**United                States Securities and Exchange Commission**

**Washington,                D.C. 20549**

**Form                10-QSB**

**[X]                       **
**QUARTERLY                REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE**

**SECURITIES                EXCHANGE ACT OF 1934**

**[                ]**
**TRANSITION                REPORT UNDER SECTION 13 OR 15(d) OF THE**

**SECURITIES                EXCHANGE ACT OF 1934**

**ATLAS                AMERICA PUBLIC #12-2003 Limited Partnership**

**Delaware                                                                                                      **
**54-2113989**

**(412)                262-2830**

----

**ATLAS                AMERICA PUBLIC #12-2003 Limited Partnership**

**(A                Delaware Limited Partnership)**

**INDEX                TO QUARTERLY REPORT**

**ON                FORM 10QSB**

|                                   |                                                                                                                                                                                    | **PAGE**                                                        |
|----------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------|
| **PART                          I.**   | **FINANCIAL                          INFORMATION**                                                                                                                                      |                                                            |
|                                   |                                                                                                                                                                                    |                                                            |
| Item                          1.       | Financial                          Statements                                                                                                                                           |                                                            |
|                                   |                                                                                                                                                                                    |                                                            |
|                                   | Balance                          Sheets as of September 30, 2005 (Unaudited) and December                          31,                          2004                                    | 3                                                               |
|                                   |                                                                                                                                                                                    |                                                            |
|                                   | Statements                          of Operations for the Three and Nine Months ended September                          30, 2005 and                          2004 (Unaudited)    | 4                                                          |
|                                   |                                                                                                                                                                                    |                                                            |
|                                   | Statement                          of Partners’ Capital Accounts for the Nine Months ended September 30,                          2005                          (Unaudited)  | 5                                                               |
|                                   |                                                                                                                                                                                    |                                                            |
|                                   | Statements                          of Cash Flows for the Nine Months ended September 30, 2005                          and 2004                          (Unaudited)              | 6                                                               |
|                                   |                                                                                                                                                                                    |                                                            |
|                                   | Notes                          to Financial Statements (Unaudited)                                                                                                                      | 7                          -                          10        |
|                                   |                                                                                                                                                                                    |                                                            |
| Item                          2.       | Management’s                          Discussion and Analysis of Financial Condition and Results                          of                          Operations                  |  11                          -                          13 |
|                                   |                                                                                                                                                                                    |                                                            |
| Item                          3.       | Controls                          and Procedures                                                                                                                                        | 14                                                              |
|                                   |                                                                                                                                                                                    |                                                            |
| **PART                          II.**  | **OTHER                          INFORMATION**                                                                                                                                          |                                                            |
|                                   |                                                                                                                                                                                    |                                                            |
|  Item                          6. | Exhibits                                                                                                                                                                                | 14                                                              |
|                                   |                                                                                                                                                                                    |                                                            |
|                                   |                                                                                                                                                                                    |                                                            |
| **SIGNATURES**                         | 15                                                                                                                                                                                      |
|                                   |                                                                                                                                                                                    |
| **CERTIFICATIONS**                     | 16                          - 19                                                                                                                                                        |

----

**PART                I**

**ITEM                1.**
**FINANCIAL                STATEMENTS**

**ATLAS                AMERICA PUBLIC #12-2003 Limited Partnership**

**(A                Delaware Limited Partnership)**

**BALANCE                SHEETS**

**(Unaudited)**

|                                                                       |   | **September                          30,** |        | **December                          31,** |   |
|----------------------------------------------------------------------------|--------|--------------------------------------------|-------------|-------------------------------------------|--------|
|                                                                       |   | **2005**                                   |        | **2004**                                  |   |
|                                                                       |   |                                       |        |                                      |   |   |   |
| **ASSETS**                                                                 |   |                                       |        |                                      |   |   |   |
| Current                          Assets:                                   |   |                                       |        |                                      |   |   |   |
| Cash                          and cash equivalents                         |   | $                                          | 1,674,200   |                                      | $      | 1,024,500 |   |
| Accounts                          receivable - affiliate                   |   |                                       | 2,554,200   |                                      |   | 4,616,600 |   |
| Total                          current assets                              |   |                                       | 4,228,400   |                                      |   | 5,641,100 |   |
|                                                                       |   |                                       |        |                                      |   |   |   |
| Oil                          and gas properties (successful efforts)  |   |                                       | 53,368,000  |                                      |   | 52,218,500 |   |
| Less                          accumulated depletion and depreciation  |   |                                       | (10,409,500 | )                                         |   | (5,936,300 | ) |
|                                                                       |   |                                       | 42,958,500  |                                      |   | 46,282,200 |   |
|                                                                       |   | $                                          | 47,186,900  |                                      | $      | 51,923,300 |   |
|                                                                       |   |                                       |        |                                      |   |   |   |
|                                                                       |   |                                       |        |                                      |   |   |   |
| **LIABILITIES                          AND PARTNERS’ CAPITAL**       |   |                                       |        |                                      |   |   |   |
| Current                          liabilities:                              |   |                                       |        |                                      |   |   |   |
| Accrued                          liabilities                          |   | $                                          | 15,300      |                                      | $      | 20,400 |   |
| Total                          current liabilities                         |   |                                       | 15,300      |                                      |   | 20,400 |   |
|                                                                       |   |                                       |        |                                      |   |   |   |
| Asset                          retirement obligation                  |   |                                       | 1,238,800   |                                      |   | 1,185,400 |   |
|                                                                       |   |                                       |        |                                      |   |   |   |
|                                                                       |   |                                       |        |                                      |   |   |   |
| Partners’                          capital:                          |   |                                       |        |                                      |   |   |   |
| Managing                          General Partner                     |   |                                       | 12,044,000  |                                      |   | 11,945,500 |   |
| Limited                          Partners (4,024.015 units)           |   |                                       | 33,888,800  |                                      |   | 38,772,000 |   |
|                                                                       |   |                                       | 45,932,800  |                                      |   | 50,717,500 |   |
|                                                                       |   | $                                          | 47,186,900  |                                      | $      | 51,923,300 |   |

----

**ATLAS                AMERICA PUBLIC #12-2003 Limited Partnership**

**(A                Delaware Limited Partnership)**

**STATEMENTS                OF OPERATIONS **

**(Unaudited)**

|                                                                    |   | **Three                          Months Ended** |      | **Nine                          Months Ended** |   |
|-------------------------------------------------------------------------|--------|-------------------------------------------------|-----------|------------------------------------------------|--------|
|                                                                    |   | **September                          30,**      |      | **September                          30,**     |   |
|                                                                    |   | **2005**                                        |      | **2004**                                       |   | **2005** |   | **2004** |   |
| **REVENUES:**                                                           |   |                                            |      |                                           |   |   |   |   |   |   |   |   |   |
| Natural                          gas and oil sales                      |   | $                                               | 2,624,300 |                                           | $      | 3,988,700 |   | $ | 9,239,900 |   | $ | 7,584,300 |   |
| Interest                          income                                |   |                                            | 8,900     |                                           |   | 900 |   |   | 24,500 |   |   | 1,000 |   |
| Total                          revenues                                 |   |                                            | 2,633,200 |                                           |   | 3,989,600 |   |   | 9,264,400 |   |   | 7,585,300 |   |
|                                                                    |   |                                            |      |                                           |   |   |   |   |   |   |   |   |   |
| **COSTS                          AND EXPENSES:**                        |   |                                            |      |                                           |   |   |   |   |   |   |   |   |   |
| Production                          expenses                       |   |                                            | 365,200   |                                           |   | 390,500 |   |   | 1,166,000 |   |   | 708,600 |   |
| Depletion                          and depreciation of oil and gas      |   |                                            |      |                                           |   |   |   |   |   |   |   |   |   |
| properties                                                              |   |                                            | 1,373,100 |                                           |   | 3,204,500 |   |   | 4,469,300 |   |   | 5,037,800 |   |
| Accretion                          of asset retirement obligation  |   |                                            | 17,800    |                                           |   | 25,000 |   |   | 53,400 |   |   | 45,000 |   |
| General                          and administrative expenses       |   |                                            | 56,600    |                                           |   | 52,300 |   |   | 173,900 |   |   | 116,100 |   |
| Total                          expenses                                 |   |                                            | 1,812,700 |                                           |   | 3,672,300 |   |   | 5,862,600 |   |   | 5,907,500 |   |
| **Net                          earnings**                          |   | $                                               | 820,500   |                                           | $      | 317,300 |   | $ | 3,401,800 |   | $ | 1,677,800 |   |
|                                                                    |   |                                            |      |                                           |   |   |   |   |   |   |   |   |   |
|                                                                    |   |                                            |      |                                           |   |   |   |   |   |   |   |   |   |
|                                                                    |   |                                            |      |                                           |   |   |   |   |   |   |   |   |   |
|                                                                    |   |                                            |      |                                           |   |   |   |   |   |   |   |   |   |
| **Allocation                          of net earnings:**                |   |                                            |      |                                           |   |   |   |   |   |   |   |   |   |
| Managing                          general partner                       |   | $                                               | 578,700   |                                           | $      | 553,000 |   | $ | 2,137,600 |   | $ | 1,353,300 |   |
| Limited                          partners                               |   | $                                               | 241,800   |                                           | $      | (235,700 | ) | $ | 1,264,200 |   | $ | 324,300 |   |
| Net                          earnings (loss) per limited                |   |                                            |      |                                           |   |   |   |   |   |   |   |   |   |
| partnership                          unit                          |   | $                                               | 60        |                                           | $      | (58 | ) | $ | 314 |   | $ | 81 |   |

----

**ATLAS                AMERICA PUBLIC #12-2003 Limited                Partnership**

**(A                Delaware Limited Partnership)**

**STATEMENTS                OF PARTNERS’ CAPITAL ACCOUNTS **

**FOR                THE NINE MONTHS ENDED September 30, 2005**

**(Unaudited)**

|                                                                    |   |  **Managing** |       |               |   |            |   |
|-------------------------------------------------------------------------|--------|--------------------|------------|--------------------|--------|-----------------|--------|
|                                                                    |   |  **General**  |       |  **Limited**  |   |            |   |
|                                                                    |   |  **Partner**  |       |  **Partners** |   |  **Total** |   |
|  **Balance                          at January 1, 2005**           |   | $                  | 11,945,500 |               | $      | 38,772,000      |   | $ | 50,717,500 |   |
|                                                                    |   |               |       |               |   |            |   |   |   |   |
|  Participation                          in revenues and expenses:  |   |               |       |               |   |            |   |   |   |   |
|  Net                          production revenues                  |   |               | 2,825,900  |               |   | 5,248,000       |   |   | 8,073,900 |   |
|  Interest                          income                          |   |               | 8,600      |               |   | 15,900          |   |   | 24,500 |   |
|  Depletion                          and depreciation               |   |               | (617,300   | )                  |   | (3,852,000      | )      |   | (4,469,300 | ) |
|  Accretion                          of asset retirement obligation |   |               | (18,700    | )                  |   | (34,700         | )      |   | (53,400 | ) |
|  General                          and administrative               |   |               | (60,900    | )                  |   | (113,000        | )      |   | (173,900 | ) |
|  Net                          earnings                             |   |               | 2,137,600  |               |   | 1,264,200       |   |   | 3,401,800 |   |
|                                                                    |   |               |       |               |   |            |   |   |   |   |
|  MGP                          adjusted asset contribution          |   |               | 1,149,500  |               |   | ─         |   |   | 1,149,500 |   |
|                                                                    |   |               |       |               |   |            |   |   |   |   |
|  Distributions                                                |   |               | (3,188,600 | )                  |   | (6,147,400      | )      |   | (9,336,000 | ) |
|                                                                    |   |               |       |               |   |            |   |   |   |   |
|  **Balance                          at September 30, 2005**        |   | $                  | 12,044,000 |               | $      | 33,888,800      |   | $ | 45,932,800 |   |

----

**ATLAS                AMERICA PUBLIC #12-2003 Limited Partnership**

**(A                Delaware Limited Partnership)**

**STATEMENT                OF CASH FLOWS **

**(Unaudited)**

|                                                                                                                                        |   | **Nine                          Months Ended** |       |
|---------------------------------------------------------------------------------------------------------------------------------------------|--------|------------------------------------------------|------------|
|                                                                                                                                        |   | **September                          30,**     |       |
|                                                                                                                                        |   | **2005**                                       |       | **2004** |   |
| **Cash                          flows from operating activities:**                                                                          |   |                                           |       |   |   |   |   |
| Net                          earnings                                                                                                       |   | $                                              | 3,401,800  |   | $ | 1,677,800 |   |
| Adjustments                          to reconcile net earnings to net cash provided by operating                          activities:       |   |                                           |       |   |   |   |   |
| Depletion                          and depreciation                                                                                         |   |                                           | 4,469,300  |   |   | 5,037,800 |   |
| Accretion                          of asset retirement obligation                                                                           |   |                                           | 53,400     |   |   | 45,000 |   |
| Decrease                          (Increase) in accounts receivable - affiliate                                                             |   |                                           | 2,062,400  |   |   | (3,448,900 | ) |
| (Decrease)                          Increase in accrued liabilities                                                                         |   |                                           | (5,100     | ) |   | 15,300 |   |
|                                                                                                                                        |   |                                           |       |   |   |   |   |
| Net                          cash provided by operating activities                                                                     |   |                                           | 9,981,800  |   |   | 3,327,000 |   |
|                                                                                                                                        |   |                                           |       |   |   |   |   |
| **Cash                          flows from investing activities:**                                                                          |   |                                           |       |   |   |   |   |
| Proceeds                          from asset sales                                                                                     |   |                                           | 3,900      |   |   | ─ |   |
| Capital                          expenditure                                                                                           |   |                                           | ─    |   |   | (2,000 | ) |
|                                                                                                                                        |   |                                           |       |   |   |   |   |
| Net                          cash provided by (used in) investing activities                                                           |   |                                           | 3,900      |   |   | (2,000 | ) |
|                                                                                                                                        |   |                                           |       |   |   |   |   |
| **Cash                          flows from financing activities:**                                                                          |   |                                           |       |   |   |   |   |
| Partners                          distribution                                                                                              |   |                                           | (9,336,000 | ) |   | (1,269,500 | ) |
| Additional                          limited partner contribution                                                                            |   |                                           | ─    |   |   | 1,800 |   |
|                                                                                                                                        |   |                                           |       |   |   |   |   |
| Net                          cash used in financing activities                                                                              |   |                                           | (9,336,000 | ) |   | (1,267,700 | ) |
|                                                                                                                                        |   |                                           |       |   |   |   |   |
| Net                          increase in cash and cash equivalents                                                                     |   |                                           | 649,700    |   |   | 2,057,300 |   |
| Cash                          and cash equivalents at beginning of period                                                              |   |                                           | 1,024,500  |   |   | 100 |   |
| Cash                          and cash equivalents at end of period                                                                    |   | $                                              | 1,674,200  |   | $ | 2,057,400 |   |
|                                                                                                                                        |   |                                           |       |   |   |   |   |
| **Supplemental                          schedule of non-cash investing and financing                          activities:**                 |   |                                           |       |   |   |   |   |
|                                                                                                                                        |   |                                           |       |   |   |   |   |
|                                Managing General Partner adjusted asset contributions:                              |   |                                           |       |   |   |   |   |
|      Tangible                          equipment cost included in oil and gas properties                      |   | $                                              | 229,100    |   | $ | 6,602,700 |   |
|                                   Intangible drilling cost included in oil and gas properties  |   |                                           | 920,400    |   |   | ─ |   |
|                                                                                                                                        |   | $                                              | 1,149,500  |   | $ | 6,602,700 |   |
|                                                                                                                                        |   |                                           |       |   |   |   |   |
| Asset                          retirement obligation                                                                                   |   | $                                              | -          |   | $ | 1,000,000 |   |

----

** ATLAS              AMERICA PUBLIC #12-2003 Limited Partnership**
**(A                Delaware Limited Partnership)**

**NOTES                TO FINANCIAL STATEMENTS **

**September                30, 2005**

**(Unaudited)**

**NOTE                1 **
**-**
**                BASIS OF PRESENTATION**

**NOTE                2 - SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES**

**Receivables**

**Revenue                Recognition**

**Recently                Issued Financial Accounting Standards **

*Accounting                Changes and Error Corrections*

----

**ATLAS                AMERICA PUBLIC #12-2003 Limited Partnership**

**(A                Delaware Limited Partnership)**

**NOTES                TO FINANCIAL STATEMENTS **

**September                30, 2005**

**(Unaudited)**

**NOTE                2 - SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES - (Continued)**

**Recently                Issued Financial Accounting Standards (Continued)**

*Accounting                for Conditional Asset*
*Retirement                Obligations*
*Accounting                for Asset Retirement*
*Obligations,*

**Fair                Value of Financial Instruments**

**Asset                Retirement Obligation**

|                                                                              |   | **Three                          Months** |      | **Nine                          Months** |   |
|-----------------------------------------------------------------------------------|--------|-------------------------------------------|-----------|------------------------------------------|--------|
|                                                                              |   | **2005**                                  |      | **2004**                                 |   | **2005** |   | **2004** |   |
|                                                                              |   |                                      |      |                                     |   |   |   |   |   |   |   |   |   |
| Asset                          retirement obligation at beginning of period       |   | $                                         | 1,221,000 |                                     | $      | 665,200 |   | $ | 1,185,400 |   | $ | ─ |   |
| Adoption                          of SFAS No. 143                                 |   |                                      | ─   |                                     |   | 354,800 |   |   | ─ |   |   | 1,000,000 |   |
| Accretion                          expense                                   |   |                                      | 17,800    |                                     |   | 25,000 |   |   | 53,400 |   |   | 45,000 |   |
| Total                          asset retirement obligation at end of period  |   | $                                         | 1,238,800 |                                     | $      | 1,045,000 |   | $ | 1,238,800 |   | $ | 1,045,000 |   |

----

**ATLAS                AMERICA PUBLIC #12-2003 Limited Partnership**

**(A                Delaware Limited Partnership)**

**NOTES                TO FINANCIAL STATEMENTS **

**September                30, 2005**

**(Unaudited)**

**NOTE                2 - SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES -                (Continued)**

**Supplemental                Cash Flow Information**

**Credit                Risk**

**Comprehensive                Income**

**Property                and Equipment**

|                                                            |   | **At                          September 30,** |        | **At                          December 31,** |   |
|-----------------------------------------------------------------|--------|-----------------------------------------------|-------------|----------------------------------------------|--------|
|                                                            |   | **2005**                                      |        | **2004**                                     |   |
| Capitalized                          costs of properties:       |   |                                          |        |                                         |   |   |   |
| Proved                          properties                      |   | $                                             | 1,169,700   |                                         | $      | 1,169,700 |   |
| Wells                          and related equipment            |   |                                          | 52,198,300  |                                         |   | 51,048,800 |   |
|                                                            |   |                                          | 53,368,000  |                                         |   | 52,218,500 |   |
|                                                            |   |                                          |        |                                         |   |   |   |
| Accumulated                          depreciation and depletion |   |                                          | (10,409,500 | )                                            |   | (5,936,300 | ) |
|                                                            |   | $                                             | 42,958,500  |                                         | $      | 46,282,200 |   |

----

**ATLAS                AMERICA PUBLIC #12-2003 Limited Partnership**

**(A                Delaware Limited Partnership)**

**NOTES                TO FINANCIAL STATEMENTS **

**September                30, 2005**

**(Unaudited)**

**NOTE                2 - SUMMARY OF SIGNIFICANT ACCOUNTING POLICIES -                (Continued)**

**Property                and Equipment (Continued)**

**NOTE                3 **
**-**
**                TRANSACTIONS WITH ATLAS RESOURCES, INC. AND ITS AFFILIATES**

| ·   | Administrative                          costs which are included in general and administrative                          costs in the                          Statements of Operations are payable to Atlas at $75 per                          well per month.                          Administrative costs incurred for the three months ended                          September 30,                          2005 and 2004 were $46,400 and $39,500, respectively; and                          $135,700 and                          $72,600 for the nine months ended September 30, 2005 and                          2004,                          respectively. |
|--------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| ·   | Monthly                          well supervision fees which are included in production                          expenses in the                          Statements of Operations are payable to Atlas at $275 per                          well per month                          for operating and maintaining the wells. Well supervision                          fees incurred                          for the three months ended September 30, 2005 and 2004                          were $170,200 and                          $137,000, respectively; and $503,900 and $241,000 for the                          nine months                          ended September 30, 2005 and 2004,                          respectively. |
|--------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| ·   | Transportation                          fees which are included in production expenses in the Statements                          of                          Operations are payable to Atlas at $.29-$.35 per mcf (one                          thousand cubic                          feet). Transportation costs incurred for the three months                          ended September                          30, 2005 and 2004 were $115,900 and $218,800, respectively;                          and $394,300                          and $351,800 for the nine months ended September 30, 2005                          and 2004,                          respectively. |
|--------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| ·   | Adjusted                          asset contributions from the managing general partner which                          are included                          on the Statement of Cash Flows for the nine months ended                          September 30,                          2005 are $1,149,500. |
|--------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

**Major                Customers**

**Subordination                of Managing General Partner’s Revenue Share**

----

**ITEM                2. MANAGEMENT’S DISCUSSION AND ANALYSIS AND RESULTS OF                OPERATIONS**

**(UNAUDITED)**

**Forward-Looking                Statements**

**Results                of Operations**

|                                                                                                                   |   | **Three                          Months Ended** |   | **Nine                          Months Ended** |   |
|------------------------------------------------------------------------------------------------------------------------|--------|-------------------------------------------------|--------|------------------------------------------------|--------|
|                                                                                                                   |   | **September                          30,**      |   | **September                          30,**     |   |
|                                                                                                                   |   | **2005**                                        |   | **2004**                                       |   | **2005** |   | **2004** |   |
| Production                          revenues: (in thousands)                                                           |   |                                            |   |                                           |   |   |   |   |   |
|     Gas                                                                                            |   | $                                               | 2,506  |                                           | $      | 3,757 |   | $ | 8,887 |   | $ | 7,297 |   |
|     Oil                                                                                            |   | $                                               | 119    |                                           | $      | 232 |   | $ | 353 |   | $ | 288 |   |
|                                                                                                                   |   | $                                               | 2,625  |                                           | $      | 3,989 |   | $ | 9,240 |   | $ | 7,585 |   |
|                                                                                                                   |   |                                            |   |                                           |   |   |   |   |   |   |   |   |   |
| Production                          volumes:                                                                           |   |                                            |   |                                           |   |   |   |   |   |   |   |   |   |
|      Gas                          (thousands of cubic feet (“mcf”)/day)           |   |                                            | 3,948  |                                           |   | 6,011 |   |   | 4,620 |   |   | 4,215 |   |
|      Oil                          (barrels (“bbls”)/day)                          |   |                                            | 22     |                                           |   | 67 |   |   | 26 |   |   | 28 |   |
|                                                                                                                   |   |                                            |   |                                           |   |   |   |   |   |   |   |   |   |
| Average                          sales prices:                                                                         |   |                                            |   |                                           |   |   |   |   |   |   |   |   |   |
|     Gas                          (per mcf)                                                         |   | $                                               | 6.90   |                                           | $      | 6.79 |   | $ | 7.05 |   | $ | 6.32 |   |
|     Oil                          (per bbl)                                                         |   | $                                               | 58.85  |                                           | $      | 37.82 |   | $ | 50.67 |   | $ | 37.57 |   |
|                                                                                                                   |   |                                            |   |                                           |   |   |   |   |   |   |   |   |   |
| Average                          production costs:                                                                     |   |                                            |   |                                           |   |   |   |   |   |   |   |   |   |
|     As                          a                          percent of sales                        |   |                                            | 14     | %                                              |   | 10 | % |   | 13 | % |   | 9 | % |
|     Per                          mcf                          equivalent unit (“mcfe”) |   | $                                               | .97    |                                           | $      | .66 |   | $ | .89 |   | $ | .59 |   |
|                                                                                                                   |   |                                            |   |                                           |   |   |   |   |   |   |   |   |   |
| Depletion                          per mcfe                                                                            |   | $                                               | 3.66   |                                           | $      | 5.43 |   | $ | 3.43 |   | $ | 4.19 |   |

----

**Revenues**

**Expenses.                **

**Liquidity                and Capital Resources. **

----

**Critical                Accounting Policies**

**Recently                Issued Financial Accounting Standards **

*Accounting                Changes and Error Corrections*

*Accounting                for Conditional Assets*
*Retirement                Obligations*
*Accounting                for Asset Retirement*
*Obligations,*

----

**ITEM                3. CONTROLS AND PROCEDURES**

**Evaluation                of Disclosure Controls and Procedures**

**PART                II.**
**OTHER                INFORMATION**

**ITEM                6. Exhibits**

**EXHIBIT                INDEX**

| **Exhibit                          No.** | **Description**                                                                                                                                                                                   |
|------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
|                                     |                                                                                                                                                                                              |
| 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 |

----

| **SIGNATURES**                                                                                                                                                                                                                                                                                                         |
|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
|                                                                                                                                                                                                                                                                                                                   |
|                                                                                                                                                                                                                                                                                                                   |
| Pursuant                          to the requirements of the Securities 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                                                                                                                                                                                                                                             |
|                                                                                                                                                                                                                                                                                                                   |
| By: (Signature                          and Title):         Atlas                          Resources, Inc., Managing General Partner                                                                                                                                 |
|                                                                                                                                                                                                                                                                                                                   |
|                                                                                                                                                                                                                                                                                                                   |
| By: (Signature                          and Title):                                     /s/                          Freddie M. Kotek                                                                                                                      |
| Freddie                          M. Kotek, Chairman of the Board of Directors,                                                                                                                                                                                                                                         |
| Chief                          Executive Officer and President                                                                                                                                                                                                                                                         |
|                                                                                                                                                                                                                                                                                                                   |
| Date: November                          14, 2005                                                                                                                                                                                                                                                                  |
|                                                                                                                                                                                                                                                                                                                   |
| 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.                   |
|                                                                                                                                                                                                                                                                                                                   |
|                                                                                                                                                                                                                                                                                                                   |
| By: (Signature                          and Title):               /s/                          Freddie M. Kotek                                                                                                                        |
| Freddie                          M. Kotek, Chairman of the Board of Directors,                                                                                                                                                                                                                                         |
| Chief                          Executive Officer and President                                                                                                                                                                                                                                                         |
|                                                                                                                                                                                                                                                                                                                   |
| Date: November                          14, 2005                                                                                                                                                                                                                                                                  |
|                                                                                                                                                                                                                                                                                                                   |
|                                                                                                                                                                                                                                                                                                                   |
| By: (Signature                          and Title):               /s/                          Nancy J. McGurk                                                                                                                         |
| Nancy                          J. McGurk, Senior Vice President,                                                                                                                                                                                                                                                       |
| Chief                          Financial Officer and Chief Accounting Officer                                                                                                                                                                                                                                          |
|                                                                                                                                                                                                                                                                                                                   |
|                                                                                                                                                                                                                                                                                                                   |
| Date: November                          14, 2005                                                                                                                                                                                                                                                                  |
|                                                                                                                                                                                                                                                                                                                   |
|                                                                                                                                                                                                                                                                                                                   |

----

**CERTIFICATIONS**

| 1.   | I                          have reviewed this quarterly report on Form 10-QSB for                          the quarter ended                          September 30, 2005 of Atlas America Public #12-2003 Limited                          Partnership. |
|----------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| 2.   | Based                          on my knowledge, this report does not contain any untrue                          statement of a                          material fact or omit to state a material fact necessary                          to make the                          statements made, in light of the circumstances under which                          such statements                          were made, not misleading with respect to the period covered                          by this                          report; |
|----------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| 3.   | Based                          on my knowledge, the financial statements, and other financial                          information                          included in this report, fairly present in all material                          respects the                          financial condition, results of operations and cash flows                          of the                          registrant as of, and for, the periods presented in this                          report; |
|----------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| 4.   | The                          registrant’s other certifying officer(s) and I are responsible for                          establishing and maintaining disclosure controls and procedures                          (as                          defined in Exchange Act Rules 13a-15(e) and 15d-15(e))                          and internal                          control over Financial Reporting (as defined in Exchange                          Act Rules                          13a-15(f) and 15d-15(f)) for the registrant and                          have: |
|----------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| a)   | Designed                          such disclosure controls and procedures, or caused such                          disclosure                          controls and procedures to be designed under our supervision,                          to ensure                          that material information relating to the registrant, including                          its                          consolidated subsidiaries, is made known to us by others                          within those                          entities, particularly during the period in which this                          report is being                          prepared; |
|----------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| b)   | Designed                          such internal control over financial reporting, or caused                          such internal                          control over financial reporting to be designed under our                          supervision, to                          provide reasonable assurance regarding the reliability                          of financial                          reporting and the preparation of financial statements for                          external                          purposes in accordance with generally accepted accounting                          principles; |
|----------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| c)   | Evaluated                          the effectiveness of the registrant’s disclosure controls and procedures                          and presented in this report our conclusions about the                          effectiveness of                          the disclosure controls and procedures, as of the end of                          the period                          covered by this report based on such evaluation;                          and |
|----------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| d)   | Disclosed                          in this report any change in the registrant’s internal control over                          financial reporting that occurred during the registrant’s most recent                          fiscal quarter (the registrant’s fourth fiscal quarter in the case of an                          annual report) that has materially affected, or is reasonably                          likely to                          materially affect, the registrant’s internal control over financial                          reporting; and |
|----------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| 5.   | The                          registrant’s other certifying officer(s) and I have disclosed, based                          on                          our most recent evaluation of internal control over financial                          reporting,                          to the registrant’s auditors and the audit committee of the registrant’s                          board of directors (or persons performing the equivalent                          functions): |
|----------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| a)   | All                          significant deficiencies and material weaknesses in the                          design or                          operation of internal control over financial reporting                          which are                          reasonably likely to adversely affect the registrant’s ability to record,                          process, summarize and report financial information;                          and |
|----------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| b)   | Any                          fraud, whether or not material, that involves management                          or other                          employees who have a significant role in the registrant’s internal control                          over financial reporting. |
|----------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| By:    |   | /s/                          Freddie M. Kotek                                    |
|--------|--------|----------------------------------------------------------------------------------|
| Name:  |   | Freddie                          M. Kotek                                        |
| Title: |   | Chief                          Executive Officer of the Managing General Partner |
| Date:  |   | November                          14, 2005                                       |
|   |   |                                                                             |

----

**EXHIBIT                31.2**

**CERTIFICATIONS**

| 1.   | I                          have reviewed this quarterly report on Form 10-QSB for                          the quarter ended,                          September 30, 2005 of Atlas America Public #12-2003 Limited                          Partnership. |
|----------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| 2.   | Based                          on my knowledge, this report does not contain any untrue                          statement of a                          material fact or omit to state a material fact necessary                          to make the                          statements made, in light of the circumstances under which                          such statements                          were made, not misleading with respect to the period covered                          by this                          report; |
|----------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| 3.   | Based                          on my knowledge, the financial statements, and other financial                          information                          included in this report, fairly present in all material                          respects the                          financial condition, results of operations and cash flows                          of the                          registrant as of, and for, the periods presented in this                          report; |
|----------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| 4.   | The                          registrant’s other certifying officer(s) and I are responsible for                          establishing and maintaining disclosure controls and procedures                          (as                          defined in Exchange Act Rules 13a-15(e) and 15d-15(e))                          and internal                          control over Financial Reporting (as defined in Exchange                          Act Rules                          13a-15(f) and 15d-15(f)) for the registrant and                          have: |
|----------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| a)   | Designed                          such disclosure controls and procedures, or caused such                          disclosure                          controls and procedures to be designed under our supervision,                          to ensure                          that material information relating to the registrant, including                          its                          consolidated subsidiaries, is made known to us by others                          within those                          entities, particularly during the period in which this                          report is being                          prepared; |
|----------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| b)   | Designed                          such internal control over financial reporting, or caused                          such internal                          control over financial reporting to be designed under our                          supervision, to                          provide reasonable assurance regarding the reliability                          of financial                          reporting and the preparation of financial statements for                          external                          purposes in accordance with generally accepted accounting                          principles; |
|----------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| c)   | Evaluated                          the effectiveness of the registrant’s disclosure controls and procedures                          and presented in this report our conclusions about the                          effectiveness of                          the disclosure controls and procedures, as of the end of                          the period                          covered by this report based on such evaluation;                          and |
|----------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| d)   | Disclosed                          in this report any change in the registrant’s internal control over                          financial reporting that occurred during the registrant’s most recent                          fiscal quarter (the registrant’s fourth fiscal quarter in the case of an                          annual report) that has materially affected, or is reasonably                          likely to                          materially affect, the registrant’s internal control over financial                          reporting; and |
|----------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| 5.   | The                          registrant’s other certifying officer(s) and I have disclosed, based                          on                          our most recent evaluation of internal control over financial                          reporting,                          to the registrant’s auditors and the audit committee of the registrant’s                          board of directors (or persons performing the equivalent                          functions): |
|----------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| a)   | All                          significant deficiencies and material weaknesses in the                          design or                          operation of internal control over financial reporting                          which are                          reasonably likely to adversely affect the registrant’s ability to record,                          process, summarize and report financial information;                          and |
|----------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| b)   | Any                          fraud, whether or not material, that involves management                          or other                          employees who have a significant role in the registrant’s internal control                          over financial reporting. |
|----------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| By:    |   | /s/                          Nancy J. McGurk                                     |
|--------|--------|----------------------------------------------------------------------------------|
| Name:  |   | Nancy                          J. McGurk                                         |
| Title: |   | Chief                          Financial Officer of the Managing General Partner |
| Date:  |   | Date:                          November 14, 2005                                 |
|   |   |                                                                             |

----

| **EXHIBIT                          32.1**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |
|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   |
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   |
|  **CERTIFICATION                          PURSUANT TO**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
|  **18                          U.S.C. SECTION 1350,**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |
|  **AS                          ADOPTED PURSUANT TO**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              |
|  **SECTION                          906 OF THE SARBANES-OXLEY ACT OF 2002**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       |
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   |
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   |
| In                          connection with the Quarterly Report of Atlas America Public                          #12-2003                          Limited Partnership (the “Partnership”) on Form 10-QSB for the period                          ended September 30, 2005 as filed with the Securities and                          Exchange                          Commission on the date hereof (the “Report”), I, Freddie M. Kotek, Chief                          Executive Officer of the Managing General Partner, certify,                          pursuant to 18                          U.S.C. § 1350, as adopted pursuant to § 906 of the Sarbanes-Oxley Act of                          2002, that: |
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   |
|  (1)  The                          Report fully complies with the requirements of section                          13 (a) or 15 (d) of                          the Securities Exchange Act of 1934; and                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                |
|  (2)  The                          information contained in the Report fairly presents, in                          all material                          respects, the financial condition and results of operations                                    of  the Partnership.                                                                                                                                                                                                                                                                                                                                                                                                    |
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   |
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   |
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   |
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   |
|                                  By:    /s/                          Freddie M. Kotek                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
|                            Name:    Freddie                          M. Kotek                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
|  Title:                                  Chief                          Executive Officer                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
|  Date:                            November                          14, 2005    18                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   |
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   |
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   |

|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| **EXHIBIT                          32.2**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
|  **CERTIFICATION                          PURSUANT TO**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          |
|  **18                          U.S.C. SECTION 1350,**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            |
|  **AS                          ADOPTED PURSUANT TO**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |
|  **SECTION                          906 OF THE SARBANES-OXLEY ACT OF 2002**                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
| In                          connection with the Quarterly Report of Atlas America Public                          #12-2003                          Limited Partnership (the “Partnership”) on Form 10-QSB for the period                          ended September 30, 2005 as filed with the Securities and                          Exchange                          Commission on the date hereof (the “Report”), I, Nancy J. McGurk, Chief                          Financial Officer of the Managing General Partner, certify,                          pursuant to 18                          U.S.C. § 1350, as adopted pursuant to § 906 of the Sarbanes-Oxley Act of                          2002, that: |
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
|  (1)  The                          Report fully complies with the requirements of section                          13 (a) or 15 (d) of                          the Securities Exchange Act of 1934; and                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |
|  (2)  The                          information contained in the Report fairly presents, in                          all material                          respects, the financial condition and results of operations                          of                                     the Partnership.                                                                                                                                                                                                                                                                                                                                                                          |
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
| By:     /s/                          Nancy J. McGurk                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
| Name:    Nancy                          J. McGurk                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| Title:                                 Chief                          Financial Officer                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            |
| Date:                                 November                          14, 2005                19                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |