| Round of 16 — Direct Qualification | ||||||||||
| 1 | Rennes | 8 | 8 | 0 | 0 | 25 | 5 | +20 | 24 | Direct |
| 2 | Augsburg | 8 | 7 | 0 | 1 | 23 | 7 | +16 | 21 | Direct |
| 3 | Villarreal | 8 | 7 | 0 | 1 | 22 | 7 | +15 | 21 | Direct |
| 4 | Lyon | 8 | 6 | 1 | 1 | 25 | 10 | +15 | 19 | Direct |
| 5 | Valencia | 8 | 6 | 1 | 1 | 21 | 6 | +15 | 19 | Direct |
| 6 | Eintracht Frankfurt | 8 | 5 | 2 | 1 | 13 | 8 | +5 | 17 | Direct |
| 7 | Twente | 8 | 5 | 1 | 2 | 20 | 10 | +10 | 16 | Direct |
| 8 | Tottenham | 8 | 5 | 1 | 2 | 14 | 6 | +8 | 16 | Direct |
| Knockout Playoff Round | ||||||||||
| 9 | Rapid Wien 2 | 8 | 5 | 1 | 2 | 13 | 8 | +5 | 16 | Playoff |
| 10 | Gent | 8 | 5 | 1 | 2 | 16 | 12 | +4 | 16 | Playoff |
| 11 | Monaco | 8 | 4 | 3 | 1 | 18 | 7 | +11 | 15 | Playoff |
| 12 | Braga | 8 | 5 | 0 | 3 | 14 | 6 | +8 | 15 | Playoff |
| 13 | Club Brugge 2 | 8 | 3 | 4 | 1 | 18 | 16 | +2 | 13 | Playoff |
| 14 | FK Liepaja | 8 | 4 | 1 | 3 | 18 | 19 | -1 | 13 | Playoff |
| 15 | AZ Alkmaar | 8 | 3 | 3 | 2 | 15 | 13 | +2 | 12 | Playoff |
| 16 | Manchester United | 8 | 4 | 0 | 4 | 16 | 15 | +1 | 12 | Playoff |
| 17 | Vitesse | 8 | 3 | 3 | 2 | 17 | 19 | -2 | 12 | Playoff |
| 18 | Sfintul Gheorghe | 8 | 3 | 2 | 3 | 13 | 13 | 0 | 11 | Playoff |
| 19 | Crusaders | 8 | 3 | 1 | 4 | 16 | 15 | +1 | 10 | Playoff |
| 20 | CSKA Sofia | 8 | 3 | 1 | 4 | 18 | 23 | -5 | 10 | Playoff |
| 21 | Waterford | 8 | 3 | 1 | 4 | 9 | 16 | -7 | 10 | Playoff |
| 22 | LASK | 8 | 3 | 0 | 5 | 16 | 19 | -3 | 9 | Playoff |
| 23 | Banik Ostrava | 8 | 2 | 3 | 3 | 12 | 15 | -3 | 9 | Playoff |
| 24 | Austria Wien | 8 | 2 | 2 | 4 | 13 | 15 | -2 | 8 | Playoff |
| Eliminated | ||||||||||
| 25 | AS Roma | 8 | 2 | 2 | 4 | 9 | 18 | -9 | 8 | Out |
| 26 | Real Betis | 8 | 2 | 1 | 5 | 14 | 20 | -6 | 7 | Out |
| 27 | Sparta Prague | 8 | 2 | 1 | 5 | 17 | 24 | -7 | 7 | Out |
| 28 | Ajax 2 | 8 | 2 | 1 | 5 | 12 | 19 | -7 | 7 | Out |
| 29 | Slavia Prague 2 | 8 | 2 | 1 | 5 | 9 | 21 | -12 | 7 | Out |
| 30 | Kairat | 8 | 2 | 0 | 6 | 15 | 22 | -7 | 6 | Out |
| 31 | Basel | 8 | 1 | 3 | 4 | 10 | 18 | -8 | 6 | Out |
| 32 | Wisla Krakow | 8 | 1 | 2 | 5 | 10 | 19 | -9 | 5 | Out |
| 33 | Sparta Prague 2 | 8 | 1 | 1 | 6 | 13 | 21 | -8 | 4 | Out |
| 34 | Midtjylland | 8 | 1 | 1 | 6 | 11 | 20 | -9 | 4 | Out |
| 35 | Lincoln Red Imps | 8 | 1 | 0 | 7 | 8 | 25 | -17 | 3 | Out |
| 36 | Drogheda | 8 | 0 | 1 | 7 | 10 | 26 | -16 | 1 | Out |