| 3. Round | 30/08/2008 | TSV 1860 München [Youth B] | - | 1. FSV Mainz 05 [Youth B] | 3:1 |  |
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| 4. Round | 14/09/2008 | 1. FSV Mainz 05 [Youth B] | - | SSV Ulm 1846 [Youth B] | 1:1 | ||||
| 5. Round | 28/09/2008 | 1. FSV Mainz 05 [Youth B] | - | Kickers Offenbach [Youth B] | 2:0 | ||||
| 21. Round | 08/10/2008 | 1. FSV Mainz 05 [Youth B] | - | Eintracht Frankfurt [Youth B] | 1:1 | ||||
| 14. Round | 11/10/2008 | 1. FSV Mainz 05 [Youth B] | - | Karlsruher SC [Youth B] | 2:1 | ||||
| 7. Round | 26/10/2008 | 1. FSV Mainz 05 [Youth B] | - | 1. FC Kaiserslautern [Youth B] | 0:2 | ||||
| 8. Round | 01/11/2008 | Eintracht Frankfurt [Youth B] | - | 1. FSV Mainz 05 [Youth B] | 4:2 | ||||
| 9. Round | 09/11/2008 | 1. FSV Mainz 05 [Youth B] | - | 1. FC Nürnberg [Youth B] | 2:2 | |
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| 10. Round | 15/11/2008 | Bayern München [Youth B] | - | 1. FSV Mainz 05 [Youth B] | 2:1 | ||||
| 13. Round | 14/12/2008 | 1. FSV Mainz 05 [Youth B] | - | SpVgg Greuther Fürth [Youth B] | 0:0 |
Germany