| 18. Round | 18/01/2009 | OFI Heraklion | - | Panionios GSS | 2:0 |  |
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| 19. Round | 24/01/2009 | Olympiakos Piraeus | - | OFI Heraklion | 2:1 | ||||
| 20. Round | 31/01/2009 | OFI Heraklion | - | AE Lárissa | 1:2 | |
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| 21. Round | 08/02/2009 | Thrasyvoulos Fylis | - | OFI Heraklion | 1:2 | ||||
| 22. Round | 15/02/2009 | OFI Heraklion | - | Asteras Tripolis | 1:1 | ||||
| 23. Round | 21/02/2009 | Skoda Xanthi | - | OFI Heraklion | 0:0 | |
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| 24. Round | 01/03/2009 | OFI Heraklion | - | Panserraikos | 0:0 | ||||
| 25. Round | 08/03/2009 | OFI Heraklion | - | Levadiakos | 0:2 | ||||
| 26. Round | 14/03/2009 | AEK Athen | - | OFI Heraklion | 1:0 | |
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| 27. Round | 22/03/2009 | OFI Heraklion | - | Panthrakikos | 4:3 | |
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| 28. Round | 05/04/2009 | Aris Saloniki | - | OFI Heraklion | 4:1 | |
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| 29. Round | 12/04/2009 | OFI Heraklion | - | Ergotelis | 0:0 |
Spain