|                                                                                                                                             | 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 June 30, 2009                                              |
|                                                                                                                                             |                                                                                      |
| o                                                                                                                                                | TRANSITION REPORT PURSUANT TO SECTION 13 OR 15 (d) OF THE SECURITIES EXCHANGE ACT OF 1934 |
|                                                                                                                                             |                                                                                      |
|                                                                                                                                             | For the transition period from _____ to _____                                             |
|                                                                                                                                             |                                                                                      |
|                                                                                                                                             | Commission file number 333-105811                                                         |
|                                                                                                                                             |                                                                                      |
|                                                                                                                                             |                                                                                      |
|                                                                                                                                             | ATLAS AMERICA PUBLIC #12-2003 Limited Partnership                                         |
|                                                                                                                                             | (Name of small business issuer in its charter)                                            |
|                                                                                                                                             |                                                                                      |
|                                                                                                                                             |                                                                                      |
|                                                                                                                                             |                                                                                      |
| Delaware                                                                                                                                         | 54-2113989                                                                                |
| (State or other jurisdiction ofincorporation or organization)                                                                                    | (I.R.S. EmployerIdentification No.)                                                       |
|                                                                                                                                             |                                                                                      |
| Westpointe Corporate Center One                                                                                                                  |                                                                                      |
| 1550 Coraopolis Heights Rd. 2nd Floor                                                                                                            |                                                                                      |
| Moon Township, PA                                                                                                                                | 15108                                                                                     |
| (Address of principal executive offices)                                                                                                         | (zip code)                                                                                |
|                                                                                                                                             |                                                                                      |
| Issuer’s telephone number, including area code: (412) 262-2830                                                                             |
|                                                                                                                                             |
| Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15 (d) of the Securities Exchange  |
| Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports),                   |
| and (2) has been subject to such filing requirements for the past 90 days. Yes R No o                                                       |
|                                                                                                                                             |
| Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive       |
| Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12     |
| months (or for such shorter period that the registrant was required to submit and post such files). Yes o No R                                   |
|                                                                                                                                             |
| Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer or a smaller reporting |
| company. See the definitions of "large accelerated filer", "accelerated filer", 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 June 30, 2009 and December 31, 2008                                  | 3      |
|           |   |                                                                                      |   |
|           |   | Statements of Operations for the Three Months and Six Months Ended June 30, 2009 and 2008 | 4      |
|           |   |                                                                                      |   |
|           |   | Statement of Changes in Partners’ Capital for the Six Months ended June 30, 2009    | 5      |
|           |   |                                                                                      |   |
|           |   | Statements of Cash Flows for the Six Months ended June 30, 2009 and 2008                  | 6      |
|           |   |                                                                                      |   |
|           |   | Notes to Financial Statements                                                             | 7-17   |
|           |   |                                                                                      |   |
| Item 2:        |   | Management’s Discussion and Analysis of Financial Condition or Plan of Operations   | 17-22  |
|           |   |                                                                                      |   |
| Item 4:        |   | Controls and Procedures                                                                   | 22     |
|           |   |                                                                                      |   |
| PART II.       |   | OTHER INFORMATION                                                                         |   |
|           |   |                                                                                      |   |
| Item 6:        |   | Exhibits                                                                                  | 23     |
|           |   |                                                                                      |   |
|           |   |                                                                                      |   |
| SIGNATURES     | 24     |
|           |   |                                                                                      |   |
| CERTIFICATIONS | 25-28  |

|                                           |   | June 30,    |       |   | December 31, |   |
|------------------------------------------------|--------|-------------|------------|--------|--------------|--------|
|                                           |   | 2009        |       |   | 2008         |   |
|                                           |   | (Unaudited) |       |   |         |   |
| ASSETS                                         |   |        |       |   |         |   |
| Current assets:                                |   |        |       |   |         |   |
| Cash and cash equivalents                      |   | $           | 301,300    |   |         | $      | 574,000 |   |
| Accounts receivable-affiliate                  |   |        | 626,400    |   |         |   | 1,003,000 |   |
| Short-term hedge receivable due from affiliate |   |        | 724,600    |   |         |   | 1,071,500 |   |
| Total current assets                           |   |        | 1,652,300  |   |         |   | 2,648,500 |   |
|                                           |   |        |       |   |         |   |   |   |
| Oil and gas properties, net                    |   |        | 26,360,700 |   |         |   | 27,285,200 |   |
| Long-term hedge receivable due from affiliate  |   |        | 435,700    |   |         |   | 666,900 |   |
|                                           |   | $           | 28,448,700 |   |         | $      | 30,600,600 |   |
|                                           |   |        |       |   |         |   |   |   |
| LIABILITIES AND PARTNERS’ CAPITAL        |   |        |       |   |         |   |   |   |
| Current liabilities:                           |   |        |       |   |         |   |   |   |
| Accrued liabilities                            |   | $           | 17,100     |   |         | $      | 22,200 |   |
| Short-term hedge liability due to affiliate    |   |        | 2,300      |   |         |   | 95,700 |   |
| Total current liabilities                      |   |        | 19,400     |   |         |   | 117,900 |   |
|                                           |   |        |       |   |         |   |   |   |
| Asset retirement obligation                    |   |        | 2,160,800  |   |         |   | 2,097,900 |   |
| Long-term hedge liability due to affiliate     |   |        | 109,500    |   |         |   | 86,100 |   |
|                                           |   |        |       |   |         |   |   |   |
| Partners’ capital:                       |   |        |       |   |         |   |   |   |
| Managing general partner                       |   |        | 8,619,000  |   |         |   | 8,999,800 |   |
| Limited partners (4,024 units)                 |   |        | 16,515,200 |   |         |   | 17,776,000 |   |
| Accumulated other comprehensive income         |   |        | 1,024,800  |   |         |   | 1,522,900 |   |
| Total partners' capital                        |   |        | 26,159,000 |   |         |   | 28,298,700 |   |
|                                           |   | $           | 28,448,700 |   |         | $      | 30,600,600 |   |

|                                             |   | Three Months Ended |     |   | Six Months Ended |   |
|--------------------------------------------------|--------|--------------------|----------|--------|------------------|--------|
|                                             |   | June 30,           |     |   | June 30,         |   |
|                                             |   | 2009               |     |   | 2008             |   |   | 2009 |   |   | 2008 |   |
| REVENUES                                         |   |               |     |   |             |   |   |   |   |   |   |   |
| Natural gas and oil                              |   | $                  | 765,100  |   |             | $      | 1,738,100 |   |   | $ | 1,781,400 |   |   | $ | 3,245,100 |   |
| Interest income                                  |   |               | 200      |   |             |   | 1,600 |   |   |   | 600 |   |   |   | 5,000 |   |
| Total revenues                                   |   |               | 765,300  |   |             |   | 1,739,700 |   |   |   | 1,782,000 |   |   |   | 3,250,100 |   |
|                                             |   |               |     |   |             |   |   |   |   |   |   |   |   |   |   |   |
| COSTS AND EXPENSES                               |   |               |     |   |             |   |   |   |   |   |   |   |   |   |   |   |
| Production                                       |   |               | 367,000  |   |             |   | 490,000 |   |   |   | 727,300 |   |   |   | 919,400 |   |
| Depletion                                        |   |               | 441,100  |   |             |   | 828,700 |   |   |   | 924,500 |   |   |   | 1,582,900 |   |
| Accretion of asset retirement obligation         |   |               | 31,400   |   |             |   | 29,700 |   |   |   | 62,900 |   |   |   | 59,300 |   |
| General and administrative                       |   |               | 56,900   |   |             |   | 66,900 |   |   |   | 110,000 |   |   |   | 121,100 |   |
| Total expenses                                   |   |               | 896,400  |   |             |   | 1,415,300 |   |   |   | 1,824,700 |   |   |   | 2,682,700 |   |
| Net (loss) earnings                              |   | $                  | (131,100 | )      |             | $      | 324,400 |   |   | $ | (42,700 | ) |   | $ | 567,400 |   |
|                                             |   |               |     |   |             |   |   |   |   |   |   |   |   |   |   |   |
| Allocation of net (loss) earnings :              |   |               |     |   |             |   |   |   |   |   |   |   |   |   |   |   |
| Managing general partner                         |   | $                  | 46,600   |   |             | $      | 313,500 |   |   | $ | 178,800 |   |   | $ | 580,600 |   |
| Limited partners                                 |   | $                  | (177,700 | )      |             | $      | 10,900 |   |   | $ | (221,500 | ) |   | $ | (13,200 | ) |
| Net (loss) earnings per limited partnership unit |   | $                  | (44      | )      |             | $      | 3 |   |   | $ | (55 | ) |   | $ | (3 | ) |

|                                     |   |     |      |   |     |   |       | 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                  |   |     | 368,900   |   |     |   | 685,200    |          |   |   | —   |   |   |   | 1,054,100 |   |
| Interest income                          |   |     | 200       |   |     |   | 400        |          |   |   | —   |   |   |   | 600 |   |
| Depletion                                |   |     | (129,800  | )      |     |   | (794,700   | )             |   |   | —   |   |   |   | (924,500 | ) |
| Accretion of asset retirement obligation |   |     | (22,000   | )      |     |   | (40,900    | )             |   |   | —   |   |   |   | (62,900 | ) |
| General and administrative               |   |     | (38,500   | )      |     |   | (71,500    | )             |   |   | —   |   |   |   | (110,000 | ) |
| Net (loss) earnings                      |   |     | 178,800   |   |     |   | (221,500   | )             |   |   | —   |   |   |   | (42,700 | ) |
|                                     |   |     |      |   |     |   |       |          |   |   |      |   |   |   |   |   |
| Other comprehensive loss                 |   |     | —   |   |     |   | —    |          |   |   | (498,100  | )      |   |   | (498,100 | ) |
|                                     |   |     |      |   |     |   |       |          |   |   |      |   |   |   |   |   |
| Distributions to partners                |   |     | (559,600  | )      |     |   | (1,039,300 | )             |   |   | —   |   |   |   | (1,598,900 | ) |
|                                     |   |     |      |   |     |   |       |          |   |   |      |   |   |   |   |   |
| Balance at June 30, 2009                 |   | $        | 8,619,000 |   |     | $      | 16,515,200 |          |   | $      | 1,024,800 |   |   | $ | 26,159,000 |   |

|                                                                                |   | Six Months Ended |       |
|-------------------------------------------------------------------------------------|--------|------------------|------------|
|                                                                                |   | June 30,         |       |
|                                                                                |   | 2009             |       |   | 2008 |   |
| Cash flows from operating activities:                                               |   |             |       |   |   |   |
| Net (loss) earnings                                                                 |   | $                | (42,700    | ) |   | $ | 567,400 |   |
| Adjustments to reconcile net earnings to net cash provided by operating activities: |   |             |       |   |   |   |   |   |
| Depletion                                                                           |   |             | 924,500    |   |   |   | 1,582,900 |   |
| Non-cash loss on derivative value                                                   |   |             | 10,000     |   |   |   | 20,700 |   |
| Accretion of asset retirement obligation                                            |   |             | 62,900     |   |   |   | 59,300 |   |
| Decrease (increase) in accounts receivable – affiliate                        |   |             | 376,600    |   |   |   | (232,700 | ) |
| Decrease in accrued liabilities                                                     |   |             | (5,100     | ) |   |   | (1,900 | ) |
| Net cash provided by operating activities                                           |   |             | 1,326,200  |   |   |   | 1,995,700 |   |
|                                                                                |   |             |       |   |   |   |   |   |
| Cash flows from financing activities:                                               |   |             |       |   |   |   |   |   |
| Distributions to partners                                                           |   |             | (1,598,900 | ) |   |   | (2,026,400 | ) |
| Net cash used in financing activities                                               |   |             | (1,598,900 | ) |   |   | (2,026,400 | ) |
|                                                                                |   |             |       |   |   |   |   |   |
| Net decrease in cash and cash equivalents                                           |   |             | (272,700   | ) |   |   | (30,700 | ) |
| Cash and cash equivalents at beginning of period                                    |   |             | 574,000    |   |   |   | 750,100 |   |
| Cash and cash equivalents at end of period                                          |   | $                | 301,300    |   |   | $ | 719,400 |   |

| Oil and gas properties consist of the following at the dates indicated:                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |   | June 30, |        |   | December 31, |   |
|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|--------|----------|-------------|--------|--------------|--------|
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |   | 2009     |        |   | 2008         |   |
| Natural gas and oil properties:                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       |   |     |        |   |         |   |
| Proved properties:                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |   |     |        |   |         |   |
| Leasehold interests                                                                                                                            |   | $        | 1,137,100   |   |         | $      | 1,137,100 |   |
| Wells and related equipment                                                                                                                    |   |     | 51,580,600  |   |         |   | 51,580,600 |   |
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |   |     | 52,717,700  |   |         |   | 52,717,700 |   |
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |   |     |        |   |         |   |   |   |
| Accumulated depletion                                                                                                 |   |     | (26,357,000 | )      |         |   | (25,432,500 | ) |
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |   | $        | 26,360,700  |   |         | $      | 27,285,200 |   |

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

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

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

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

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

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

| ·   | Administrative costs which are included in general and administrative expenses in the Partnership’s Statements of Operations are payable at $75 per well per month. Administrative costs incurred for the three months and six months ended June 30, 2009 were $44,700 and $89,800, respectively. Administrative costs incurred for the three months and sixmonths ended June 30, 2008 were $45,300 and $90,400, respectively. |
|--------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| ·   | Monthly well supervision fees which are included in production expenses in the Partnership’s Statements of Operations are payable at $313 per well per month in 2009 and 2008, respectively, for operating and maintaining the wells. Well supervision fees incurred for the three months and six months ended June 30, 2009 were $187,000 and $375,200, respectively.Well supervision fees incurred for the three months and six months ended June 30, 2008 were $189,100 and $377,700, respectively. |
|--------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| ·   | Transportation fees which are included in production expenses in the Partnership’s Statements of Operations are generally payable at 13% of the natural gas sales price. Transportation fees incurred for the three months and six months ended June 30, 2009 were $84,600 and $199,800, respectively. Transportation fees incurred for the three months andsix months ended June 30, 2008 were $205,600 and $381,600, respectively. |
|--------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

|                                                                          |   | Three Months Ended |     |   | Six Months Ended |   |
|-------------------------------------------------------------------------------|--------|--------------------|----------|--------|------------------|--------|
|                                                                          |   | June 30,           |     |   | June 30,         |   |
|                                                                          |   | 2009               |     |   | 2008             |   |   | 2009 |   |   | 2008 |   |
|                                                                          |   |               |     |   |             |   |   |   |   |   |   |   |
| Net (loss) earnings                                                           |   | $                  | (131,100 | )      |             | $      | 324,400 |   |   | $ | (42,700 | ) |   | $ | 567,400 |   |
| Other comprehensive income (loss):                                            |   |               |     |   |             |   |   |   |   |   |   |   |   |   |   |   |
| Unrealized holding (loss) gain on hedging contracts                           |   |               | (54,000  | )      |             |   | (2,323,200 | ) |   |   | 26,200 |   |   |   | (3,764,100 | ) |
| Less: reclassification adjustment for (gains) losses realized in net earnings |   |               | (298,200 | )      |             |   | 36,400 |   |   |   | (524,300 | ) |   |   | (110,500 | ) |
| Total other comprehensive loss                                                |   |               | (352,200 | )      |             |   | (2,286,800 | ) |   |   | (498,100 | ) |   |   | (3,874,600 | ) |
| Comprehensive loss                                                            |   | $                  | (483,300 | )      |             | $      | (1,962,400 | ) |   | $ | (540,800 | ) |   | $ | (3,307,200 | ) |

| Fair Value of Derivative Instruments: |   |
|---------------------------------------|--------|
|                                  |   | Asset Derivatives |   | Liability Derivatives |   |
| Derivatives in                        |   |   |   | Fair Value |   |   |   | Fair Value |   |
| SFAS 133 Cash Flow                    |   | Balance Sheet |   | June 30, |   |   | December 31, |   | Balance Sheet |   | June 30, |   |   | December 31, |   |
| Hedging Relationships                 |   | Location |   | 2009 |   |   | 2008 |   | Location |   | 2009 |   |   | 2008 |   |
|                                  |   |   |   |   |   |   |   |   |   |
| Commodity contracts:                  |   | Current assets |   | $ | 724,600 |   |   | $ | 1,071,500 |   | Current liabilities |   | $ | (2,300 | ) |   | $ | (95,700 | ) |
|                                  |   | Long-term assets |   |   | 435,700 |   |   |   | 666,900 |   | Long-term liabilities |   |   | (109,500 | ) |   |   | (86,100 | ) |
|                                  |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
| Total derivatives under SFAS No. 133  |   | $ | 1,160,300 |   |   | $ | 1,738,400 |   |   |   | $ | (111,800 | ) |   | $ | (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   |   | June 30,                                                                        |    |                                                 | June 30, |                                                                              | OCI into Income     |   | June 30, |   |   | June 30, |   |
| Hedging Relationship |   | 2009                                                                            |    |                                                 | 2008     |                                                                              | (Effective Portion) |   | 2009 |   |   | 2008 |   |
|                 |   |                                                                            |    |                                                 |     |                                                                              |                |
| Commodity contracts  |   | $                                                                               | (54,000 | )                                                    |     | $                                                                                 | (2,323,200          | ) | Natural gas and oil revenue |   | $ | 298,200 |   |   | $ | (36,400 | ) |

| Derivatives in       |   | Gain/(Loss)Recognized in OCI on Derivative(Effective Portion)Six Months Ended |   | Location of Gain/(Loss)Reclassified from Accumulated |     | Gain/(Loss)Reclassified from OCI into Income(Effective Portion)Six Months Ended |                |
|----------------------|--------|-------------------------------------------------------------------------------|--------|------------------------------------------------------|----------|---------------------------------------------------------------------------------|---------------------|
| SFAS 133 Cash Flow   |   | June 30,                                                                      |   |                                                 | June 30, |                                                                            | OCI into Income     |   | June 30, |   |   | June 30, |   |
| Hedging Relationship |   | 2009                                                                          |   |                                                 | 2008     |                                                                            | (Effective Portion) |   | 2009 |   |   | 2008 |   |
|                 |   |                                                                          |   |                                                 |     |                                                                            |                |
| Commodity contracts  |   | $                                                                             | 26,200 |                                                 |     | $                                                                               | (3,764,100          | ) | Natural gas and oil revenue |   | $ | 524,300 |   |   | $ | 110,500 |   |

|          |   |   |        |    |   |        |   |   |       |   |
|---------------|--------|--------|-------------|---------|--------|-------------|--------|--------|------------|--------|
| Production    |   |   |        |    |   | Average     |   |   |       |   |
| Period Ending |   |   | Volumes     |    |   | Fixed Price |   |   | Fair Value |   |
| December 31,  |   |   | (MMbtu) (1) |    |   | (per MMbtu) |   |   | Asset (2)  |   |
|          |   |   |        |    |   |        |   |   |       |   |
| 2009          |   |   |        | 136,200 |   |        | $      | 8.04   |       |   | $ | 500,400 |   |
| 2010          |   |   |        | 188,000 |   |        |   | 7.71   |       |   |   | 309,900 |   |
| 2011          |   |   |        | 114,700 |   |        |   | 7.04   |       |   |   | 91,900 |   |
| 2012          |   |   |        | 101,100 |   |        |   | 7.22   |       |   |   | 55,600 |   |
| 2013          |   |   |        | 48,200  |   |        |   | 7.13   |       |   |   | 300 |   |
|          |   |   |        |    |   |        |   |   |       |   | $ | 958,100 |   |

|          |   |           |   |        |   |   |            |   |   |            |   |
|---------------|--------|----------------|--------|-------------|--------|--------|-----------------|--------|--------|-----------------|--------|
| Production    |   |           |   |        |   |   | Average         |   |   | Fair Value      |   |
| Period Ending |   | Option         |   | Volumes     |   |   | Floor & Cap |   |   | Asset           |   |
| December 31,  |   | Type           |   | (MMbtu) (1) |   |   | (per MMbtu)     |   |   | (Liability) (2) |   |
|          |   |           |   |        |   |   |            |   |   |            |   |
| 2009          |   | Puts purchased |   |        | 700    |   |            | $      | 11.00  |            |   | $ | 5,000 |   |
| 2009          |   | Calls sold     |   |        | 700    |   |            |   | 15.35  |            |   |   | — |   |
| 2010          |   | Puts purchased |   |        | 19,600 |   |            |   | 7.84   |            |   |   | 39,000 |   |
| 2010          |   | Calls sold     |   |        | 19,600 |   |            |   | 9.01   |            |   |   | — |   |
| 2011          |   | Puts purchased |   |        | 51,800 |   |            |   | 6.52   |            |   |   | 31,100 |   |
| 2011          |   | Calls sold     |   |        | 51,800 |   |            |   | 7.67   |            |   |   | — |   |
| 2012          |   | Puts purchased |   |        | 19,700 |   |            |   | 6.51   |            |   |   | — |   |
| 2012          |   | Calls sold     |   |        | 19,700 |   |            |   | 7.72   |            |   |   | (3,200 | ) |
| 2013          |   | Puts purchased |   |        | 24,600 |   |            |   | 6.52   |            |   |   | — |   |
| 2013          |   | Calls sold     |   |        | 24,600 |   |            |   | 7.81   |            |   |   | (7,700 | ) |
|          |   |           |   |        |   |   |            |   |   |            |   | $ | 64,200 |   |

|          |   |   |    |   |   |        |   |   |       |   |
|---------------|--------|--------|---------|--------|--------|-------------|--------|--------|------------|--------|
| Production    |   |   |    |   |   | Average     |   |   |       |   |
| Period Ending |   |   | Volumes |   |   | Fixed Price |   |   | Fair Value |   |
| December 31,  |   |   | (Bbl)   |   |   | (per Bbl)   |   |   | Asset (3)  |   |
|          |   |   |    |   |   |        |   |   |       |   |
| 2009          |   |   |    | 200    |   |        | $      | 99.50  |       |   | $ | 5,300 |   |
| 2010          |   |   |    | 300    |   |        |   | 97.40  |       |   |   | 6,100 |   |
| 2011          |   |   |    | 200    |   |        |   | 77.46  |       |   |   | 4,000 |   |
| 2012          |   |   |    | 100    |   |        |   | 76.86  |       |   |   | 2,500 |   |
| 2013          |   |   |    | 100    |   |        |   | 77.36  |       |   |   | 700 |   |
|          |   |   |    |   |   |        |   |   |       |   | $ | 18,600 |   |

|          |   |           |   |    |   |   |            |            |   |       |   |
|---------------|--------|----------------|--------|---------|--------|--------|-----------------|-----------------|--------|------------|--------|
| Production    |   |           |   |    |   |   | Average         |            |   |       |   |
| Period Ending |   | Option         |   | Volumes |   |   | Floor & Cap |            |   | Fair Value |   |
| December 31,  |   | Type           |   | (Bbl)   |   |   | (per Bbl)       |            |   | Asset (3)  |   |
|          |   |           |   |    |   |   |            |            |   |       |   |
| 2009          |   | Puts purchased |   |    | 100    |   |            | $               | 85.00  |       |   | $ | 1,700 |   |
| 2009          |   | Calls sold     |   |    | 100    |   |            |            | 116.88 |       |   |   | — |   |
| 2010          |   | Puts purchased |   |    | 200    |   |            |            | 85.00  |       |   |   | 2,500 |   |
| 2010          |   | Calls sold     |   |    | 200    |   |            |            | 112.92 |       |   |   | — |   |
| 2011          |   | Puts purchased |   |    | 100    |   |            |            | 67.22  |       |   |   | 1,900 |   |
| 2011          |   | Calls sold     |   |    | 100    |   |            |            | 89.44  |       |   |   | — |   |
| 2012          |   | Puts purchased |   |    | 100    |   |            |            | 65.51  |       |   |   | 1,200 |   |
| 2012          |   | Calls sold     |   |    | 100    |   |            |            | 91.45  |       |   |   | — |   |
| 2013          |   | Puts purchased |   |    | 100    |   |            |            | 65.36  |       |   |   | 300 |   |
| 2013          |   | Calls sold     |   |    | 100    |   |            |            | 93.44  |       |   |   | — |   |
|          |   |           |   |    |   |   |            |            |   |       |   | $ | 7,600 |   |
|          |   |           |   |    |   |   |            |            |   |       |   |   |   |   |
|          |   |           |   |    |   |   |            | Total Net Asset |   |       | $      | 1,048,500 |   |

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

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

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

|                                                                                                                                                                                                                                                                                                                                                      |   | Fair Value Measurements at June 30, 2009 Using |    |
|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|--------|------------------------------------------------|---------|
|                                                                                                                                                                                                                                                                                                                                                      |   | Quoted prices                                  |    |   | Significant other |   |   | Significant |   |
|                                                                                                                                                                                                                                                                                                                                                      |   | in active                                      |    |   | observable |   |   | unobservable |   |
|                                                                                                                                                                                                                                                                                                                                                      |   | markets                                        |    |   | inputs |   |   | inputs |   |
|                                                                                                                                                                                                                                                                                                                                                      |   | (Level 1)                                      |    |   | (Level 2) |   |   | (Level 3) |   |
|                                                                                                                                                                                                                                                                                                                                                      |   |                                           |    |   |   |   |   |   |   |
| Commodity-based derivatives                                                      |   | $                                              | — |   |   | $ | 1,048,500 |   |   | $ | — |   |
|                                                                                                                                                                                                                                                                                                                                                      |   |                                           |    |   |   |   |   |   |   |   |   |   |
| Total                                                                            |   | $                                              | — |   |   | $ | 1,048,500 |   |   | $ | — |   |

|                                               |   | Three Months Ended |      |   | Six Months Ended |   |
|----------------------------------------------------|--------|--------------------|-----------|--------|------------------|--------|
|                                               |   | June 30,           |      |   | June 30,         |   |
|                                               |   | 2009               |      |   | 2008             |   |   | 2009 |   |   | 2008 |   |
|                                               |   |               |      |   |             |   |   |   |   |   |   |   |
| Asset retirement obligation at beginning of period |   | $                  | 2,129,400 |   |             | $      | 2,005,600 |   |   | $ | 2,097,900 |   |   | $ | 1,976,000 |   |
| Accretion expense                                  |   |               | 31,400    |   |             |   | 29,700 |   |   |   | 62,900 |   |   |   | 59,300 |   |
| Asset retirement obligation at end of period       |   | $                  | 2,160,800 |   |             | $      | 2,035,300 |   |   | $ | 2,160,800 |   |   | $ | 2,035,300 |   |

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

|                                |   | Three Months Ended |   |   | Six Months Ended |   |
|-------------------------------------|--------|--------------------|--------|--------|------------------|--------|
|                                |   | June 30,           |   |   | June 30,         |   |
|                                |   | 2009               |   |   | 2008             |   |   | 2009 |   |   | 2008 |   |
|                                |   |               |   |   |             |   |   |   |   |   |   |   |
| Production revenues (in thousands): |   |               |   |   |             |   |   |   |   |   |   |   |
| Gas                                 |   | $                  | 758    |   |             | $      | 1,698 |   |   | $ | 1,746 |   |   | $ | 3,154 |   |
| Oil                                 |   |               | 7      |   |             |   | 40 |   |   |   | 35 |   |   |   | 91 |   |
| Total                               |   | $                  | 765    |   |             | $      | 1,738 |   |   | $ | 1,781 |   |   | $ | 3,245 |   |
|                                |   |               |   |   |             |   |   |   |   |   |   |   |   |   |   |   |
| Production volumes:                 |   |               |   |   |             |   |   |   |   |   |   |   |   |   |   |   |
| Gas (mcf/day) (1)                   |   |               | 1,100  |   |             |   | 1,994 |   |   |   | 1,148 |   |   |   | 1,899 |   |
| Oil (bbls/day) (1)                  |   |               | 2      |   |             |   | 4 |   |   |   | 4 |   |   |   | 5 |   |
| Total (mcfe/day) (1)                |   |               | 1,112  |   |             |   | 2,018 |   |   |   | 1,172 |   |   |   | 1,929 |   |
|                                |   |               |   |   |             |   |   |   |   |   |   |   |   |   |   |   |
| Average sales prices: (2)           |   |               |   |   |             |   |   |   |   |   |   |   |   |   |   |   |
| Gas (per mcf) (1) (3)               |   | $                  | 7.72   |   |             | $      | 9.47 |   |   | $ | 8.45 |   |   | $ | 9.18 |   |
| Oil (per bbl) (1)                   |   | $                  | 42.40  |   |             | $      | 109.77 |   |   | $ | 50.44 |   |   | $ | 99.33 |   |
|                                |   |               |   |   |             |   |   |   |   |   |   |   |   |   |   |   |
| Average production costs:           |   |               |   |   |             |   |   |   |   |   |   |   |   |   |   |   |
| As a percent of revenues            |   |               | 48     | %      |             |   | 28 | % |   |   | 41 | % |   |   | 28 | % |
| Per mcfe (1)                        |   | $                  | 3.63   |   |             | $      | 2.67 |   |   | $ | 3.43 |   |   | $ | 2.62 |   |
|                                |   |               |   |   |             |   |   |   |   |   |   |   |   |   |   |   |
| Depletion per mcfe                  |   | $                  | 4.36   |   |             | $      | 4.51 |   |   | $ | 4.36 |   |   | $ | 4.51 |   |

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

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

| (3)   | Average gas prices are calculated by including in total revenue gains previously recognized into income and dividing by the total volume for the period. Gas revenue was adjusted for previously recognized gains of $15,600 and $10,000 for the three and six months June 30, 2009. Gas revenue was adjusted for previously recognized gains of $21,100 and $20,700for the three and six months ended June 30, 2008. |
|-----------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

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

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

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

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

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

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

| 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:  August 13, 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:  August 13, 2009                                                                                                                                                                 |   | By:/s/ Freddie M. Kotek |
|                                                                                                                                                                                             |   | Freddie M. Kotek, Chairman of the Board of Directors, Chief Executive |
|                                                                                                                                                                                             |   | Officer and President |
|                                                                                                                                                                                             |   |   |
|                                                                                                                                                                                             |   |   |
| Date:  August 13, 2009                                                                                                                                                                 |   | By:/s/ Matthew A. Jones |
|                                                                                                                                                                                             |   | Matthew A. Jones, Chief Financial Officer |
|                                                                                                                                                                                             |   |   |
|                                                                                                                                                                                             |   |   |
| Date:  August 13, 2009                                                                                                                                                                 |   | By:/s/ Sean P. McGrath |
|                                                                                                                                                                                             |   | Sean P. McGrath, Chief Accounting Officer |
|                                                                                                                                                                                             |   |   |
|                                                                                                                                                                                             |   |   |
|                                                                                                                                                                                             |   |   |
|                                                                                                                                                                                             |   |   |
|                                                                                                                                                                                             |   |   |