| Round of 16 — Direct Qualification | ||||||||||
| 1 | Braga | 8 | 8 | 0 | 0 | 26 | 5 | +21 | 24 | Direct |
| 2 | Lyon | 8 | 7 | 1 | 0 | 24 | 5 | +19 | 22 | Direct |
| 3 | Tottenham | 8 | 7 | 1 | 0 | 18 | 3 | +15 | 22 | Direct |
| 4 | Valencia | 8 | 7 | 0 | 1 | 30 | 8 | +22 | 21 | Direct |
| 5 | Monaco | 8 | 6 | 2 | 0 | 14 | 3 | +11 | 20 | Direct |
| 6 | Augsburg | 8 | 6 | 1 | 1 | 22 | 14 | +8 | 19 | Direct |
| 7 | Lincoln Red Imps | 8 | 6 | 0 | 2 | 20 | 11 | +9 | 18 | Direct |
| 8 | Villarreal | 8 | 5 | 1 | 2 | 19 | 7 | +12 | 16 | Direct |
| Knockout Playoff Round | ||||||||||
| 9 | Crusaders | 8 | 5 | 1 | 2 | 17 | 12 | +5 | 16 | Playoff |
| 10 | Ferencvaros | 8 | 5 | 1 | 2 | 12 | 8 | +4 | 16 | Playoff |
| 11 | Rennes | 8 | 5 | 0 | 3 | 20 | 11 | +9 | 15 | Playoff |
| 12 | Hajduk Split | 8 | 5 | 0 | 3 | 23 | 16 | +7 | 15 | Playoff |
| 13 | Rapid Wien 2 | 8 | 4 | 2 | 2 | 19 | 15 | +4 | 14 | Playoff |
| 14 | Panathinaikos | 8 | 4 | 1 | 3 | 18 | 10 | +8 | 13 | Playoff |
| 15 | Sfintul Gheorghe | 8 | 4 | 1 | 3 | 19 | 16 | +3 | 13 | Playoff |
| 16 | Real Betis | 8 | 4 | 1 | 3 | 16 | 13 | +3 | 13 | Playoff |
| 17 | Manchester United | 8 | 4 | 1 | 3 | 11 | 13 | -2 | 13 | Playoff |
| 18 | Eintracht Frankfurt | 8 | 4 | 1 | 3 | 13 | 17 | -4 | 13 | Playoff |
| 19 | Sparta Prague | 8 | 3 | 2 | 3 | 14 | 16 | -2 | 11 | Playoff |
| 20 | Club Brugge 2 | 8 | 3 | 1 | 4 | 12 | 10 | +2 | 10 | Playoff |
| 21 | Austria Wien | 8 | 2 | 3 | 3 | 11 | 15 | -4 | 9 | Playoff |
| 22 | Rio Ave | 8 | 3 | 0 | 5 | 14 | 20 | -6 | 9 | Playoff |
| 23 | CFR Cluj | 8 | 3 | 0 | 5 | 15 | 23 | -8 | 9 | Playoff |
| 24 | SS Murata | 8 | 2 | 2 | 4 | 11 | 19 | -8 | 8 | Playoff |
| Eliminated | ||||||||||
| 25 | Vitesse | 8 | 2 | 1 | 5 | 13 | 21 | -8 | 7 | Out |
| 26 | Young Boys | 8 | 2 | 1 | 5 | 11 | 20 | -9 | 7 | Out |
| 27 | LASK | 8 | 2 | 1 | 5 | 9 | 26 | -17 | 7 | Out |
| 28 | Basel | 8 | 2 | 0 | 6 | 10 | 16 | -6 | 6 | Out |
| 29 | AS Roma | 8 | 2 | 0 | 6 | 8 | 19 | -11 | 6 | Out |
| 30 | Brondby | 8 | 1 | 2 | 5 | 12 | 23 | -11 | 5 | Out |
| 31 | FCSB | 8 | 1 | 1 | 6 | 11 | 18 | -7 | 4 | Out |
| 32 | Hibernians | 8 | 1 | 1 | 6 | 17 | 25 | -8 | 4 | Out |
| 33 | Slavia Prague 2 | 8 | 1 | 1 | 6 | 8 | 17 | -9 | 4 | Out |
| 34 | Rosenborg | 8 | 1 | 1 | 6 | 11 | 23 | -12 | 4 | Out |
| 35 | Ajax 2 | 8 | 1 | 0 | 7 | 7 | 17 | -10 | 3 | Out |
| 36 | Sparta Prague 2 | 8 | 0 | 0 | 8 | 3 | 23 | -20 | 0 | Out |