| 4. Round | 28/09/2008 | Skoda Xanthi | - | Thrasyvoulos Fylis | 1:0 |  |
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| 5. Round | 05/10/2008 | Asteras Tripolis | - | Skoda Xanthi | 0:0 | ||||
| 6. Round | 19/10/2008 | Levadiakos | - | Skoda Xanthi | 0:0 | |
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| 8. Round | 02/11/2008 | OFI Heraklion | - | Skoda Xanthi | 0:2 | ||||
| 14. Round | 13/12/2008 | PAOK Saloniki | - | Skoda Xanthi | 1:0 | |
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| 15. Round | 20/12/2008 | Iraklis Saloniki | - | Skoda Xanthi | 1:0 | ||||
| 16. Round | 03/01/2009 | Skoda Xanthi | - | Panionios GSS | 0:0 | |
Greece