| Round of 16 — Direct Qualification | ||||||||||
| 1 | Aston Villa | 6 | 5 | 1 | 0 | 12 | 1 | +11 | 16 | Direct |
| 2 | Sliema Wanderers | 6 | 5 | 0 | 1 | 16 | 8 | +8 | 15 | Direct |
| 3 | Red Star | 6 | 5 | 0 | 1 | 14 | 8 | +6 | 15 | Direct |
| 4 | Bohemian | 6 | 4 | 1 | 1 | 12 | 6 | +6 | 13 | Direct |
| 5 | Zalgiris Vilnius | 6 | 4 | 1 | 1 | 14 | 9 | +5 | 13 | Direct |
| 6 | Kayserispor | 6 | 4 | 1 | 1 | 13 | 8 | +5 | 13 | Direct |
| 7 | West Ham | 6 | 3 | 3 | 0 | 12 | 4 | +8 | 12 | Direct |
| 8 | Panathinaikos 2 | 6 | 3 | 2 | 1 | 22 | 14 | +8 | 11 | Direct |
| Knockout Playoff Round | ||||||||||
| 9 | Real Betis 2 | 6 | 3 | 2 | 1 | 16 | 14 | +2 | 11 | Playoff |
| 10 | Fiorentina 2 | 6 | 3 | 2 | 1 | 9 | 8 | +1 | 11 | Playoff |
| 11 | Breidablik | 6 | 3 | 1 | 2 | 11 | 7 | +4 | 10 | Playoff |
| 12 | Rigas FS | 6 | 3 | 1 | 2 | 11 | 9 | +2 | 10 | Playoff |
| 13 | Kairat | 6 | 3 | 1 | 2 | 10 | 10 | 0 | 10 | Playoff |
| 14 | Glentoran | 6 | 3 | 0 | 3 | 18 | 17 | +1 | 9 | Playoff |
| 15 | Sivasspor | 6 | 3 | 0 | 3 | 10 | 9 | +1 | 9 | Playoff |
| 16 | OFK Beograd | 6 | 2 | 3 | 1 | 12 | 12 | 0 | 9 | Playoff |
| 17 | Hamrun Spartans | 6 | 3 | 0 | 3 | 10 | 11 | -1 | 9 | Playoff |
| 18 | PAOK 2 | 6 | 3 | 0 | 3 | 15 | 17 | -2 | 9 | Playoff |
| 19 | Real Sociedad 2 | 6 | 2 | 3 | 1 | 11 | 14 | -3 | 9 | Playoff |
| 20 | Lazio 2 | 6 | 2 | 2 | 2 | 13 | 12 | +1 | 8 | Playoff |
| 21 | Anderlecht 2 | 6 | 2 | 2 | 2 | 12 | 12 | 0 | 8 | Playoff |
| 22 | FK Valmiera | 6 | 2 | 2 | 2 | 10 | 10 | 0 | 8 | Playoff |
| 23 | Lech Poznan | 6 | 2 | 2 | 2 | 16 | 19 | -3 | 8 | Playoff |
| 24 | Sarajevo | 6 | 2 | 2 | 2 | 12 | 17 | -5 | 8 | Playoff |
| Eliminated | ||||||||||
| 25 | Buducnost | 6 | 2 | 2 | 2 | 10 | 17 | -7 | 8 | Out |
| 26 | Lyon 2 | 6 | 2 | 1 | 3 | 16 | 12 | +4 | 7 | Out |
| 27 | Sparta Prague | 6 | 2 | 1 | 3 | 13 | 11 | +2 | 7 | Out |
| 28 | Trans | 6 | 2 | 0 | 4 | 11 | 11 | 0 | 6 | Out |
| 29 | Crusaders | 6 | 1 | 3 | 2 | 7 | 8 | -1 | 6 | Out |
| 30 | Partizan | 6 | 1 | 1 | 4 | 4 | 8 | -4 | 4 | Out |
| 31 | Drogheda | 6 | 1 | 1 | 4 | 10 | 17 | -7 | 4 | Out |
| 32 | Rennes 2 | 6 | 1 | 0 | 5 | 10 | 14 | -4 | 3 | Out |
| 33 | Jagiellonia Bialystok | 6 | 0 | 2 | 4 | 7 | 14 | -7 | 2 | Out |
| 34 | Gent 2 | 6 | 0 | 1 | 5 | 11 | 22 | -11 | 1 | Out |
| 35 | Glenavon | 6 | 0 | 0 | 6 | 4 | 13 | -9 | 0 | Out |
| 36 | RFS | 6 | 0 | 0 | 6 | 7 | 18 | -11 | 0 | Out |