| Round of 16 — Direct Qualification | ||||||||||
| 1 | Lyon | 8 | 7 | 1 | 0 | 25 | 4 | +21 | 22 | Direct |
| 2 | Monaco | 8 | 6 | 2 | 0 | 23 | 7 | +16 | 20 | Direct |
| 3 | Valencia | 8 | 6 | 2 | 0 | 19 | 8 | +11 | 20 | Direct |
| 4 | Villarreal | 8 | 6 | 1 | 1 | 20 | 8 | +12 | 19 | Direct |
| 5 | Augsburg | 8 | 6 | 1 | 1 | 18 | 17 | +1 | 19 | Direct |
| 6 | Rennes | 8 | 6 | 0 | 2 | 19 | 9 | +10 | 18 | Direct |
| 7 | Braga | 8 | 5 | 2 | 1 | 16 | 11 | +5 | 17 | Direct |
| 8 | Brondby | 8 | 4 | 4 | 0 | 13 | 7 | +6 | 16 | Direct |
| Knockout Playoff Round | ||||||||||
| 9 | Ajax 2 | 8 | 5 | 0 | 3 | 11 | 16 | -5 | 15 | Playoff |
| 10 | Austria Wien | 8 | 4 | 2 | 2 | 23 | 18 | +5 | 14 | Playoff |
| 11 | Tottenham | 8 | 4 | 2 | 2 | 18 | 13 | +5 | 14 | Playoff |
| 12 | Nomme Kalju | 8 | 4 | 1 | 3 | 25 | 17 | +8 | 13 | Playoff |
| 13 | Club Brugge 2 | 8 | 4 | 0 | 4 | 14 | 12 | +2 | 12 | Playoff |
| 14 | Rosenborg | 8 | 3 | 2 | 3 | 19 | 16 | +3 | 11 | Playoff |
| 15 | Sturm Graz | 8 | 3 | 2 | 3 | 18 | 18 | 0 | 11 | Playoff |
| 16 | Genk | 8 | 3 | 2 | 3 | 16 | 16 | 0 | 11 | Playoff |
| 17 | Skenderbeu | 8 | 3 | 2 | 3 | 15 | 16 | -1 | 11 | Playoff |
| 18 | Manchester United | 8 | 3 | 2 | 3 | 14 | 17 | -3 | 11 | Playoff |
| 19 | Ordabasy | 8 | 2 | 4 | 2 | 9 | 7 | +2 | 10 | Playoff |
| 20 | Cercle Brugge | 8 | 3 | 1 | 4 | 12 | 11 | +1 | 10 | Playoff |
| 21 | CSKA Sofia | 8 | 2 | 4 | 2 | 15 | 20 | -5 | 10 | Playoff |
| 22 | AS Roma | 8 | 3 | 1 | 4 | 15 | 21 | -6 | 10 | Playoff |
| 23 | Vitesse | 8 | 2 | 2 | 4 | 17 | 14 | +3 | 8 | Playoff |
| 24 | Real Betis | 8 | 2 | 2 | 4 | 13 | 15 | -2 | 8 | Playoff |
| Eliminated | ||||||||||
| 25 | Sparta Prague | 8 | 2 | 2 | 4 | 17 | 20 | -3 | 8 | Out |
| 26 | Slavia Prague | 8 | 2 | 2 | 4 | 9 | 13 | -4 | 8 | Out |
| 27 | Zalgiris Vilnius | 8 | 2 | 2 | 4 | 7 | 15 | -8 | 8 | Out |
| 28 | Eintracht Frankfurt | 8 | 2 | 1 | 5 | 12 | 17 | -5 | 7 | Out |
| 29 | Rigas FS | 8 | 2 | 1 | 5 | 12 | 17 | -5 | 7 | Out |
| 30 | Sparta Prague 2 | 8 | 2 | 1 | 5 | 12 | 19 | -7 | 7 | Out |
| 31 | Slavia Prague 2 | 8 | 1 | 3 | 4 | 13 | 19 | -6 | 6 | Out |
| 32 | Rapid Wien | 8 | 0 | 5 | 3 | 10 | 14 | -4 | 5 | Out |
| 33 | Rapid Wien 2 | 8 | 1 | 2 | 5 | 13 | 18 | -5 | 5 | Out |
| 34 | Hamrun Spartans | 8 | 1 | 1 | 6 | 9 | 20 | -11 | 4 | Out |
| 35 | Panevezys | 8 | 1 | 0 | 7 | 8 | 27 | -19 | 3 | Out |
| 36 | Twente | 8 | 0 | 2 | 6 | 9 | 21 | -12 | 2 | Out |