                                                  |   | September      30,      |      |   | September      30,     |   |
|                                                  |   | 2008                    |      |   | 2007                   |   |   | 2008 |   |   | 2007 |   |
| REVENUES                                              |   |                    |      |   |                   |   |   |   |   |   |   |   |
| Natural      gas and oil                              |   | $                       | 1,550,400 |   |                   | $      | 1,579,400 |   |   | $ | 4,795,500 |   |   | $ | 4,953,700 |   |
| Interest      income                                  |   |                    | 1,400     |   |                   |   | 13,300 |   |   |   | 6,400 |   |   |   | 34,900 |   |
| Total      revenues                                   |   |                    | 1,551,800 |   |                   |   | 1,592,700 |   |   |   | 4,801,900 |   |   |   | 4,988,600 |   |
|                                                  |   |                    |      |   |                   |   |   |   |   |   |   |   |   |   |   |   |
| COSTS      AND EXPENSES                               |   |                    |      |   |                   |   |   |   |   |   |   |   |   |   |   |   |
| Production                                            |   |                    | 422,500   |   |                   |   | 418,600 |   |   |   | 1,341,900 |   |   |   | 1,311,600 |   |
| Depletion                                             |   |                    | 618,100   |   |                   |   | 838,700 |   |   |   | 2,201,000 |   |   |   | 2,671,300 |   |
| Accretion      of asset retirement obligation         |   |                    | 29,600    |   |                   |   | 29,200 |   |   |   | 88,900 |   |   |   | 87,700 |   |
| General      and administrative                       |   |                    | 56,700    |   |                   |   | 71,000 |   |   |   | 177,800 |   |   |   | 179,800 |   |
| Total      expenses                                   |   |                    | 1,126,900 |   |                   |   | 1,357,500 |   |   |   | 3,809,600 |   |   |   | 4,250,400 |   |
| Net      earnings                                     |   | $                       | 424,900   |   |                   | $      | 235,200 |   |   | $ | 992,300 |   |   | $ | 738,200 |   |
|                                                  |   |                    |      |   |                   |   |   |   |   |   |   |   |   |   |   |   |
| Allocation      of net earnings (loss):               |   |                    |      |   |                   |   |   |   |   |   |   |   |   |   |   |   |
| Managing      general partner                         |   | $                       | 298,000   |   |                   | $      | 280,700 |   |   | $ | 878,600 |   |   | $ | 890,600 |   |
| Limited      partners                                 |   | $                       | 126,900   |   |                   | $      | (45,500 | ) |   | $ | 113,700 |   |   | $ | (152,400 | ) |
| Net      earnings (loss) per limited partnership unit |   | $                       | 31        |   |                   | $      | (11 | ) |   | $ | 28 |   |   | $ | (38 | ) |

|                                          |   |     |       |   |     |   |       | Accumulated        |   |   |     |   |
|-----------------------------------------------|--------|----------|------------|--------|----------|--------|------------|--------------------|--------|--------|----------|--------|
|                                          |   | Managing |       |   |     |   |       | Other              |   |   |     |   |
|                                          |   | General  |       |   | Limited  |   |       | Comprehensive      |   |   |     |   |
|                                          |   | Partner  |       |   | Partners |   |       | Income      (Loss) |   |   | Total    |   |
|                                          |   |     |       |   |     |   |       |               |   |   |     |   |
| Balance      at January 1, 2008               |   | $        | 9,548,500  |   |     | $      | 20,450,900 |               |   | $      | (235,700 | )      |   | $ | 29,763,700 |   |
|                                          |   |     |       |   |     |   |       |               |   |   |     |   |   |   |   |   |
| Participation      in revenues and expenses:  |   |     |       |   |     |   |       |               |   |   |     |   |   |   |   |   |
| Net      production revenues                  |   |     | 1,208,800  |   |     |   | 2,244,800  |               |   |   | —  |   |   |   | 3,453,600 |   |
| Interest      income                          |   |     | 2,200      |   |     |   | 4,200      |               |   |   | —  |   |   |   | 6,400 |   |
| Depletion                                     |   |     | (239,100   | )      |     |   | (1,961,900 | )                  |   |   | —  |   |   |   | (2,201,000 | ) |
| Accretion      of asset retirement obligation |   |     | (31,100    | )      |     |   | (57,800    | )                  |   |   | —  |   |   |   | (88,900 | ) |
| General      and administrative               |   |     | (62,200    | )      |     |   | (115,600   | )                  |   |   | —  |   |   |   | (177,800 | ) |
| Net      earnings                             |   |     | 878,600    |   |     |   | 113,700    |               |   |   | —  |   |   |   | 992,300 |   |
|                                          |   |     |       |   |     |   |       |               |   |   |     |   |   |   |   |   |
| Other      comprehensive income               |   |     | —    |   |     |   | —    |               |   |   | 162,200  |   |   |   | 162,200 |   |
|                                          |   |     |       |   |     |   |       |               |   |   |     |   |   |   |   |   |
| Distributions      to partners                |   |     | (1,087,200 | )      |     |   | (2,019,000 | )                  |   |   | —  |   |   |   | (3,106,200 | ) |
|                                          |   |     |       |   |     |   |       |               |   |   |     |   |   |   |   |   |
| Balance      at September 30, 2008            |   | $        | 9,339,900  |   |     | $      | 18,545,600 |               |   | $      | (73,500  | )      |   | $ | 27,812,000 |   |

|                                                                                          |   | Nine      Months Ended |       |
|-----------------------------------------------------------------------------------------------|--------|------------------------|------------|
|                                                                                          |   | September      30,     |       |
|                                                                                          |   | 2008                   |       |   | 2007 |   |
| Cash      flows from operating activities:                                                    |   |                   |       |   |   |   |
| Net      earnings                                                                             |   | $                      | 992,300    |   |   | $ | 738,200 |   |
| Adjustments      to reconcile net earnings to net cash provided by operating      activities: |   |                   |       |   |   |   |   |   |
| Depletion                                                                                     |   |                   | 2,201,000  |   |   |   | 2,671,300 |   |
| Non-cash      loss on derivative value                                                        |   |                   | 39,100     |   |   |   | 97,700 |   |
| Accretion      of asset retirement obligation                                                 |   |                   | 88,900     |   |   |   | 87,700 |   |
| (Increase)      decrease in accounts receivable – affiliate                             |   |                   | (108,100   | ) |   |   | 81,200 |   |
| Increase      (decrease) in accrued liabilities                                               |   |                   | 4,900      |   |   |   | (1,300 | ) |
| Net      cash provided by operating activities                                                |   |                   | 3,218,100  |   |   |   | 3,674,800 |   |
|                                                                                          |   |                   |       |   |   |   |   |   |
| Cash      flows from investing activities:                                                    |   |                   |       |   |   |   |   |   |
| Purchase      of tangible equipment                                                           |   |                   | —    |   |   |   | (7,800 | ) |
| Net      cash used in investing activities                                                    |   |                   | —    |   |   |   | (7,800 | ) |
|                                                                                          |   |                   |       |   |   |   |   |   |
| Cash      flows from financing activities:                                                    |   |                   |       |   |   |   |   |   |
| Distributions      to partners                                                                |   |                   | (3,106,200 | ) |   |   | (3,809,400 | ) |
| Net      cash used in financing activities                                                    |   |                   | (3,106,200 | ) |   |   | (3,809,400 | ) |
|                                                                                          |   |                   |       |   |   |   |   |   |
| Net      increase (decrease) in cash and cash equivalents                                     |   |                   | 111,900    |   |   |   | (142,400 | ) |
| Cash      and cash equivalents at beginning of period                                         |   |                   | 750,100    |   |   |   | 1,041,200 |   |
| Cash      and cash equivalents at end of period                                               |   | $                      | 862,000    |   |   | $ | 898,800 |   |

| Oil      and gas properties consist of the following at the dates      indicated:                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          |   | September      30, |        |   | December      31, |   |
|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|--------|--------------------|-------------|--------|-------------------|--------|
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       |   | 2008               |        |   | 2007              |   |
| Natural      gas and oil properties:                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       |   |               |        |   |              |   |
| Proved      properties:                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |   |               |        |   |              |   |
| Leasehold      interests                                                                                                                            |   | $                  | 1,169,700   |   |              | $      | 1,169,700 |   |
| Wells      and related      equipment                                                                                                               |   |               | 52,709,800  |   |              |   | 52,709,800 |   |
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       |   |               | 53,879,500  |   |              |   | 53,879,500 |   |
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       |   |               |        |   |              |   |   |   |
| Accumulated      depletion                                                                                                 |   |               | (26,043,900 | )      |              |   | (23,842,900 | ) |
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       |   | $                  | 27,835,600  |   |              | $      | 30,036,600 |   |

| ·   | 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 the three months and nine months      ended September 30, 2008 were $45,300 and $135,700, respectively.      Administrative costs incurred for the three months and nine months ended      September 30, 2007 were $44,800 and $135,500,  respectively. |
|--------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| ·   | Monthly      well supervision fees which are included in production expenses in the      Partnership’s Statements of Net Earnings are payable at $313 and $301 per      well per month in 2008 and 2007, respectively, for operating and      maintaining the wells. Well supervision fees incurred for the three months      and nine months ended September 30, 2008 were $189,200 and $566,900,      respectively. Well supervision fees incurred for the three months and nine      months ended September 30, 2007 were $179,800 and $544,200,      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 and nine      months ended September 30, 2008 were $161,400 and $543,000, respectively.      Transportation fees incurred for the three months and nine months ended      September 30, 2007 were $185,200 and $580,400,    respectively. |
|--------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

|                                                                                                                                                                                                                                                                                                                                                                                                          |   | Three      Months Ended |      |   | Nine      Months Ended |   |
|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|--------|-------------------------|-----------|--------|------------------------|--------|
|                                                                                                                                                                                                                                                                                                                                                                                                          |   | September      30,      |      |   | September      30,     |   |
|                                                                                                                                                                                                                                                                                                                                                                                                          |   | 2008                    |      |   | 2007                   |   |   | 2008 |   |   | 2007 |   |
|                                                                                                                                                                                                                                                                                                                                                                                                          |   |                    |      |   |                   |   |   |   |   |   |   |   |
| Net      earnings                                                                                 |   | $                       | 424,900   |   |                   | $      | 235,200 |   |   | $ | 992,300 |   |   | $ | 738,200 |   |
| Other      comprehensive income (loss):                                                                                                                                                                                                                                                                                                                                                                       |   |                    |      |   |                   |   |   |   |   |   |   |   |   |   |   |   |
| Unrealized      holding gain (loss) on hedging contracts                                                                                                                                                                                                                                                                                                                                                      |   |                    | 3,680,800 |   |                   |   | 311,000 |   |   |   | (83,300 | ) |   |   | (1,180,400 | ) |
| Less:      reclassification adjustment for losses (gains) realized in net      earnings                                                                                                                                                                                                                                                                                                                       |   |                    | 356,000   |   |                   |   | (135,300 | ) |   |   | 245,500 |   |   |   | (463,400 | ) |
| Total      other comprehensive income (loss)                                                                                                                                                                                                                                                                                                                                                                  |   |                    | 4,036,800 |   |                   |   | 175,700 |   |   |   | 162,200 |   |   |   | (1,643,800 | ) |
| Comprehensive      income      (loss)                                                             |   | $                       | 4,461,700 |   |                   | $      | 410,900 |   |   | $ | 1,154,500 |   |   | $ | (905,600 | ) |

|               |   |             |    |   |             |   |   |                 |   |
|--------------------|--------|------------------|---------|--------|------------------|--------|--------|----------------------|--------|
| Production         |   |             |    |   | Average          |   |   | Fair      Value      |   |
| Period      Ending |   | Volumes          |    |   | Fixed      Price |   |   | Asset                |   |
| December      31,  |   | (MMbtu)      (1) |    |   | (per      MMbtu) |   |   | (Liability)      (2) |   |
|               |   |             |    |   |             |   |   |                 |   |
| 2008               |   |             | 99,900  |   |             | $      | 8.88   |                 |   | $ | 138,200 |   |
| 2009               |   |             | 455,300 |   |             |   | 8.56   |                 |   |   | 162,400 |   |
| 2010               |   |             | 340,100 |   |             |   | 8.14   |                 |   |   | (117,400 | ) |
| 2011               |   |             | 262,500 |   |             |   | 7.91   |                 |   |   | (119,600 | ) |
| 2012               |   |             | 176,200 |   |             |   | 8.13   |                 |   |   | (42,400 | ) |
| 2013               |   |             | 15,100  |   |             |   | 8.73   |                 |   |   | 4,500 |   |
|               |   |             |    |   |             |   |   |                 |   | $ | 25,700 |   |

|               |   |                |   |             |   |   |                 |   |   |                 |   |
|--------------------|--------|---------------------|--------|------------------|--------|--------|----------------------|--------|--------|----------------------|--------|
| Production         |   |                |   |             |   |   | Average              |   |   | Fair      Value      |   |
| Period      Ending |   | Option              |   | Volumes          |   |   | Floor      & Cap |   |   | Asset                |   |
| December      31,  |   | Type                |   | (MMbtu)      (1) |   |   | (per      MMbtu)     |   |   | (Liability)      (2) |   |
|               |   |                |   |             |   |   |                 |   |   |                 |   |
| 2008               |   | Puts      purchased |   |             | 3,900  |   |                 | $      | 7.50   |                 |   | $ | 800 |   |
| 2008               |   | Calls      sold     |   |             | 3,900  |   |                 |   | 9.40   |                 |   |   | — |   |
| 2009               |   | Puts      purchased |   |             | 2,400  |   |                 |   | 11.00  |                 |   |   | 7,200 |   |
| 2009               |   | Calls      sold     |   |             | 2,400  |   |                 |   | 15.35  |                 |   |   | — |   |
| 2010               |   | Puts      purchased |   |             | 31,500 |   |                 |   | 7.75   |                 |   |   | — |   |
| 2010               |   | Calls      sold     |   |             | 31,500 |   |                 |   | 8.75   |                 |   |   | (6,100 | ) |
| 2011               |   | Puts      purchased |   |             | 72,800 |   |                 |   | 7.50   |                 |   |   | — |   |
| 2011               |   | Calls      sold     |   |             | 72,800 |   |                 |   | 8.45   |                 |   |   | (38,400 | ) |
| 2012               |   | Puts      purchased |   |             | 7,300  |   |                 |   | 7.00   |                 |   |   | — |   |
| 2012               |   | Calls      sold     |   |             | 7,300  |   |                 |   | 8.37   |                 |   |   | (4,700 | ) |
|               |   |                |   |             |   |   |                 |   |   |                 |   | $ | (41,200 | ) |

|               |   |    |   |   |             |   |   |                 |   |
|--------------------|--------|---------|--------|--------|------------------|--------|--------|----------------------|--------|
| Production         |   |    |   |   | Average          |   |   | Fair      Value      |   |
| Period      Ending |   | Volumes |   |   | Fixed      Price |   |   | Asset                |   |
| December      31,  |   | (Bbl)   |   |   | (per      Bbl)   |   |   | (Liability)      (3) |   |
|               |   |    |   |   |             |   |   |                 |   |
| 2008               |   |    | 200    |   |             | $      | 103.67 |                 |   | $ | 400 |   |
| 2009               |   |    | 500    |   |             |   | 99.92  |                 |   |   | (1,300 | ) |
| 2010               |   |    | 400    |   |             |   | 97.31  |                 |   |   | (3,000 | ) |
| 2011               |   |    | 300    |   |             |   | 96.43  |                 |   |   | (2,800 | ) |
| 2012               |   |    | 300    |   |             |   | 96.00  |                 |   |   | (2,400 | ) |
| 2013               |   |    | 100    |   |             |   | 95.95  |                 |   |   | (600 | ) |
|               |   |    |   |   |             |   |   |                 |   | $ | (9,700 | ) |

|               |   |                |   |    |   |   |                 |                     |   |                 |   |
|--------------------|--------|---------------------|--------|---------|--------|--------|----------------------|--------------------------|--------|----------------------|--------|
| Production         |   |                |   |    |   |   | Average              |                     |   | Fair      Value      |   |
| Period      Ending |   | Option              |   | Volumes |   |   | Floor      & Cap |                     |   | Asset                |   |
| December      31,  |   | Type                |   | (Bbl)   |   |   | (per      Bbl)       |                     |   | (Liability)      (3) |   |
|               |   |                |   |    |   |   |                 |                     |   |                 |   |
| 2008               |   | Puts      purchased |   |    | 100    |   |                 | $                        | 85.00  |                 |   | $ | — |   |
| 2008               |   | Calls      sold     |   |    | 100    |   |                 |                     | 126.44 |                 |   |   | — |   |
| 2009               |   | Puts      purchased |   |    | 300    |   |                 |                     | 85.00  |                 |   |   | — |   |
| 2009               |   | Calls      sold     |   |    | 300    |   |                 |                     | 118.63 |                 |   |   | (700 | ) |
| 2010               |   | Puts      purchased |   |    | 300    |   |                 |                     | 85.00  |                 |   |   | — |   |
| 2010               |   | Calls      sold     |   |    | 300    |   |                 |                     | 112.92 |                 |   |   | (1,600 | ) |
| 2011               |   | Puts      purchased |   |    | 200    |   |                 |                     | 85.00  |                 |   |   | — |   |
| 2011               |   | Calls      sold     |   |    | 200    |   |                 |                     | 110.81 |                 |   |   | (1,700 | ) |
| 2012               |   | Puts      purchased |   |    | 100    |   |                 |                     | 85.00  |                 |   |   | — |   |
| 2012               |   | Calls      sold     |   |    | 100    |   |                 |                     | 110.06 |                 |   |   | (1,400 | ) |
| 2013               |   | Puts      purchased |   |    | 100    |   |                 |                     | 85.00  |                 |   |   | — |   |
| 2013               |   | Calls      sold     |   |    | 100    |   |                 |                     | 110.09 |                 |   |   | (400 | ) |
|               |   |                |   |    |   |   |                 |                     |   |                 |   | $ | (5,800 | ) |
|               |   |                |   |    |   |   |                 |                     |   |                 |   |   |   |   |
|               |   |                |   |    |   |   |                 | Total      Net Liability |   |                 | $      | (31,000 | ) |

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

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

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

|                                                |   | September      30, |     |   | December      31, |   |
|-----------------------------------------------------|--------|--------------------|----------|--------|-------------------|--------|
|                                                |   | 2008               |     |   | 2007              |   |
| Short-term      hedge receivable due from affiliate |   | $                  | 333,500  |   |              | $      | 409,300 |   |
| Long-term      hedge receivable due from affiliate  |   |               | 106,100  |   |              |   | 61,200 |   |
| Short-term      hedge liability due to affiliate    |   |               | (26,800  | )      |              |   | (9,700 | ) |
| Long-term      hedge liability due to affiliate     |   |               | (443,800 | )      |              |   | (614,900 | ) |
|                                                |   | $                  | (31,000  | )      |              | $      | (154,100 | ) |

|                                                                                                                                                                                                                                                                                                                                |   | Fair      Value Measurements at September 30, 2008 Using |    |
|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|--------|----------------------------------------------------------|---------|
|                                                                                                                                                                                                                                                                                                                                |   | Quoted      prices                                       |    |   | Significant      other |   |   | Significant |   |
|                                                                                                                                                                                                                                                                                                                                |   | in      active                                           |    |   | observable |   |   | unobservable |   |
|                                                                                                                                                                                                                                                                                                                                |   | markets                                                  |    |   | inputs |   |   | inputs |   |
|                                                                                                                                                                                                                                                                                                                                |   | (Level      1)                                           |    |   | (Level      2) |   |   | (Level      3) |   |
|                                                                                                                                                                                                                                                                                                                                |   |                                                     |    |   |   |   |   |   |   |
| Commodity-based      derivatives                                                                                                                                                                                                                                                                                                    |   | $                                                        | — |   |   | $ | (31,000 | ) |   | $ | — |   |
|                                                                                                                                                                                                                                                                                                                                |   |                                                     |    |   |   |   |   |   |   |   |   |   |
| Total                                                      |   | $                                                        | — |   |   | $ | (31,000 | ) |   | $ | — |   |

|                                                                                                                                                                                                                                                                                                                                                                                                                   |   | Three      Months Ended |      |   | Nine      Months Ended |   |
|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|--------|-------------------------|-----------|--------|------------------------|--------|
|                                                                                                                                                                                                                                                                                                                                                                                                                   |   | September      30,      |      |   | September      30,     |   |
|                                                                                                                                                                                                                                                                                                                                                                                                                   |   | 2008                    |      |   | 2007                   |   |   | 2008 |   |   | 2007 |   |
|                                                                                                                                                                                                                                                                                                                                                                                                                   |   |                    |      |   |                   |   |   |   |   |   |   |   |
| Asset      retirement obligation at beginning of period                                                                                                                                                                                                                                                                                                                                                                |   | $                       | 2,035,300 |   |                   | $      | 2,008,000 |   |   | $ | 1,976,000 |   |   | $ | 1,949,500 |   |
| Accretion      expense                                                                 |   |                    | 29,600    |   |                   |   | 29,200 |   |   |   | 88,900 |   |   |   | 87,700 |   |
| Asset      retirement obligation at end of period                                                                                                                                                                                                                                                                                                                                                                      |   | $                       | 2,064,900 |   |                   | $      | 2,037,200 |   |   | $ | 2,064,900 |   |   | $ | 2,037,200 |   |

| 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,     |   |
|                                                                                                                                                                                                                                                                                                                                                                                                                   |   | 2008                    |   |   | 2007                   |   |   | 2008 |   |   | 2007 |   |
|                                                                                                                                                                                                                                                                                                                                                                                                                   |   |                    |   |   |                   |   |   |   |   |   |   |   |
| Production      revenues (in thousands):                                                                                                                                                                                                                                                                                                                                                                               |   |                    |   |   |                   |   |   |   |   |   |   |   |
| Gas                                                                                                                  |   | $                       | 1,448  |   |                   | $      | 1,521 |   |   | $ | 4,602 |   |   | $ | 4,839 |   |
| Oil                                                                                                                  |   | $                       | 102    |   |                   | $      | 58 |   |   | $ | 193 |   |   | $ | 115 |   |
| Total                                                                                                                |   | $                       | 1,550  |   |                   | $      | 1,579 |   |   | $ | 4,795 |   |   | $ | 4,954 |   |
|                                                                                                                                                                                                                                                                                                                                                                                                                   |   |                    |   |   |                   |   |   |   |   |   |   |   |   |   |   |   |
| Production      volumes:                                                                                                                                                                                                                                                                                                                                                                                               |   |                    |   |   |                   |   |   |   |   |   |   |   |   |   |   |   |
| Gas      (mcf/day)      (3)                                                                                          |   |                    | 1,434  |   |                   |   | 1,875 |   |   |   | 1,743 |   |   |   | 2,028 |   |
| Oil      (bbls/day)      (3)                                                                                         |   |                    | 9      |   |                   |   | 9 |   |   |   | 6 |   |   |   | 7 |   |
| Total      (mcfe/day)      (3)                                                                                       |   |                    | 1,488  |   |                   |   | 1,929 |   |   |   | 1,779 |   |   |   | 2,070 |   |
|                                                                                                                                                                                                                                                                                                                                                                                                                   |   |                    |   |   |                   |   |   |   |   |   |   |   |   |   |   |   |
| Average      sales prices:                                                                                                                                                                                                                                                                                                                                                                                             |   |                    |   |   |                   |   |   |   |   |   |   |   |   |   |   |   |
| Gas      (per mcf) (1)      (3)                                                                                      |   | $                       | 10.98  |   |                   | $      | 8.82 |   |   | $ | 9.64 |   |   | $ | 8.74 |   |
| Oil      (per bbl) (2)      (3)                                                                                      |   | $                       | 126.22 |   |                   | $      | 67.81 |   |   | $ | 111.96 |   |   | $ | 62.28 |   |
|                                                                                                                                                                                                                                                                                                                                                                                                                   |   |                    |   |   |                   |   |   |   |   |   |   |   |   |   |   |   |
| Average      production costs:                                                                                                                                                                                                                                                                                                                                                                                         |   |                    |   |   |                   |   |   |   |   |   |   |   |   |   |   |   |
| As      a percent of      revenues                                                                                   |   |                    | 27     | %      |                   |   | 26 | % |   |   | 28 | % |   |   | 26 | % |
| Per      mcfe      (3)                                                                                               |   | $                       | 3.09   |   |                   | $      | 2.36 |   |   | $ | 2.75 |   |   | $ | 2.32 |   |
|                                                                                                                                                                                                                                                                                                                                                                                                                   |   |                    |   |   |                   |   |   |   |   |   |   |   |   |   |   |   |
| Depletion      per      mcfe                                                                |   | $                       | 4.52   |   |                   | $      | 4.72 |   |   | $ | 4.51 |   |   | $ | 4.73 |   |

| (1)   | The      average sales price per mcf before the effects of hedging was $13.62 and      $8.04 for the three months ended September 30, 2008 and 2007,      respectively, and $10.13 and $7.90 for the nine months ended September 30,      2008 and 2007, respectively. |
|-----------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| (2)   | The      average sales price per bbl before the effects of hedging was $135.31 and      $116.35 for the three months and nine months ended September 30, 2008,      respectively. There was no hedging for oil in  2007. |
|-----------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| (3)   | “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:  November      13, 2008                                                                                                                                                                         |   | 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      13, 2008                                                                                                                                                                         |   | By:/s/ Freddie M.      Kotek |
|                                                                                                                                                                                                            |   | Freddie      M. Kotek, Chairman of the Board of Directors, Chief    Executive |
|                                                                                                                                                                                                            |   | Officer      and President |
|                                                                                                                                                                                                            |   |   |
|                                                                                                                                                                                                            |   |   |
| Date:  November      13, 2008                                                                                                                                                                         |   | By:/s/ Matthew A.      Jones |
|                                                                                                                                                                                                            |   | Matthew      A. Jones, Chief Financial Officer |
|                                                                                                                                                                                                            |   |   |
|                                                                                                                                                                                                            |   |   |
| Date:  November      13, 2008                                                                                                                                                                         |   | By:/s/ Nancy J.      McGurk |
|                                                                                                                                                                                                            |   | Nancy      J. McGurk, Vice President, Chief Accounting Officer |
|                                                                                                                                                                                                            |   |   |
|                                                                                                                                                                                                            |   |   |
|                                                                                                                                                                                                            |   |   |
|                                                                                                                                                                                                            |   |   |
|                                                                                                                                                                                                            |   |   |