|                        | **United                  States Securities and Exchange Commission**         |
|-----------------------------|-------------------------------------------------------------------------------|
|                        |                                                                          |
|                        | **Washington,                  D.C. 20549**                                   |
|                        |                                                                          |
|                        | **Form                  10 QSB**                                              |
|                        |                                                                          |
| (Mark                  One) |                                                                          |
|                        |                                                                          |
| **R**                       | **QUARTERLY                  REPORT PURSUANT TO SECTION 13 OR 15 (d) OF THE** |
|                        | **SECURITIES                  EXCHANGE ACT OF 1934**                          |
|                        |                                                                          |
|                        | For                  the quarterly period ended September 30, 2006            |
|                        |                                                                          |
| o                           | **TRANSITION                  REPORT UNDER SECTION 13 OR 15 (d) OF THE**      |
|                        | **SECURITIES                  EXCHANGE ACT OF 1934**                          |
|                        |                                                                          |
|                        | For                  the transition period from _____ to _____                |
|                        |                                                                          |
|                        | Commission                  file number 333-105811                            |
|                        |                                                                          |
|                        |                                                                          |
|                        | **ATLAS                  AMERICA PUBLIC #12-2003 Limited Partnership**        |
|                        | (Name                  of small business issuer in its charter)               |
|                        |                                                                          |

|                                                                                                                                                                                    |                                                                  |
|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------|
|                                                                                                                                                                                    |                                                                  |
| **Delaware**                                                                                                                                                                            | **54-2113989**                                                        |
| (State                  or other jurisdiction ofincorporation                  or organization)                                                                                         | (I.R.S.                  EmployerIdentification                  No.) |
|                                                                                                                                                                                    |                                                                  |
| 311                  Rouser Road                                                                                                                                                        | 15108                                                                 |
| Moon                  Township, PA                                                                                                                                                      | (zip                  code)                                           |
| (Address                  of principal executive offices)                                                                                                                               |                                                                  |
|                                                                                                                                                                                    |                                                                  |
| Issuer’s                  telephone number, including area code: **(412)                  262-2830**                                                                              |
|                                                                                                                                                                                    |
| Check                  whether the issuer (1) filed all reports required to be filed by                  Section                  13 or 15 (d) of the Exchange Act                      |
| during                  the past 12 months (or for such shorter period that the registrant                  was                  required to file such reports),                        |
| and                  (2) has been subject to such filing requirements for the past 90                  days.                  Yes** ****R**                  No                  o |
|                                                                                                                                                                                    |
| Indicate                  by check mark whether the registrant is a shell company (as defined                  in                  Rule 12b-2 of the Exchange                           |
| Act).Yes                  o                  No                  **R**                                                                                                                  |
|                                                                                                                                                                                    |
| Transitional                  Small Business Disclosure Format (check one): Yes o                  No                  **R**                                                            |

----

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

**(A        Delaware Limited Partnership)**

**INDEX        TO QUARTERLY REPORT**

**ON        FORM 10-QSB**

| **PART                    I.** |   | **FINANCIAL                    INFORMATION**                                                                                                      | **PAGE** |
|--------------------------------|--------|---------------------------------------------------------------------------------------------------------------------------------------------------|----------|
|                           |   |                                                                                                                                              |     |
| Item                    1:     |   | Financial                    Statements                                                                                                           |     |
|                           |   |                                                                                                                                              |     |
|                           |   | Balance                    Sheets as of September 30, 2006 and December 31, 2005                    (Unaudited)                                   | 3        |
|                           |   |                                                                                                                                              |     |
|                           |   | Statements                    of Operations for the Three and Nine Months ended September 30,                    2006 and                    2005 |     |
|                           |   | (Unaudited)                                                                                                                                       | 4        |
|                           |   |                                                                                                                                              |     |
|                           |   | Statement                    of Partners’ Capital Accounts for the Nine Months ended September 30,                    2006                  |     |
|                           |   | (Unaudited)                                                                                                                                       | 5        |
|                           |   |                                                                                                                                              |     |
|                           |   | Statements                    of Cash Flows for the Nine Months ended September 30, 2006 and                    2005                              |     |
|                           |   | (Unaudited)                                                                                                                                       | 6        |
|                           |   |                                                                                                                                              |     |
|                           |   | Notes                    to Financial Statements (Unaudited)                                                                                      | 7-12     |
|                           |   |                                                                                                                                              |     |
| Item                    2:     |   | Management’s                    Discussion and Analysis of Financial Condition or Plan of                    Operations                     | 12-16    |
|                           |   |                                                                                                                                              |     |
| Item                    3:     |   | Controls                    and Procedures                                                                                                        | 16       |
|                           |   |                                                                                                                                              |     |
| **PART.II**                    |   | **OTHER                    INFORMATION**                                                                                                          |     |
|                           |   |                                                                                                                                              |     |
| Item                    6:     |   | Exhibits                                                                                                                                          | 16       |
|                           |   |                                                                                                                                              |     |
|                           |   |                                                                                                                                              |     |
| **SIGNATURES**                 | 17     |
|                           |   |                                                                                                                                              |     |
| **CERTIFICATIONS**             | 18-21  |

----

**PART        I**

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

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

**BALANCE        SHEETS**

**(Unaudited)**

|                                                         |   | **September                  30,** |       | **December                  31,** |   |
|--------------------------------------------------------------|--------|------------------------------------|------------|-----------------------------------|--------|
|                                                         |   | **2006**                           |       | **2005**                          |   |
|                                                         |   |                               |       |                              |   |   |   |
| **ASSETS**                                                   |   |                               |       |                              |   |   |   |
| Current                  Assets:                             |   |                               |       |                              |   |   |   |
| Cash                  and cash equivalents                   |   | $                                  | 1,197,500  |                              | $      | 1,938,700 |   |
| Accounts                  receivable-affiliate               |   |                               | 1,562,300  |                              |   | 3,249,700 |   |
| Hedge                  receivable short-term-affiliate       |   |                               | 938,400    |                              |   | 161,900 |   |
| Total                  current assets                        |   |                               | 3,698,200  |                              |   | 5,350,300 |   |
|                                                         |   |                               |       |                              |   |   |   |
| Oil                  and gas properties, net                 |   |                               | 38,313,700 |                              |   | 41,014,300 |   |
|                                                         |   |                               |       |                              |   |   |   |
| Hedge                  receivable long-term-affiliate        |   |                               | 1,004,000  |                              |   | ― |   |
|                                                         |   | $                                  | 43,015,900 |                              | $      | 46,364,600 |   |
|                                                         |   |                               |       |                              |   |   |   |
| **LIABILITIES                  AND PARTNERS’ CAPITAL** |   |                               |       |                              |   |   |   |
| Current                  liabilities:                        |   |                               |       |                              |   |   |   |
| Accrued                  liabilities                         |   | $                                  | 14,300     |                              | $      | 33,000 |   |
| Hedge                  liability short-term-affiliate        |   |                               | ―    |                              |   | 15,800 |   |
| Total                  current liabilities                   |   |                               | 14,300     |                              |   | 48,800 |   |
|                                                         |   |                               |       |                              |   |   |   |
| Asset                  retirement obligation                 |   |                               | 1,980,200  |                              |   | 1,894,900 |   |
| Hedge                  liability long-term-affiliate         |   |                               | 96,300     |                              |   | 708,400 |   |
|                                                         |   |                               |       |                              |   |   |   |
|                                                         |   |                               |       |                              |   |   |   |
| Partners’                  capital:                    |   |                               |       |                              |   |   |   |
| Managing                  general partner                    |   |                               | 10,845,800 |                              |   | 11,997,500 |   |
| Limited                  partners (4,024.15 units)           |   |                               | 28,233,200 |                              |   | 32,277,300 |   |
| Accumulated                  comprehensive income (loss)     |   |                               | 1,846,100  |                              |   | (562,300 | ) |
|                                                         |   |                               | 40,925,100 |                              |   | 43,712,500 |   |
|                                                         |   | $                                  | 43,015,900 |                              | $      | 46,364,600 |   |

----

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

**STATEMENTS        OF OPERATIONS**

**(Unaudited)**

|                                                       |   | **Three                  Months Ended** |      | **Nine                  Months Ended** |   |
|------------------------------------------------------------|--------|-----------------------------------------|-----------|----------------------------------------|--------|
|                                                       |   | **September                  30,**      |      | **September                  30,**     |   |
|                                                       |   | **2006**                                |      | **2005**                               |   | **2006** |   | **2005** |   |
| **REVENUES:**                                              |   |                                    |      |                                   |   |   |   |   |   |   |   |   |   |
| Natural                  gas and oil sales                 |   | $                                       | 1,762,200 |                                   | $      | 2,624,300 |   | $ | 6,852,100 |   | $ | 9,239,900 |   |
| Interest                  income                           |   |                                    | 11,900    |                                   |   | 8,900 |   |   | 40,500 |   |   | 24,500 |   |
| Total                  revenues                            |   |                                    | 1,774,100 |                                   |   | 2,633,200 |   |   | 6,892,600 |   |   | 9,264,400 |   |
|                                                       |   |                                    |      |                                   |   |   |   |   |   |   |   |   |   |
| **COSTS                  AND EXPENSES:**                   |   |                                    |      |                                   |   |   |   |   |   |   |   |   |   |
| Production                  expenses                       |   |                                    | 424,700   |                                   |   | 365,200 |   |   | 1,381,500 |   |   | 1,166,000 |   |
| Depletion                                                  |   |                                    | 807,900   |                                   |   | 1,373,100 |   |   | 2,715,300 |   |   | 4,469,300 |   |
| Accretion                  of asset retirement obligation  |   |                                    | 27,300    |                                   |   | 17,800 |   |   | 85,300 |   |   | 53,400 |   |
| General                  and administrative expenses       |   |                                    | 53,900    |                                   |   | 56,600 |   |   | 167,400 |   |   | 173,900 |   |
| Total                  expenses                            |   |                                    | 1,313,800 |                                   |   | 1,812,700 |   |   | 4,349,500 |   |   | 5,862,600 |   |
| **Net                  earnings**                          |   | $                                       | 460,300   |                                   | $      | 820,500 |   | $ | 2,543,100 |   | $ | 3,401,800 |   |
|                                                       |   |                                    |      |                                   |   |   |   |   |   |   |   |   |   |
| **Allocation                  of net earnings:**           |   |                                    |      |                                   |   |   |   |   |   |   |   |   |   |
| Managing                  general partner                  |   | $                                       | 358,300   |                                   | $      | 578,700 |   | $ | 1,551,900 |   | $ | 2,137,600 |   |
| Limited                  partners                          |   | $                                       | 102,000   |                                   | $      | 241,800 |   | $ | 991,200 |   | $ | 1,264,200 |   |
| Net                  earnings per limited partnership unit |   | $                                       | 25        |                                   | $      | 60 |   | $ | 246 |   | $ | 314 |   |

----

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

**STATEMENT        OF PARTNERS’ CAPITAL ACCOUNTS**

**FOR        THE NINE MONTHS ENDED September 30, 2006**

**(Unaudited)**

|                                                      |   | **Managing** |       |         |   | **Accumulated**   |   |      |      |
|-----------------------------------------------------------|--------|--------------|------------|--------------|--------|-------------------|--------|-----------|-----------|
|                                                      |   | **General**  |       | **Limited**  |   | **Comprehensive** |   |      |      |
|                                                      |   | **Partner**  |       | **Partners** |   | **(Loss)/Income** |   | **Total** |      |
|                                                      |   |         |       |         |   |              |   |      |      |   |   |   |   |
| **Balance                  at January 1, 2006**           |   | $            | 11,997,500 |         | $      | 32,277,300        |   | $         | (562,300  | ) | $ | 43,712,500 |   |
|                                                      |   |         |       |         |   |              |   |      |      |   |   |   |   |
| Participation                  in revenues and expenses:  |   |         |       |         |   |              |   |      |      |   |   |   |   |
| Net                  production revenues                  |   |         | 1,914,700  |         |   | 3,555,900         |   |      | ―   |   |   | 5,470,600 |   |
| Interest                  income                          |   |         | 14,200     |         |   | 26,300            |   |      | ―   |   |   | 40,500 |   |
| Depletion                                                 |   |         | (288,500   | )            |   | (2,426,800        | )      |      | ―   |   |   | (2,715,300 | ) |
| Accretion                  of asset retirement obligation |   |         | (29,900    | )            |   | (55,400           | )      |      | ―   |   |   | (85,300 | ) |
| General                  and administrative               |   |         | (58,600    | )            |   | (108,800          | )      |      | ―   |   |   | (167,400 | ) |
| Net                  earnings                             |   |         | 1,551,900  |         |   | 991,200           |   |      | ―   |   |   | 2,543,100 |   |
|                                                      |   |         |       |         |   |              |   |      |      |   |   |   |   |
|                                                      |   |         |       |         |   |              |   |      |      |   |   |   |   |
| Other                  comprehensive income               |   |         | ―    |         |   | ―           |   |      | 2,408,400 |   |   | 2,408,400 |   |
|                                                      |   |         |       |         |   |              |   |      |      |   |   |   |   |
|                                                      |   |         |       |         |   |              |   |      |      |   |   |   |   |
| Distributions                  to partners                |   |         | (2,703,600 | )            |   | (5,035,300        | )      |      | ―   |   |   | (7,738,900 | ) |
|                                                      |   |         |       |         |   |              |   |      |      |   |   |   |   |
| **Balance                  at September 30, 2006**        |   | $            | 10,845,800 |         | $      | 28,233,200        |   | $         | 1,846,100 |   | $ | 40,925,100 |   |

----

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

**STATEMENTS        OF CASH FLOWS **

**(Unaudited)**

|                                                                                                                  |   | **Nine                  Months Ended** |                            |
|-----------------------------------------------------------------------------------------------------------------------|--------|----------------------------------------|---------------------------------|
|                                                                                                                  |   | **September                  30,**     |                            |
|                                                                                                                  |   | **2006**                               |                            | **2005** |   |
| **Cash                  flows from operating activities:**                                                            |   |                                   |                            |   |   |   |   |
| Net                  earnings                                                                                         |   | $                                      | 2,543,100                       |   | $ | 3,401,800 |   |
| Adjustments                  to reconcile net earnings to net cash provided by operating                  activities: |   |                                   |                            |   |   |   |   |
| Depletion                                                                                                             |   |                                   | 2,715,300                       |   |   | 4,469,300 |   |
| Accretion                  of asset retirement obligation                                                             |   |                                   | 85,300                          |   |   | 53,400 |   |
| Decrease                  in accounts receivable - affiliate                                                          |   |                                   | 1,687,400                       |   |   | 2,062,400 |   |
| Decrease                  in accrued liabilities                                                                      |   |                                   | (18,700                         | ) |   | (5,100 | ) |
| Net                  cash provided by operating activities                                                            |   |                                   | 7,012,400                       |   |   | 9,981,800 |   |
|                                                                                                                  |   |                                   |                            |   |   |   |   |
| **Cash                  flows from investing activities:**                                                            |   |                                   |                            |   |   |   |   |
| Proceeds                  from asset sale                                                                             |   |                                   | 1,200                           |   |   | 3,900 |   |
| Purchase                  of tangible equipment                                                                       |   |                                   | (15,900                         | ) |   | — |   |
| Net                  cash (used in) provided by investing activities                                                  |   |                                   | (14,700                         | ) |   | 3,900 |   |
|                                                                                                                  |   |                                   |                            |   |   |   |   |
| **Cash                  flows from financing activities:**                                                            |   |                                   |                            |   |   |   |   |
| Distributions                  to partners                                                                            |   |                                   | (7,738,900                      | ) |   | (9,336,000 | ) |
| Net                  cash used in financing activities                                                                |   |                                   | (7,738,900                      | ) |   | (9,336,000 | ) |
|                                                                                                                  |   |                                   |                            |   |   |   |   |
| Net                  (decrease) increase in cash and cash equivalents                                                 |   |                                   | (741,200                        | ) |   | 649,700 |   |
| Cash                  and cash equivalents at beginning of period                                                     |   |                                   | 1,938,700                       |   |   | 1,024,500 |   |
| Cash                  and cash equivalents at end of period                                                           |   | $                                      | 1,197,500                       |   | $ | 1,674,200 |   |
|                                                                                                                  |   |                                   |                            |   |   |   |   |
| **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 |   |
| Intangible                  drilling cost included in oil and gas properties                                          |   |                                   | —                         |   |   | 920,400 |   |
|                                                                                                                  |   | $                                      |     — |   | $ | 1,149,500 |   |

----

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

**NOTES        TO FINANCIAL STATEMENTS**

**September        30, 2006**

**(Unaudited)**

**NOTE        1 **
**-**
**        NATURE OF OPERATIONS**

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

**Recently        Issued Financial Accounting Standards**

*Considering        the Effects of Prior Year Misstatements when Quantifying Misstatements in        Current Year Financial Statements*

*Fair        Value*
*Measurement*

----

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

**NOTES        TO FINANCIAL STATEMENTS**

**September        30, 2006**

**(Unaudited)**

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

**Receivables**

**Revenue        Recognition**

**Reclassifications**

**Asset        Retirement Obligation**

*Accounting        for Asset Retirement Obligations*

|                                                                |   | **Three                  Months** |      | **Nine                  Months** |   |
|---------------------------------------------------------------------|--------|-----------------------------------|-----------|----------------------------------|--------|
|                                                                |   | **2006**                          |      | **2005**                         |   | **2006** |   | **2005** |   |
|                                                                |   |                              |      |                             |   |   |   |   |   |   |   |   |   |
| Asset                  retirement obligation at beginning of period |   | $                                 | 1,952,900 |                             | $      | 1,221,000 |   | $ | 1,894,900 |   | $ | 1,185,400 |   |
| Accretion                  expense                                  |   |                              | 27,300    |                             |   | 17,800 |   |   | 85,300 |   |   | 53,400 |   |
| Total                  asset retirement obligation at end of period |   | $                                 | 1,980,200 |                             | $      | 1,238,800 |   | $ | 1,980,200 |   | $ | 1,238,800 |   |

**Concentration        of Credit Risk**

----

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

**NOTES        TO FINANCIAL STATEMENTS **

**September        30, 2006**

**(Unaudited)**

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

**Property        and Equipment**

| Oil                  and gas properties consist of the following at the dates                  indicated: |   | **September                  30,** |        | **December                  31,** |   |
|-----------------------------------------------------------------------------------------------------------|--------|------------------------------------|-------------|-----------------------------------|--------|
|                                                                                                      |   | **2006**                           |        | **2005**                          |   |
| Capitalized                  costs of properties:                                                         |   |                               |        |                              |   |   |   |
| Proved                  properties                                                                        |   | $                                  | 1,169,700   |                              | $      | 1,169,700 |   |
| Wells                  and related equipment                                                              |   |                               | 52,851,700  |                              |   | 52,837,000 |   |
|                                                                                                      |   |                               | 54,021,400  |                              |   | 54,006,700 |   |
|                                                                                                      |   |                               |        |                              |   |   |   |
| Accumulated                  depletion                                                                    |   |                               | (15,707,700 | )                                 |   | (12,992,400 | ) |
|                                                                                                      |   | $                                  | 38,313,700  |                              | $      | 41,014,300 |   |

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

| ·   | Administrative                costs which are included in general and administrative expenses in                the                Partnership’s Statements of Operations are payable at $75 per well per                month. Administrative costs incurred for the three months ended September                30, 2006 and 2005 were $46,100 and $46,400, respectively; and $137,700                and                $135,700 for the nine months ended September 30, 2006 and 2005,                respectively. |
|--------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| ·   | Monthly                well supervision fees which are included in production expenses in                the                Partnership’s Statements of Operations are payable at $289 per well per                month for operating and maintaining the wells. Well supervision fees                incurred for the three months ended September 30, 2006 and 2005 were                $186,200 and $170,200, respectively; and $527,800 and $503,900 for                the                nine months ended September 30, 2006 and 2005,                respectively. |
|--------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| ·   | Transportation                fees which are included in production expenses in the Partnership’s                Statements of Operations are payable at rates ranging from $.29-$.35                per                mcf (one thousand cubic feet) to 10% of the natural gas sales price.                Transportation costs incurred for the three months ended September                30,                2006 and 2005 were $162,900 and $115,900, respectively; and $609,400                and                $394,300 for the nine months ended September 30, 2006 and 2005,                respectively. |
|--------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

----

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

**NOTES        TO FINANCIAL STATEMENTS **

**September        30, 2006**

**(Unaudited)**

**NOTE        3 **
**-**
**        TRANSACTIONS WITH ATLAS RESOURCES, LLC AND ITS AFFILIATES        (CONTINUED)**

**Comprehensive        Income**

|                                                          |   | **Three                  Months Ended** |      | **Nine                  Months Ended** |   |
|---------------------------------------------------------------|--------|-----------------------------------------|-----------|----------------------------------------|--------|
|                                                          |   | **September                  30,**      |      | **September                  30,**     |   |
|                                                          |   | **2006**                                |      | **2005**                               |   | **2006** |   | **2005** |   |
|                                                          |   |                                    |      |                                   |   |   |   |   |   |   |   |   |   |
| Net                  earnings                                 |   | $                                       | 460,300   |                                   | $      | 820,500 |   | $ | 2,543,100 |   | $ | 3,401,800 |   |
| Other                  comprehensive income:                  |   |                                    |      |                                   |   |   |   |   |   |   |   |   |   |
| Unrealized                  holding gain on hedging contracts |   |                                    | 1,668,400 |                                   |   | ― |   |   | 2,986,900 |   |   | ― |   |
| Less:                  reclassification adjustment for gains  |   |                                    |      |                                   |   |   |   |   |   |   |   |   |   |
| realized                  in net earnings                     |   |                                    | (215,500  | )                                      |   | ― |   |   | (578,500 | ) |   | ― |   |
| Total                  other comprehensive income             |   |                                    | 1,452,900 |                                   |   | ― |   |   | 2,408,400 |   |   | ― |   |
| Comprehensive                  income                         |   | $                                       | 1,913,200 |                                   | $      | 820,500 |   | $ | 4,951,500 |   | $ | 3,401,800 |   |

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

**NOTE        4 - DERIVATIVE INSTRUMENTS**

----

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

**NOTES        TO FINANCIAL STATEMENTS **

**September        30, 2006**

**(Unaudited)**

**NOTE        4 - DERIVATIVE INSTRUMENTS (CONTINUED)**

| **Natural                  Gas Fixed - Price Swaps** |   |               |    |                             |   |
|------------------------------------------------------|--------|--------------------|---------|----------------------------------|--------|
|                                                 |   |               |    |                             |   |   |   |
| **Twelve                  Month**                    |   |               |    | **Average**                      |   | **Fair                  Value** |   |
| **Production                  Period**               |   | **Volumes**        |    | **Fixed                  Price** |   | **Asset****(2)** |   |
| **Ended                  September 30,**             |   | **(MMBTU)****(1)** |    | **(per                  MMBTU)** |   | **(in                  thousands)** |   |
|                                                 |   |               |    |                             |   |   |   |   |   |   |
| 2007                                                 |   |               | 471,700 |                             | $      | 9.26 |   | $ | 938 |   |
| 2008                                                 |   |               | 683,000 |                             |   | 8.75 |   |   | 464 |   |
| 2009                                                 |   |               | 510,800 |                             |   | 8.65 |   |   | 367 |   |
| 2010                                                 |   |               | 113,300 |                             |   | 8.61 |   |   | 77 |   |
|                                                 |   |               |    |                             |   |   |   |   |   |   |
| Total                  asset                         | $      | 1,846              |    |

| (1)   | MMBTU                represents million British Thermal Units. |
|-----------------|----------------------------------------------------------------|
| (2)   | Fair                value based on forward NYMEX natural gas prices, as                applicable. |
|-----------------|----------------------------------------------------------------------------------------------------|

----

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

**NOTES        TO FINANCIAL STATEMENTS **

**September        30, 2006**

**(Unaudited)**

**NOTE        4 - DERIVATIVE INSTRUMENTS (CONTINUED)**

|                                    |   | **September                  30, 2006** |   | **December                  31, 2005** |   |
|-----------------------------------------|--------|-----------------------------------------|--------|----------------------------------------|--------|
|                                    |   | **Book                  Value**         |   | **Fair                  Value**        |   | **Book                  Value** |   | **Fair                  Value** |   |
| Assets                                  |   |                                    |   |                                   |   |   |   |   |   |   |   |   |   |
| Derivative                  instruments |   | $                                       | 1,942  |                                   | $      | 1,942 |   | $ | 162 |   | $ | 162 |   |
|                                    |   | $                                       | 1,942  |                                   | $      | 1,942 |   | $ | 162 |   | $ | 162 |   |
| Liabilities                             |   |                                    |   |                                   |   |   |   |   |   |   |   |   |   |
| Derivative                  instruments |   | $                                       | (96    | )                                      | $      | (96 | ) | $ | (724 | ) | $ | (724 | ) |
|                                    |   | $                                       | 1,846  |                                   | $      | 1,846 |   | $ | (562 | ) | $ | (562 | ) |

**NOTE        5 - SUBSEQUENT EVENT**

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

**Forward-Looking        Statements**

**General**

----

**Results        of Operations**

|                                                 |   | **Three                  Months Ended** |   | **Nine                  Months Ended** |   |
|------------------------------------------------------|--------|-----------------------------------------|--------|----------------------------------------|--------|
|                                                 |   | **September                  30,**      |   | **September                  30,**     |   |
|                                                 |   | **2006**                                |   | **2005**                               |   | **2006** |   | **2005** |   |
|                                                 |   |                                    |   |                                   |   |   |   |   |   |   |   |   |   |
| Production                  revenues (in thousands): |   |                                    |   |                                   |   |   |   |   |   |   |   |   |   |
| Gas                                                  |   | $                                       | 1,718  |                                   | $      | 2,506 |   | $ | 6,738 |   | $ | 8,887 |   |
| Oil                                                  |   | $                                       | 44     |                                   | $      | 119 |   | $ | 114 |   | $ | 353 |   |
| Total                                                |   | $                                       | 1,762  |                                   | $      | 2,625 |   | $ | 6,852 |   | $ | 9,240 |   |
|                                                 |   |                                    |   |                                   |   |   |   |   |   |   |   |   |   |
| Production                  volumes:                 |   |                                    |   |                                   |   |   |   |   |   |   |   |   |   |
| Gas                  (mcf/day) (2)                   |   |                                    | 2,263  |                                   |   | 3,948 |   |   | 2,630 |   |   | 4,620 |   |
| Oil                  (bbls/day) (2)                  |   |                                    | 7      |                                   |   | 22 |   |   | 7 |   |   | 26 |   |
| Total                  (mcfe/day) (2)                |   |                                    | 2,305  |                                   |   | 4,080 |   |   | 2,672 |   |   | 4,776 |   |
|                                                 |   |                                    |   |                                   |   |   |   |   |   |   |   |   |   |
| Average                  sales prices:               |   |                                    |   |                                   |   |   |   |   |   |   |   |   |   |
| Gas                  (per mcf) (1) (2)               |   | $                                       | 8.25   |                                   | $      | 6.90 |   | $ | 9.38 |   | $ | 7.05 |   |
| Oil                  (per bbl) (2)                   |   | $                                       | 67.12  |                                   | $      | 58.85 |   | $ | 62.84 |   | $ | 50.67 |   |
|                                                 |   |                                    |   |                                   |   |   |   |   |   |   |   |   |   |
| Average                  production costs:           |   |                                    |   |                                   |   |   |   |   |   |   |   |   |   |
| As                  a percent of sales               |   |                                    | 24     | %                                      |   | 14 | % |   | 20 | % |   | 13 | % |
| Per                  mcfe (2)                        |   | $                                       | 2.00   |                                   | $      | .97 |   | $ | 1.90 |   | $ | .89 |   |
|                                                 |   |                                    |   |                                   |   |   |   |   |   |   |   |   |   |
| Depletion                  per mcfe                  |   | $                                       | 3.81   |                                   | $      | 3.66 |   | $ | 3.73 |   | $ | 3.43 |   |

| (1)   | The                average sales price per mcf before the effects of hedging was $7.22                and                $8.50 for the three and nine months ended September 30, 2006,                respectively. There were no hedging transactions in the three and                nine                months ended September 30, 2005. |
|-----------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| (2)   | “Mcf”                means thousand cubic feet, “mcfe” means thousand cubic feet equivalent and                “bbls” means barrels. Bbls are converted to mcfe using the ratio of six                mcfs to one bbl. |
|-----------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

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**Natural        Gas Revenues**

**Oil        Revenues**

**Expenses.        **

----

**Liquidity        and Capital Resources. **

**Critical        Accounting Policies**

**Recently        Issued Financial Accounting Standards**

*Considering        the Effects of Prior Year Misstatements when Quantifying Misstatements in        Current Year Financial Statements*

*Fair        Value*
*Measurement*

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**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 of the Exchange Act of                    1934, the                    registrant has duly caused this |
|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| report                    to be signed on its behalf by the undersigned, thereunto duly                    authorized.                                                   |
|                                                                                                                                                                     |   |   |
|                                                                                                                                                                     |   |   |
| Atlas                    America Public #12-2003 Limited Partnership                                                                                                     |   |   |
|                                                                                                                                                                     |   |   |
|                                                                                                                                                                     |   | Atlas                    Resources, LLC, Managing General Partner |
|                                                                                                                                                                     |   |   |
| Date:                    November 13, 2006                                                                                                                               |   | By:/s/                    Freddie M. Kotek |
|                                                                                                                                                                     |   | Freddie                    M. Kotek, Chairman of the Board of Directors, |
|                                                                                                                                                                     |   | Chief                    Executive Officer and President |
|                                                                                                                                                                     |   |   |
|                                                                                                                                                                     |   |   |
| In                    accordance with the Exchange Act, this report has been signed                    by the                    following persons on behalf of the      |
| registrant                    and in the capacities and on the dates indicated.                                                                                          |
|                                                                                                                                                                     |   |   |
|                                                                                                                                                                     |   |   |
| Date:                    November 13, 2006                                                                                                                               |   | By:/s/                    Freddie M. Kotek |
|                                                                                                                                                                     |   | Freddie                    M. Kotek, Chairman of the Board of Directors, |
|                                                                                                                                                                     |   | Chief                    Executive Officer and President |
|                                                                                                                                                                     |   |   |
|                                                                                                                                                                     |   |   |
| Date:                    November 13, 2006                                                                                                                               |   | By:/s/                    Nancy J. McGurk |
|                                                                                                                                                                     |   | Nancy                    J. McGurk, Vice President, Chief Financial Officer and                    Chief |
|                                                                                                                                                                     |   | Accounting                    Officer |
|                                                                                                                                                                     |   |   |
|                                                                                                                                                                     |   |   |

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