| Round of 16 — Direct Qualification | ||||||||||
| 1 | SS Murata | 6 | 5 | 1 | 0 | 19 | 10 | +9 | 16 | Direct |
| 2 | Narva Trans | 6 | 5 | 0 | 1 | 16 | 10 | +6 | 15 | Direct |
| 3 | Real Betis 2 | 6 | 4 | 1 | 1 | 15 | 7 | +8 | 13 | Direct |
| 4 | Aston Villa | 6 | 3 | 3 | 0 | 14 | 6 | +8 | 12 | Direct |
| 5 | Twente | 6 | 4 | 0 | 2 | 14 | 10 | +4 | 12 | Direct |
| 6 | Real Sociedad 2 | 6 | 4 | 0 | 2 | 12 | 9 | +3 | 12 | Direct |
| 7 | Sheriff | 6 | 3 | 1 | 2 | 16 | 10 | +6 | 10 | Direct |
| 8 | West Ham | 6 | 3 | 1 | 2 | 10 | 4 | +6 | 10 | Direct |
| Knockout Playoff Round | ||||||||||
| 9 | Gent 2 | 6 | 3 | 1 | 2 | 18 | 13 | +5 | 10 | Playoff |
| 10 | Kayserispor | 6 | 3 | 1 | 2 | 15 | 11 | +4 | 10 | Playoff |
| 11 | Rennes 2 | 6 | 3 | 1 | 2 | 16 | 13 | +3 | 10 | Playoff |
| 12 | Lech Poznan | 6 | 3 | 1 | 2 | 13 | 12 | +1 | 10 | Playoff |
| 13 | Besiktas | 6 | 3 | 1 | 2 | 10 | 9 | +1 | 10 | Playoff |
| 14 | Sivasspor | 6 | 3 | 1 | 2 | 11 | 13 | -2 | 10 | Playoff |
| 15 | Lazio 2 | 6 | 3 | 0 | 3 | 13 | 10 | +3 | 9 | Playoff |
| 16 | Fiorentina 2 | 6 | 3 | 0 | 3 | 14 | 12 | +2 | 9 | Playoff |
| 17 | CSKA Sofia | 6 | 2 | 3 | 1 | 13 | 11 | +2 | 9 | Playoff |
| 18 | Motherwell | 6 | 2 | 3 | 1 | 11 | 10 | +1 | 9 | Playoff |
| 19 | Sutjeska | 6 | 3 | 0 | 3 | 11 | 11 | 0 | 9 | Playoff |
| 20 | Slavia Prague | 6 | 3 | 0 | 3 | 10 | 10 | 0 | 9 | Playoff |
| 21 | PAOK 2 | 6 | 2 | 2 | 2 | 13 | 11 | +2 | 8 | Playoff |
| 22 | Bohemian | 6 | 2 | 2 | 2 | 9 | 11 | -2 | 8 | Playoff |
| 23 | Hearts | 6 | 2 | 1 | 3 | 11 | 10 | +1 | 7 | Playoff |
| 24 | Tirana | 6 | 2 | 1 | 3 | 13 | 13 | 0 | 7 | Playoff |
| Eliminated | ||||||||||
| 25 | Copenhagen | 6 | 2 | 1 | 3 | 13 | 15 | -2 | 7 | Out |
| 26 | Anderlecht 2 | 6 | 2 | 1 | 3 | 10 | 12 | -2 | 7 | Out |
| 27 | Jagiellonia Bialystok | 6 | 1 | 3 | 2 | 11 | 12 | -1 | 6 | Out |
| 28 | Aberdeen | 6 | 2 | 0 | 4 | 13 | 18 | -5 | 6 | Out |
| 29 | Longford Town | 6 | 2 | 0 | 4 | 9 | 14 | -5 | 6 | Out |
| 30 | Lyon 2 | 6 | 2 | 0 | 4 | 6 | 11 | -5 | 6 | Out |
| 31 | Panathinaikos 2 | 6 | 2 | 0 | 4 | 8 | 14 | -6 | 6 | Out |
| 32 | F91 Dudelange | 6 | 2 | 0 | 4 | 10 | 17 | -7 | 6 | Out |
| 33 | Sturm Graz | 6 | 1 | 1 | 4 | 10 | 14 | -4 | 4 | Out |
| 34 | Waterford | 6 | 1 | 1 | 4 | 8 | 14 | -6 | 4 | Out |
| 35 | Crusaders | 6 | 1 | 1 | 4 | 5 | 18 | -13 | 4 | Out |
| 36 | OFK Beograd | 6 | 0 | 1 | 5 | 3 | 18 | -15 | 1 | Out |