| 1. Round | 11/08/2006 | Kickers Offenbach | - | FC Carl Zeiss Jena | 2:2 |  |
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| 2. Round | 18/08/2006 | FC Carl Zeiss Jena | - | Eintracht Braunschweig | 0:0 | ||||
| 3. Round | 25/08/2006 | FC Carl Zeiss Jena | - | 1. FC Köln | 3:2 | ||||
| 6. Round | 01/10/2006 | TSV 1860 München | - | FC Carl Zeiss Jena | 2:0 | ||||
| 7. Round | 15/10/2006 | FC Carl Zeiss Jena | - | SpVgg Unterhaching | 0:2 | ||||
| 8. Round | 20/10/2006 | Karlsruher SC | - | FC Carl Zeiss Jena | 4:1 | |
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| 9. Round | 27/10/2006 | FC Carl Zeiss Jena | - | TuS Koblenz | 2:0 | ||||
| 10. Round | 03/11/2006 | Hansa Rostock | - | FC Carl Zeiss Jena | 1:1 |  |
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| 11. Round | 08/11/2006 | FC Carl Zeiss Jena | - | SpVgg Greuther Fürth | 1:1 | ||||
| 12. Round | 12/11/2006 | Erzgebirge Aue | - | FC Carl Zeiss Jena | 5:1 |  |
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| 15. Round | 03/12/2006 | FC Carl Zeiss Jena | - | Wacker Burghausen | 0:2 | |
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| 16. Round | 08/12/2006 | 1. FC Kaiserslautern | - | FC Carl Zeiss Jena | 0:0 | ||||
| 17. Round | 15/12/2006 | FC Carl Zeiss Jena | - | FC Augsburg | 0:2 | |
Germany