|        |
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|        |  |
| o      | Annual report pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934. |
|   |   |
| x      | Transition report pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934. |
|   |   |
|   | For the transition period from January 1, 2011 to September 30, 2011 |
|   |   |
|   | COMMISSION FILE NUMBER 000-52033 |

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|                                                                                                |  |  |  |  |
| North Dakota                                                                                   |   | 76-0742311 |
| (State or other jurisdiction ofincorporation or organization)                                  |   | (I.R.S. Employer Identification No.) |
|                                                                                           |   |   |
| 3682 Highway 8 South, P.O. Box 11, Richardton, ND 58652                                        |
| (Address of principal executive offices)                                                       |
|                                                                                           |
| (701) 974-3308                                                                                 |
| (Registrant's telephone number, including area code)                                           |
|                                                                                           |   |   |   |   |
| Securities registered pursuant to Section 12(b) of the Act: None.                    |
|                                                                                           |   |   |   |   |
| Securities registered pursuant to Section 12(g) of the Act: Class A Membership Units |

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|--------------------------------|
|                                |  |
| Large Accelerated Filer o | Accelerated Filer  o |
| Non-Accelerated Filer x        | Smaller Reporting Company o |

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|     |                           |
|-----|---------------------------|
| (1) | Financial Statements  |

|     |                                    |
|-----|------------------------------------|
| (2) | Financial Statement Schedules  |

|     |          |
|-----|----------|
| (3) | Exhibits |

|             |
|-------------|
|             |  |  |  |  |  |
| Exhibit No. | Exhibit |   | Filed Herewith |   | Incorporated by Reference |
| 3.1         | Articles of Organization, as filed with the North Dakota Secretary of State on July 16, 2003. |   |   |   | Filed as Exhibit 3.1 to the registrant's registration statement on Form 10-12G (000-52033) and incorporated by reference herein. |
| 3.2         | Amended and Restated Operating Agreement of Red Trail Energy, LLC. |   |   |   | Filed as exhibit 3.1 to our Current Report on Form 8-K on August 6, 2008. (000-52033) and incorporated by reference herein. |
| 4.1         | Membership Unit Certificate Specimen. |   |   |   | Filed as Exhibit 4.1 to the registrant's registration statement on Form 10-12G (000-52033) and incorporated by reference herein. |
| 4.2         | Member Control Agreement of Red Trail Energy, LLC. |   |   |   | Filed as Exhibit 4.2 to our Annual Report on Form 10-K for the year ended December 31, 2006. (000-52033) and incorporated by reference herein. |
| 10.1        | The Burlington Northern and Santa Fe Railway Company Lease of Land for Construction/ Rehabilitation of Track made as of May 12, 2003 by and between The Burlington Northern and Santa Fe Railway Company and Red Trail Energy, LLC. |   |   |   | Filed as Exhibit 10.1 to the registrant's registration statement on Form 10-12G (000-52033) and incorporated by reference herein. |
| 10.2        | Management Agreement made and entered into as of December 17, 2003 by and between Red Trail Energy, LLC, and Greenway Consulting, LLC. |   |   |   | Filed as Exhibit 10.2 to the registrant's registration statement on Form 10-12G (000-52033) and incorporated by reference herein. |
| 10.3        | Development Services Agreement entered into as of December 17, 2003 by and between Red Trail Energy, LLC, and Greenway Consulting, LLC. |   |   |   | Filed as Exhibit 10.3 to the registrant's registration statement on Form 10-12G (000-52033) and incorporated by reference herein. |
| 10.4        | The Burlington Northern and Santa Fe Railway Company Real Estate Purchase and Sale Agreement with Red Trail Energy, LLC, dated January 14, 2004. |   |   |   | Filed as Exhibit 10.4 to the registrant's registration statement on Form 10-12G (000-52033) and incorporated by reference herein. |
| 10.5        | Warranty Deed made as of January 13, 2005 between Victor Tormaschy and Lucille Tormaschy, Husband and Wife, as Grantors, and Red Trail Energy, LLC, as Grantee. |   |   |   | Filed as Exhibit 10.8 to the registrant's registration statement on Form 10-12G (000-52033) and incorporated by reference herein. |
| 10.6        | Warranty Deed made as of July 11, 2005 between Neal C. Messer and Bonnie M. Messer, Husband and Wife, as Grantors, and Red Trail Energy, LLC, as Grantee. |   |   |   | Filed as Exhibit 10.9 to the registrant's registration statement on Form 10-12G (000-52033) and incorporated by reference herein. |
| 10.7        | Agreement for Electric Service made the dated August 18, 2005, by and between West Plains Electric Cooperative, Inc. and Red Trail Energy, LLC. |   |   |   | Filed as Exhibit 10.10 to the registrant's registration statement on Form 10-12G (000-52033) and incorporated by reference herein. |

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|-------|
|       |  |  |  |  |  |
| 10.8  | Lump Sum Design-Build Agreement between Red Trail Energy, LLC, and Fagen, Inc. dated August 29, 2005. |   |   |   | Filed as Exhibit 10.12 to the registrant's registration statement on Form 10-12G/A-3 (000-52033) and incorporated by reference herein. |
| 10.9  | Construction Loan Agreement dated as of the December 16, 2005 by and between Red Trail Energy, LLC, and First National Bank of Omaha. |   |   |   | Filed as Exhibit 10.14 to the registrant's registration statement on Form 10-12G (000-52033) and incorporated by reference herein. |
| 10.10 | Construction Note for $55,211,740.00 dated December 16, 2005, between Red Trail Energy, LLC, as Borrower, and First National Bank of Omaha, as Bank. |   |   |   | Filed as Exhibit 10.15 to the registrant's registration statement on Form 10-12G (000-52033) and incorporated by reference herein. |
| 10.11 | International Swap Dealers Association, Inc. Master Agreement dated as of December 16, 2005, signed by First National Bank of Omaha and Red Trial Energy, LLC. |   |   |   | Filed as Exhibit 10.18 to the registrant's registration statement on Form 10-12G (000-52033) and incorporated by reference herein. |
| 10.12 | Security Agreement and Deposit Account Control Agreement made December 16, 2005, by and among First National Bank of Omaha, Red Trail Energy, LLC, and Bank of North Dakota. |   |   |   | Filed as Exhibit 10.19 to the registrant's registration statement on Form 10-12G (000-52033) and incorporated by reference herein. |
| 10.13 | Security Agreement given as of December 16, 2005, by Red Trail Energy, LLC, to First National Bank of Omaha. |   |   |   | Filed as Exhibit 10.20 to the registrant's registration statement on Form 10-12G (000-52033) and incorporated by reference herein. |
| 10.14 | Control Agreement Regarding Security Interest in Investment Property, made as of December 16, 2005, by and between First National Bank of Omaha, Red Trail Energy, LLC, and First National Capital Markets, Inc. |   |   |   | Filed as Exhibit 10.21 to the registrant's registration statement on Form 10-12G (000-52033) and incorporated by reference herein. |
| 10.15 | Loan Agreement between Greenway Consulting, LLC, and Red Trail Energy, LLC, dated February 26, 2006. |   |   |   | Filed as Exhibit 10.22 to the registrant's registration statement on Form 10-12G (000-52033) and incorporated by reference herein. |
| 10.16 | Promissory Note for $1,525,000.00, dated February 28, 2006, given by Red Trail Energy, LLC, to Greenway Consulting, LLC. |   |   |   | Filed as Exhibit 10.23 to the registrant's registration statement on Form 10-12G (000-52033) and incorporated by reference herein. |
| 10.17 | Loan Agreement between ICM Inc. and Red Trail Energy, LLC, dated February 28, 2006. |   |   |   | Filed as Exhibit 10.24 to the registrant's registration statement on Form 10-12G (000-52033) and incorporated by reference herein. |
| 10.18 | Promissory Note for $3,000,000.00, dated February 28, 2006, given by Red Trail Energy, LLC, to ICM Inc. |   |   |   | Filed as Exhibit 10.25 to the registrant's registration statement on Form 10-12G (000-52033) and incorporated by reference herein. |
| 10.19 | Loan Agreement between Fagen, Inc. and Red Trail Energy, LLC, dated February 28, 2006. |   |   |   | Filed as Exhibit 10.26 to the registrant's registration statement on Form 10-12G (000-52033) and incorporated by reference herein. |
| 10.20 |  Promissory Note for $1,000,000.00, dated February 28, 2006, given by Red Trail Energy, LLC, to Fagen, Inc. |   |   |   | Filed as Exhibit 10.27 to the registrant's registration statement on Form 10-12G (000-52033) and incorporated by reference herein. |
| 10.21 | Southwest Pipeline Project Raw Water Service Contract, executed by Red Trail Energy, LLC, on March 8, 2006, by the Secretary of the North Dakota State Water Commission on March 31, 2006, and by the Chairman of the Southwest Water Authority on April 2, 2006. |   |   |   | Filed as Exhibit 10.28 to the registrant's registration statement on Form 10-12G (000-52033) and incorporated by reference herein. |
| 10.22 | Contract dated April 26, 2006, by and between the North Dakota Industrial Commission and Red Trail Energy, LLC. |   |   |   | Filed as Exhibit 10.29 to the registrant's second amended registration statement on Form 10-12G/A (000-52033) and incorporated by reference herein. |
| 10.23 | Subordination Agreement, dated May 16, 2006, among the State of North Dakota, by and through its Industrial Commission, First National Bank and Red Trail Energy, LLC. |   |   |   | Filed as Exhibit 10.30 to the registrant's second amended registration statement on Form 10-12G/A (000-52033) and incorporated by reference herein. |
| 10.24 | Firm Gas Service Extension Agreement, dated June 7, 2006, by and between Montana-Dakota Utilities Co. and Red Trail Energy, LLC. |   |   |   | Filed as Exhibit 10.31 to the registrant's second amended registration statement on Form 10-12G/A (000-52033) and incorporated by reference herein. |

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|       |
|-------|
|       |  |  |  |  |  |
| 10.25 | First Amendment to Construction Loan Agreement dated August 16, 2006 by and between Red Trail Energy, LLC and First National Bank of Omaha.   |   |   |   | Filed as Exhibit 10.32 to the registrant's Annual Report on Form 10-K for the year ended December 31, 2006. (000-52033) and incorporated by reference herein. |
| 10.26 | Security Agreement and Deposit Account Control Agreement effective August 16, 2006 by and among First National Bank of Omaha and Red Trail Energy, LLC. |   |   |   | Filed as Exhibit 10.34 to our Annual Report on Form 10-K for the year ended December 31, 2006. (000-52033) and incorporated by reference herein. |
| 10.27 | Equity Grant Agreement dated September 8, 2006 by and between Red Trail Energy, LLC and Mickey Miller. |   |   |   | Filed as Exhibit 10.35 to our Annual Report on Form 10-K for the year ended December 31, 2006. (000-52033) and incorporated by reference herein. |
| 10.28 | Option to Purchase 200,000 Class A Membership Units of Red Trail Energy, LLC by Red Trail Energy, LLC from North Dakota Development Fund and Stark County dated December 11, 2006. |   |   |   | Filed as Exhibit 10.36 to our Annual Report on Form 10-K for the year ended December 31, 2006. (000-52033) and incorporated by reference herein. |
| 10.29 | Audit Committee Charter adopted April 9, 2007. |   |   |   | Filed as Exhibit 10.37 to our Annual Report on Form 10-K for the year ended December 31, 2006. (000-52033) and incorporated by reference herein. |
| 10.30 | Senior Financial Officer Code of Conduct adopted March 28, 2007. |   |   |   | Filed as Exhibit 10.38 to our Annual Report on Form 10-K for the year ended December 31, 2006. (000-52033) and incorporated by reference herein. |
| 10.31 | Long Term Revolving Note for $10,000,000, dated April 16, 2007 between Red Trail Energy, LLC, as Borrower, and First National Bank of Omaha, as Bank.   |   |   |   | Filed as Exhibit 10.1 to our Quarterly Report on Form 10-Q for the quarter ended March 31, 2007 (000-52033) and incorporated by reference herein. |
| 10.32 | Variable Rate Note for $17,065,870, dated April 16, 2007 between Red Trail Energy, LLC, as Borrower, and First National Bank of Omaha, as Bank.   |   |   |   | Filed as Exhibit 10.2 to our Quarterly Report on Form 10-Q for the quarter ended March 31, 2007 (000-52033). |
| 10.33 | Fixed Rate Note for $27,605,870, dated April 16, 2007 between Red Trail Energy, LLC, as Borrower, and First National Bank of Omaha, as Bank.   |   |   |   | Filed as Exhibit 10.3 to our Quarterly Report on Form 10-Q for the quarter ended March 31, 2007 (000-52033) and incorporated by reference herein. |
| 10.34 | $3,500,000 Revolving Promissory Note given by the Company to First National Bank of Omaha dated July 18, 2007.   |   |   |   | Filed as Exhibit 10.1 to our Quarterly Report on Form 10-Q for the quarter ended September 30, 2007 (000-52033) and incorporated by reference herein. |
| 10.35 | Second Amendment to Construction Loan Agreement by and between the Company and First National Bank of Omaha dated July 18, 2007.   |   |   |   | Filed as Exhibit 10.2 to our Quarterly Report on Form 10-Q for the quarter ended September 30, 2007 (000-52033) and incorporated by reference herein. |
| 10.36 | Third Amendment to Construction Loan Agreement by and between the Company and First National Bank of Omaha dated November 15, 2007.   |   |   |   | Filed as Exhibit 10.38 to our Annual Report on Form 10-K for the year ended December 31, 2007 (000-52033) and incorporated by reference herein. |
| 10.37 | Fourth Amendment to Construction Loan Agreement by and between the Company and First National Bank of Omaha dated December 11, 2007.   |   |   |   | Filed as Exhibit 10.39 to our Annual Report on Form 10-K for the year ended December 31, 2007 (000-52033) and incorporated by reference herein. |
| 10.38 | Interest Rate Swap Agreement by and between the Company and First National Bank of Omaha dated December 11, 2007.   |   |   |   | Filed as Exhibit 10.40 to our Annual Report on Form 10-K for the year ended December 31, 2007 (000-52033) and incorporated by reference herein. |
| 10.39 | Member Ethanol Fuel Marketing agreement by and between Red Trail Energy, LLC and RPMG, Inc dated January 1, 2008.   |   |   |   | Filed as Exhibit 10.41 to our Annual Report on Form 10-K for the year ended December 31, 2007 (000-52033) and incorporated by reference herein. |
| 10.40 | Contribution Agreement by and between Red Trail Energy, LLC and Renewable Products Marketing Group, LLC dated January 1, 2008.   |   |   |   | Filed as Exhibit 10.42 to our Annual Report on Form 10-K for the year ended December 31, 2007 (000-52033) and incorporated by reference herein. |
| 10.41 | Coal Sales Order by and between Red Trail Energy, LLC and Westmoreland Coal Sales Company dated December 5, 2007.   |   |   |   | Filed as Exhibit 10.43 to our Annual Report on Form 10-K for the year ended December 31, 2007 (000-52033) and incorporated by reference herein. |

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|       |
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|       |  |  |  |  |  |
| 10.42 | Distillers Grain Marketing Agreement by and between Red Trail Energy, LLC and CHS, Inc dated March 10, 2008.   |   |   |   | Filed as Exhibit 10.44 to our Annual Report on Form 10-K for the year ended December 31, 2007 (000-52033) and incorporated by reference herein. |
| 10.43 | Assignment and Assumption Agreement dated April 1, 2008, by and between Commodity Specialist Company and Red Trail Energy, LLC.   |   |   |   | Filed as Exhibit 10.1 to our Quarterly Report on Form 10-Q for the quarter ended March 31, 2008 (000-52033) and incorporated by reference herein. |
| 10.44 | $3,500,000 Revolving Promissory Note given by the Company to First National Bank of Omaha dated July 19, 2008.   |   |   |   | Filed as Exhibit 10.1 to our Quarterly Report on Form 10-Q for the quarter ended September 30, 2008 (000-52033) and incorporated by reference herein. |
| 10.45 | Fifth Amendment to Construction Loan Agreement by and between the Company and First National Bank of Omaha dated July 19, 2008.   |   |   |   | Filed as Exhibit 10.2 to our Quarterly Report on Form 10-Q for the quarter ended September 30, 2008 (000-52033) and incorporated by reference herein. |
| 10.46 | Employment Agreement dated August 8, 2008 by and between Red Trail Energy, LLC and Mark Klimpel.   |   |   |   | Filed as exhibit 99.1 to our Current Report on Form 8-K filed with the SEC on August 13, 2008 (000-52033) and incorporated by reference herein. |
| 10.47 | Amended and Restated Member Control Agreement of Red Trail Energy, LLC.   |   |   |   | Filed as exhibit 4.2 to our Current Report on Form 8-K filed with the SEC on June 1, 2009 (000-52033) and incorporated by reference herein. |
| 10.48 | Sixth Amendment to Construction Loan Agreement by and between the Company and First National Bank of Omaha effective date April 16, 2009.   |   |   |   | Filed as Exhibit 10.1 to our Current Report on Form 8-K filed with the SEC on June 2, 2009 (000-52033) and incorporated by reference herein. |
| 10.49 | Coal Sales Order by and between Red Trail Energy, LLC and Westmoreland Coal Sales Company dated November 5, 2009.   |   |   |   | Filed as Exhibit 10.1 to our Quarterly Report on Form 10-Q for the quarter ended September 30, 2009 (000-52033) and incorporated by reference herein. |
| 10.50 | Amended and Restated Management Agreement made and entered into as of September 10, 2009 by and between Red Trail Energy, LLC, and Greenway Consulting, LLC. |   |   |   | Filed as Exhibit 10.2 to our Quarterly Report on Form 10-Q for the quarter ended September 30, 2009 (000-52033) and incorporated by reference herein. |
| 10.51 | Seventh Amendment to Construction Loan Agreement by and between the Company and First National Bank of Omaha dated March 1, 2010. |   |   |   | Filed as Exhibit 10.51 to our Annual Report on Form 10-K for the fiscal year ended December 31, 2009 (000-52033) and incorporated by reference herein. |
| 10.52 | Employment Agreement between Red Trail Energy, LLC and Gerald Bachmeier dated July 8, 2010. |   |   |   | Filed as Exhibit 10.1 to our Quarterly Report on Form 10-Q for the quarter ended June 30, 2010 (000-52033) and incorporated by reference herein. |
| 10.53 | Mediated Settlement Agreement between Red Trail Energy, LLC, Fagen, Inc. and Fagen Engineering, LLC, and ICM, Inc. dated November 8, 2010. + |   |   |   | Filed as Exhibit 99.1 to our Current Report on Form 8-K filed with the SEC on December 20, 2010 (000-52033) and incorporated by reference herein. |
| 10.54 | Eight Amendment to Construction Loan Agreement between First National Bank of Omaha and Red Trail Energy, LLC dated November 15, 2010. |   |   |   | Filed as Exhibit 10.54 to our Current Report on Form 10-K for the fiscal year ended December 31, 2010 (000-52033) and incorporated by reference herein. |
| 10.55 | Revolving Promissory Note between First National Bank of Omaha and Red Trail Energy, LLC dated November 15, 2010. |   |   |   | Filed as Exhibit 10.55 to our Current Report on Form 10-K for the fiscal year ended December 31, 2010 (000-52033) and incorporated by reference herein. |
| 10.56 | Letter Agreement between Greenway Consulting, LLC and Red Trail Energy, LLC dated January 13, 2011. |   |   |   | Filed as Exhibit 10.56 to our Current Report on Form 10-K for the fiscal year ended December 31, 2010 (000-52033) and incorporated by reference herein. |
| 10.57 | Ninth Amendment to Construction Loan Agreement dated June 1, 2011 by and between Red Trail Energy, LLC and First National Bank of Omaha. |   |   |   | Filed as Exhibit 99.1 to our Current Report on Form 8-K dated June 1, 2011 (000-52033) and incorporated by reference herein. |
| 10.58 | First Amended and Restated Revolving Promissory Note dated June 1, 2011 by and between Red Trail Energy, LLC and First National Bank of Omaha. |   |   |   | Filed as Exhibit 99.2 to our Current Report on Form 8-K dated June 1, 2011 (000-52033) and incorporated by reference herein. |

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| 10.59 | Equity Grant Agreement between Kent Anderson and Red Trail Energy, LLC dated July 1, 2011. |   |   |   | Filed as Exhibit 10.1 to our Current Report on Form 10-Q for the quarter ended June 30, 2011 (000-52033) and incorporated by reference herein. |
| 10.60 | Corn Oil Separation System Agreement between Solution Recovery Services, LLC and Red Trail Energy, LLC dated October 6, 2011. + |   | X |   |   |
| 31.1  | Certificate Pursuant to 17 CFR 240.13a-14(a) |   | X |   |   |
| 31.2  | Certificate Pursuant to 17 CFR 240.13a-14(a) |   | X |   |   |
| 32.1  | Certificate Pursuant to 18 U.S.C. Section 1350 |   | X |   |   |
| 32.2  | Certificate Pursuant to 18 U.S.C. Section 1350 |   | X |   |   |
| 101   | The following financial information from Red Trail Energy, LLC's Annual Report on Form 10-K for the transition period ended September 30, 2011, formatted in XBRL (eXtensible Business Reporting Language): (i) Condensed Balance Sheets as of September 30, 2011 and December 31, 2010, (ii) Statements of Operations for the transition period ended September 30, 2011 and fiscal year ended December 31, 2010 and 2009, (iii) Statement of Changes in Members' Equity; (iv)  Statements of Cash Flows for the transition period ended September 30, 2011 and fiscal year ended December 31, 2010 and 2009, and (v) the Notes to Financial Statements.** |   |   |   |   |

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|        |  |  |  |
|   |   |   | RED TRAIL ENERGY, LLC |
|   |   |   |   |
| Date:  | June 26, 2012 |   | /s/ Gerald Bachmeier |
|   |   |   | Gerald Bachmeier |
|   |   |   | President and Chief Executive Officer |
|   |   |   | (Principal Executive Officer) |
|   |   |   |   |
| Date:  | June 26, 2012 |   | /s/ Kent Anderson |
|   |   |   | Kent Anderson |
|   |   |   | Chief Financial Officer |
|   |   |   | (Principal Financial and Accounting Officer) |

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|        |  |  |  |
| Date:  | June 26, 2012 |   | /s/ Gerald Bachmeier |
|   |   |   | Gerald Bachmeier, Chief Executive Officer and President |
|   |   |   | (Principal Executive Officer) |
|   |   |   |   |
| Date:  | June 26, 2012 |   | /s/ Kent Anderson |
|   |   |   | Kent Anderson, Chief Financial Officer and Treasurer |
|   |   |   | (Principal Financial Officer) |
|   |   |   |   |
| Date:  | June 26, 2012 |   | /s/ Sid Mauch |
|   |   |   | Sid Mauch, Chairman and Governor |
|   |   |   |   |
| Date:  | June 26, 2012 |   | /s/ Tim Meuchel |
|   |   |   | Tim Meuchel, Vice Chairman and Governor |
|   |   |   |   |
| Date:  | June 26, 2012 |   | /s/ Ambrose Hoff |
|   |   |   | Ambrose Hoff, Secretary and Governor |
|   |   |   |   |
| Date:  | June 26, 2012 |   | /s/ Ron Aberle |
|   |   |   | Ron Aberle, Governor |
|   |   |   |   |
| Date:  | June 26, 2012 |   | /s/ Mike Appert |
|   |   |   | Mike Appert, Governor |
|   |   |   |   |
| Date:  | June 26, 2012 |   | /s/ Frank Kirschenheiter |
|   |   |   | Frank Kirschenheiter, Governor |
|   |   |   |   |
| Date:  | June 26, 2012 |   | /s/ William A. Price |
|   |   |   | William A. Price, Governor |