| 1. Round | 26/07/2008 | Jahn Regensburg | - | FC Carl Zeiss Jena | 2:2 |  |
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| 3. Round | 15/08/2008 | Rot-Weiß Erfurt | - | FC Carl Zeiss Jena | 2:1 |  |
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| 4. Round | 23/08/2008 | FC Carl Zeiss Jena | - | Kickers Emden | 1:1 | ||||
| 17. Round | 29/11/2008 | FC Carl Zeiss Jena | - | Fortuna Düsseldorf | 1:0 | ||||
| 33. Round | 25/04/2009 | FC Carl Zeiss Jena | - | Werder Bremen II | 3:1 |
Switzerland
France