| 5. Round | 24/10/1999 | Paniliakos Pyrgos | - | AEK Athen | 0:1 | ||||
| 7. Round | 07/11/1999 | Paniliakos Pyrgos | - | Panathinaikos | 0:1 |  |
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| 10. Round | 04/12/1999 | Paniliakos Pyrgos | - | PS Kalamata | 3:1 | ||||
| 11. Round | 11/12/1999 | Olympiakos Piraeus | - | Paniliakos Pyrgos | 2:1 | ||||
| 12. Round | 21/12/1999 | Paniliakos Pyrgos | - | Ionikos Nikea | 3:0 | |
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| 14. Round | 08/01/2000 | Paniliakos Pyrgos | - | OFI Heraklion | 1:2 | |
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| 20. Round | 18/02/2000 | AO Kavala | - | Paniliakos Pyrgos | 2:1 | ||||
| 21. Round | 26/02/2000 | Paniliakos Pyrgos | - | AO Trikala | 1:3 | ||||
| 23. Round | 10/03/2000 | Paniliakos Pyrgos | - | PAOK Saloniki | 0:4 | ||||
| 24. Round | 18/03/2000 | Panathinaikos | - | Paniliakos Pyrgos | 3:1 | |
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| 28. Round | 15/04/2000 | Paniliakos Pyrgos | - | Olympiakos Piraeus | 0:3 | ||||
| 31. Round | 06/05/2000 | OFI Heraklion | - | Paniliakos Pyrgos | 3:2 |  |
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| 33. Round | 20/05/2000 | Panachaiki GE | - | Paniliakos Pyrgos | 2:0 |
Greece