| Round of 16 — Direct Qualification | ||||||||||
| 1 | Valencia | 8 | 8 | 0 | 0 | 30 | 11 | +19 | 24 | Direct |
| 2 | Augsburg | 8 | 8 | 0 | 0 | 18 | 2 | +16 | 24 | Direct |
| 3 | Braga | 8 | 7 | 0 | 1 | 26 | 13 | +13 | 21 | Direct |
| 4 | Sutjeska | 8 | 6 | 1 | 1 | 21 | 11 | +10 | 19 | Direct |
| 5 | Villarreal | 8 | 6 | 0 | 2 | 17 | 5 | +12 | 18 | Direct |
| 6 | Rennes | 8 | 6 | 0 | 2 | 17 | 9 | +8 | 18 | Direct |
| 7 | Monaco | 8 | 5 | 2 | 1 | 17 | 6 | +11 | 17 | Direct |
| 8 | Lyon | 8 | 5 | 2 | 1 | 17 | 10 | +7 | 17 | Direct |
| Knockout Playoff Round | ||||||||||
| 9 | Tottenham | 8 | 5 | 1 | 2 | 18 | 6 | +12 | 16 | Playoff |
| 10 | AS Roma | 8 | 5 | 1 | 2 | 14 | 11 | +3 | 16 | Playoff |
| 11 | Rapid Wien 2 | 8 | 4 | 3 | 1 | 16 | 9 | +7 | 15 | Playoff |
| 12 | Sparta Prague 2 | 8 | 4 | 1 | 3 | 12 | 10 | +2 | 13 | Playoff |
| 13 | Panathinaikos | 8 | 4 | 1 | 3 | 16 | 16 | 0 | 13 | Playoff |
| 14 | Glentoran | 8 | 4 | 0 | 4 | 17 | 13 | +4 | 12 | Playoff |
| 15 | Slavia Prague 2 | 8 | 4 | 0 | 4 | 17 | 13 | +4 | 12 | Playoff |
| 16 | LASK | 8 | 3 | 3 | 2 | 11 | 10 | +1 | 12 | Playoff |
| 17 | Eintracht Frankfurt | 8 | 3 | 2 | 3 | 18 | 22 | -4 | 11 | Playoff |
| 18 | Slavia Prague | 8 | 3 | 1 | 4 | 20 | 14 | +6 | 10 | Playoff |
| 19 | Trans | 8 | 3 | 1 | 4 | 17 | 19 | -2 | 10 | Playoff |
| 20 | Vitesse | 8 | 3 | 1 | 4 | 14 | 18 | -4 | 10 | Playoff |
| 21 | Nomme Kalju | 8 | 3 | 1 | 4 | 8 | 12 | -4 | 10 | Playoff |
| 22 | Panevezys | 8 | 2 | 3 | 3 | 13 | 16 | -3 | 9 | Playoff |
| 23 | Sparta Prague | 8 | 2 | 3 | 3 | 10 | 18 | -8 | 9 | Playoff |
| 24 | Manchester United | 8 | 2 | 2 | 4 | 10 | 11 | -1 | 8 | Playoff |
| Eliminated | ||||||||||
| 25 | Club Brugge 2 | 8 | 2 | 2 | 4 | 9 | 14 | -5 | 8 | Out |
| 26 | Molde | 8 | 2 | 2 | 4 | 14 | 20 | -6 | 8 | Out |
| 27 | Levadia Tallinn | 8 | 2 | 2 | 4 | 13 | 22 | -9 | 8 | Out |
| 28 | Gent | 8 | 2 | 1 | 5 | 14 | 16 | -2 | 7 | Out |
| 29 | Banik Ostrava | 8 | 1 | 3 | 4 | 7 | 16 | -9 | 6 | Out |
| 30 | Ordabasy | 8 | 2 | 0 | 6 | 10 | 24 | -14 | 6 | Out |
| 31 | Ajax 2 | 8 | 1 | 2 | 5 | 12 | 19 | -7 | 5 | Out |
| 32 | Hibernians | 8 | 1 | 2 | 5 | 7 | 15 | -8 | 5 | Out |
| 33 | Drogheda | 8 | 1 | 1 | 6 | 14 | 21 | -7 | 4 | Out |
| 34 | Trabzonspor | 8 | 1 | 0 | 7 | 9 | 22 | -13 | 3 | Out |
| 35 | Real Betis | 8 | 0 | 3 | 5 | 6 | 21 | -15 | 3 | Out |
| 36 | Cercle Brugge | 8 | 0 | 1 | 7 | 11 | 25 | -14 | 1 | Out |