Draw
1/8-finals
| 1 | Trabzonspor | Bye | |
| 5 | Twente | Bye | |
| 6 | Vojvodina | Ferencvaros | 0 : 3, 1 : 2 |
| 8 | Bye | Gornik Zabrze | |
| 9 | KuPS | Bye | |
| 12 | Bye | Univ. Craiova | |
| 16 | Bye | Ararat-Armenia | |
| 17 | St. Truiden | Bye | |
| 21 | Lincoln Red Imps | Bye | |
| 24 | Bye | Omonia | |
| 25 | Crvena zvezda | Bye | |
| 32 | Bye | Plzen | |
| 33 | Shamrock Rovers | Bye | |
| 36 | Bye | Egnatia | |
| 40 | Bye | Lillestrom | |
| 41 | Jagiellonia | Bye | |
| 44 | Bye | Rangers | |
| 45 | Larne | Bye | |
| 48 | Bye | Iberia 1999 | |
| 49 | Mjallby | Bye | |
| 53 | Hajduk Split | Zilina | 1 : 2, 2 : 0 |
| 54 | Bye | Pafos | |
| 56 | Bye | Salzburg | |
| 57 | Kairat Almaty | Bye | |
| 61 | Dyn. Kyiv | U. Cluj | 1 : 0, 0 : 0 |
| 62 | Bye | PAOK | |
| 63 | Hammarby | Bye | |
| 64 | Bye | Anderlecht | |
| 65 | Lech Poznan | Bye | |
| 68 | Bye | Klaksvik | |
| 69 | Thun | Bye | |
| 72 | Bye | Vikingur Reykjavik | |
| 73 | Tromso | Bye | |
| 74 | Bye | Hradec Kralove | |
| 75 | Besiktas | Bye | |
| 76 | Bye | Midtjylland | |
| 80 | Bye | Kauno Zalgiris | |
| 81 | St. Gallen | Bye | |
| 82 | Bye | Benfica | |
| 84 | Bye | Hearts | |
| 88 | Bye | Aarhus | |
| 89 | OFI Crete | Bye | |
| 93 | Sheriff Tiraspol | Aluminij | 1 : 0, 0 : 0 |
| 94 | Bye | Maccabi Tel Aviv | |
| 95 | Qarabag | Vestri | 3 : 0, 3 : 0 |
| 96 | CSKA Sofia | Derry City | 2 : 1, 3 : 2 |
Quarter-finals
| 1 | Trabzonspor | Bye | |
| 3 | Twente | Ferencvaros | 2 : 2, 1 : 2 |
| 4 | Bye | Gornik Zabrze | |
| 5 | KuPS | Bye | |
| 6 | Bye | Univ. Craiova | |
| 8 | Bye | Ararat-Armenia | |
| 9 | St. Truiden | Bye | |
| 11 | Lincoln Red Imps | Bye | |
| 12 | Bye | Omonia | |
| 13 | Crvena zvezda | Bye | |
| 16 | Bye | Plzen | |
| 17 | Shamrock Rovers | Bye | |
| 18 | Bye | Egnatia | |
| 20 | Bye | Lillestrom | |
| 21 | Jagiellonia | Bye | |
| 22 | Bye | Rangers | |
| 23 | Larne | Bye | |
| 24 | Bye | Iberia 1999 | |
| 25 | Mjallby | Bye | |
| 27 | Hajduk Split | Pafos | 0 : 4, 2 : 0 |
| 28 | Bye | Salzburg | |
| 29 | Kairat Almaty | Bye | |
| 31 | Dyn. Kyiv | PAOK | 0 : 2, 2 : 3 |
| 32 | Hammarby | Anderlecht | 1 : 3, 1 : 1 |
| 33 | Lech Poznan | Bye | |
| 34 | Bye | Klaksvik | |
| 35 | Thun | Bye | |
| 36 | Bye | Vikingur Reykjavik | |
| 37 | Tromso | Hradec Kralove | 1 : 3, 0 : 1 |
| 38 | Besiktas | Midtjylland | 2 : 0, 1 : 0 |
| 40 | Bye | Kauno Zalgiris | |
| 41 | St. Gallen | Benfica | 0 : 5, 2 : 1 |
| 42 | Bye | Hearts | |
| 44 | Bye | Aarhus | |
| 45 | OFI Crete | Bye | |
| 47 | Sheriff Tiraspol | Maccabi Tel Aviv | 0 : 1, 0 : 5 |
| 48 | Qarabag | CSKA Sofia | 0 : 1, 0 : 0 |
Semi-finals
| 1 | Trabzonspor | Bye | |
| 2 | Ferencvaros | Gornik Zabrze | 1 : 1, 1 : 0 |
| 3 | KuPS | Univ. Craiova | 1 : 2, 1 : 1 |
| 4 | Bye | Ararat-Armenia | |
| 5 | St. Truiden | Bye | |
| 6 | Lincoln Red Imps | Omonia | 0 : 1, 1 : 1 |
| 7 | Crvena zvezda | Bye | |
| 8 | Bye | Plzen | |
| 9 | Shamrock Rovers | Egnatia | 1 : 5, 3 : 1 |
| 10 | Bye | Lillestrom | |
| 11 | Jagiellonia | Rangers | 1 : 1, 2 : 1 |
| 12 | Larne | Iberia 1999 | 1 : 2, 0 : 0 |
| 13 | Mjallby | Bye | |
| 14 | Pafos | Salzburg | 3 : 3, 0 : 1 |
| 15 | Kairat Almaty | Bye | |
| 16 | PAOK | Anderlecht | 2 : 3, 0 : 1 |
| 17 | Lech Poznan | Klaksvik | 5 : 0, 1 : 0 |
| 18 | Thun | Vikingur Reykjavik | 2 : 3, 3 : 0 |
| 19 | Hradec Kralove | Besiktas | 0 : 1, 0 : 1 |
| 20 | Bye | Kauno Zalgiris | |
| 21 | Benfica | Hearts | 1 : 1, 6 : 1 |
| 22 | Bye | Aarhus | |
| 23 | OFI Crete | Bye | |
| 24 | Maccabi Tel Aviv | CSKA Sofia | 3 : 1, 0 : 3 |
Final
| 1 | Trabzonspor | Ferencvaros | 0 : 1 |
| 2 | Univ. Craiova | Ararat-Armenia | 1 : 1 |
| 3 | St. Truiden | Omonia | 1 : 0 |
| 4 | Crvena zvezda | Plzen | 3 : 0 |
| 5 | Egnatia | Lillestrom | 0 : 0 |
| 6 | Jagiellonia | Iberia 1999 | 4 : 0 |
| 7 | Mjallby | Salzburg | 0 : 1 |
| 8 | Kairat Almaty | Anderlecht | 0 : 3 |
| 9 | Lech Poznan | Thun | 7 : 0 |
| 10 | Besiktas | Kauno Zalgiris | 3 : 0 |
| 11 | Benfica | Aarhus | 3 : 1 |
| 12 | OFI Crete | CSKA Sofia | 3 : 0 |
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