| Round of 16 — Direct Qualification | ||||||||||
| 1 | Monaco | 8 | 7 | 1 | 0 | 31 | 9 | +22 | 22 | Direct |
| 2 | Villarreal | 8 | 7 | 1 | 0 | 21 | 6 | +15 | 22 | Direct |
| 3 | Genk | 8 | 7 | 0 | 1 | 21 | 6 | +15 | 21 | Direct |
| 4 | Rennes | 8 | 7 | 0 | 1 | 20 | 7 | +13 | 21 | Direct |
| 5 | Lyon | 8 | 6 | 2 | 0 | 17 | 6 | +11 | 20 | Direct |
| 6 | Braga | 8 | 5 | 2 | 1 | 17 | 4 | +13 | 17 | Direct |
| 7 | Augsburg | 8 | 5 | 1 | 2 | 22 | 7 | +15 | 16 | Direct |
| 8 | Vitesse | 8 | 5 | 1 | 2 | 20 | 15 | +5 | 16 | Direct |
| Knockout Playoff Round | ||||||||||
| 9 | Rapid Wien | 8 | 5 | 1 | 2 | 15 | 15 | 0 | 16 | Playoff |
| 10 | Fenerbahce | 8 | 4 | 3 | 1 | 16 | 11 | +5 | 15 | Playoff |
| 11 | Rapid Wien 2 | 8 | 4 | 2 | 2 | 14 | 11 | +3 | 14 | Playoff |
| 12 | Drogheda | 8 | 4 | 1 | 3 | 21 | 16 | +5 | 13 | Playoff |
| 13 | Real Betis | 8 | 4 | 1 | 3 | 22 | 18 | +4 | 13 | Playoff |
| 14 | Manchester United | 8 | 4 | 1 | 3 | 14 | 12 | +2 | 13 | Playoff |
| 15 | Valencia | 8 | 4 | 0 | 4 | 21 | 17 | +4 | 12 | Playoff |
| 16 | Besiktas | 8 | 3 | 3 | 2 | 14 | 10 | +4 | 12 | Playoff |
| 17 | Cliftonville | 8 | 3 | 3 | 2 | 13 | 11 | +2 | 12 | Playoff |
| 18 | Crusaders | 8 | 4 | 0 | 4 | 17 | 20 | -3 | 12 | Playoff |
| 19 | Sparta Prague 2 | 8 | 3 | 1 | 4 | 17 | 20 | -3 | 10 | Playoff |
| 20 | Club Brugge 2 | 8 | 3 | 1 | 4 | 12 | 18 | -6 | 10 | Playoff |
| 21 | Legia Warsaw | 8 | 2 | 3 | 3 | 13 | 12 | +1 | 9 | Playoff |
| 22 | Tottenham | 8 | 2 | 3 | 3 | 8 | 7 | +1 | 9 | Playoff |
| 23 | Ajax 2 | 8 | 2 | 3 | 3 | 16 | 17 | -1 | 9 | Playoff |
| 24 | Rigas FS | 8 | 2 | 3 | 3 | 15 | 19 | -4 | 9 | Playoff |
| Eliminated | ||||||||||
| 25 | Europa FC | 8 | 3 | 0 | 5 | 12 | 25 | -13 | 9 | Out |
| 26 | AS Roma | 8 | 2 | 2 | 4 | 15 | 16 | -1 | 8 | Out |
| 27 | Brondby | 8 | 2 | 2 | 4 | 12 | 14 | -2 | 8 | Out |
| 28 | Slavia Prague 2 | 8 | 2 | 1 | 5 | 12 | 19 | -7 | 7 | Out |
| 29 | Eintracht Frankfurt | 8 | 2 | 1 | 5 | 8 | 18 | -10 | 7 | Out |
| 30 | Standard Liege | 8 | 2 | 0 | 6 | 10 | 20 | -10 | 6 | Out |
| 31 | Petrocub | 8 | 1 | 1 | 6 | 15 | 21 | -6 | 4 | Out |
| 32 | Panathinaikos | 8 | 1 | 1 | 6 | 12 | 22 | -10 | 4 | Out |
| 33 | Skenderbeu | 8 | 1 | 1 | 6 | 11 | 27 | -16 | 4 | Out |
| 34 | Austria Wien | 8 | 0 | 3 | 5 | 3 | 23 | -20 | 3 | Out |
| 35 | Ordabasy | 8 | 0 | 2 | 6 | 12 | 26 | -14 | 2 | Out |
| 36 | Banik Ostrava | 8 | 0 | 1 | 7 | 10 | 24 | -14 | 1 | Out |