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1/64-finals
1/32-finals
1/16-finals
1/8-finals
Quarter-finals
Semi-finals
Final
2008/09
1/64-finals
| 1 | AEK Athens FC | Bye | |
| 3 | PAO Neoi Epivates | Neos Asteras Rethymno | 2 : 1 |
| 4 | Bye | AO Ilisiakos | |
| 5 | Levadiakos | Bye | |
| 7 | Fokikos FC | Paraskevi | 1 : 0 |
| 8 | Bye | Kerkyra | |
| 9 | Ergotelis | Bye | |
| 11 | Odysseas | Keravnos | 3 : 2 |
| 12 | Bye | E. Asteras | |
| 13 | Athens Kallithea | Bye | |
| 14 | Ag. Dimitrios | Pyrsos | 0 : 1 |
| 16 | Bye | Xanthi FC | |
| 17 | Panathinaikos | Bye | |
| 19 | Rodos | Anagennisi Arta | 1 : 0 |
| 20 | Bye | Kavala | |
| 21 | Zakynthos | Chersonissos | 2 : 1 |
| 22 | Bye | Pierikos | |
| 24 | Bye | Panthrakikos | |
| 25 | AEL Larissa | Bye | |
| 27 | O. Volos | Bye | |
| 28 | Atsalenios | Panetolikos | 0 : 3 |
| 29 | Lamia | Aiolikos | 1 : 0 |
| 30 | Bye | Kalamata | |
| 32 | Bye | Panserraikos | |
| 33 | Asteras Tripolis | Bye | |
| 35 | Ilioupoli | Aias | 1 : 0 |
| 36 | Bye | Apollon Pontou | |
| 37 | Kastoria | Bye | |
| 38 | PAE Egaleo | Panachaiki | 0 : 3 |
| 40 | Bye | Iraklis 1908 | |
| 41 | Veria | Bye | |
| 42 | Thermaikos FC | Chaidari | 0 : 1 |
| 44 | Bye | Thrasivoulos | |
| 45 | Ethnikos Piraeus | Bye | |
| 46 | Ethnikos Katerinis | Korinthos | 0 : 3 |
| 48 | Bye | Panionios | |
| 49 | PAOK | Bye | |
| 51 | Karditsa | Bye | |
| 52 | AS Giannitsa | Makedonikos | 2 : 4 |
| 53 | Atromitos | Bye | |
| 54 | Panargiakos | Fostiras | 0 : 1 |
| 56 | Bye | Aris | |
| 57 | OFI Crete | Bye | |
| 59 | Doxa Dramas | Alexandroupoli Enosi | 3 : 0 |
| 60 | Bye | A. Asteras | |
| 61 | Diagoras | Bye | |
| 62 | Filippiada | Vyzas FC | 0 : 1 |
| 64 | Bye | Olympiacos Piraeus |
1/32-finals
| 1 | AEK Athens FC | Bye | |
| 2 | PAO Neoi Epivates | AO Ilisiakos | 0 : 1 |
| 3 | Levadiakos | Bye | |
| 4 | Fokikos FC | Kerkyra | 0 : 1 |
| 5 | Ergotelis | Bye | |
| 6 | Odysseas | E. Asteras | 0 : 2 |
| 7 | Athens Kallithea | Pyrsos | 4 : 1 |
| 8 | Bye | Xanthi FC | |
| 9 | Panathinaikos | Bye | |
| 10 | Rodos | Kavala | 0 : 1 |
| 11 | Zakynthos | Pierikos | 2 : 1 |
| 12 | Bye | Panthrakikos | |
| 13 | AEL Larissa | Bye | |
| 14 | O. Volos | Panetolikos | 1 : 2 |
| 15 | Lamia | Kalamata | 2 : 1 |
| 16 | Bye | Panserraikos | |
| 17 | Asteras Tripolis | Bye | |
| 18 | Ilioupoli | Apollon Pontou | 2 : 3 |
| 19 | Kastoria | Panachaiki | 4 : 0 |
| 20 | Bye | Iraklis 1908 | |
| 21 | Veria | Chaidari | 3 : 2 |
| 22 | Bye | Thrasivoulos | |
| 23 | Ethnikos Piraeus | Korinthos | 2 : 1 |
| 24 | Bye | Panionios | |
| 25 | PAOK | Bye | |
| 26 | Karditsa | Makedonikos | 1 : 2 |
| 27 | Atromitos | Fostiras | 3 : 1 |
| 28 | Bye | Aris | |
| 29 | OFI Crete | Bye | |
| 30 | Doxa Dramas | A. Asteras | 1 : 2 |
| 31 | Diagoras | Vyzas FC | 1 : 0 |
| 32 | Bye | Olympiacos Piraeus |
1/16-finals
| 1 | AEK Athens FC | AO Ilisiakos | 2 : 1 |
| 2 | Levadiakos | Kerkyra | 0 : 1 |
| 3 | Ergotelis | E. Asteras | 2 : 0 |
| 4 | Athens Kallithea | Xanthi FC | 1 : 3 |
| 5 | Panathinaikos | Kavala | 3 : 0 |
| 6 | Zakynthos | Panthrakikos | 0 : 2 |
| 7 | AEL Larissa | Panetolikos | 2 : 0 |
| 8 | Lamia | Panserraikos | 1 : 2 |
| 9 | Asteras Tripolis | Apollon Pontou | 1 : 0 |
| 10 | Kastoria | Iraklis 1908 | 2 : 3 |
| 11 | Veria | Thrasivoulos | 3 : 1 |
| 12 | Ethnikos Piraeus | Panionios | 0 : 2 |
| 13 | PAOK | Makedonikos | 2 : 1 |
| 14 | Atromitos | Aris | 1 : 2 |
| 15 | OFI Crete | A. Asteras | 2 : 1 |
| 16 | Diagoras | Olympiacos Piraeus | 2 : 3 |
1/8-finals
| 1 | AEK Athens FC | Kerkyra | 1 : 0 |
| 2 | Ergotelis | Xanthi FC | 0 : 3 |
| 3 | Panathinaikos | Panthrakikos | 4 : 0 |
| 4 | AEL Larissa | Panserraikos | 0 : 1 |
| 5 | Asteras Tripolis | Iraklis 1908 | 2 : 0 |
| 6 | Veria | Panionios | 0 : 2, 0 : 0 |
| 7 | PAOK | Aris | 1 : 0, 0 : 0 |
| 8 | OFI Crete | Olympiacos Piraeus | 0 : 2 |
Quarter-finals
| 1 | AEK Athens FC | Xanthi FC | 1 : 0, 1 : 2 |
| 2 | Panathinaikos | Panserraikos | 2 : 3, 0 : 0 |
| 3 | Asteras Tripolis | Panionios | 1 : 0, 1 : 0 |
| 4 | PAOK | Olympiacos Piraeus | 0 : 2, 1 : 0 |
Semi-finals
| 1 | AEK Athens FC | Panserraikos | 0 : 0, 3 : 1 |
| 2 | Asteras Tripolis | Olympiacos Piraeus | 1 : 2, 2 : 2 |
Final
| 1 | AEK Athens FC | Olympiacos Piraeus | 4 : 5 |
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