| Round of 16 — Direct Qualification | ||||||||||
| 1 | Augsburg | 8 | 7 | 1 | 0 | 23 | 4 | +19 | 22 | Direct |
| 2 | Monaco | 8 | 7 | 1 | 0 | 22 | 5 | +17 | 22 | Direct |
| 3 | Genk | 8 | 7 | 0 | 1 | 28 | 9 | +19 | 21 | Direct |
| 4 | Braga | 8 | 6 | 1 | 1 | 23 | 9 | +14 | 19 | Direct |
| 5 | Valencia | 8 | 6 | 0 | 2 | 20 | 9 | +11 | 18 | Direct |
| 6 | Villarreal | 8 | 5 | 2 | 1 | 16 | 8 | +8 | 17 | Direct |
| 7 | Paide | 8 | 5 | 2 | 1 | 13 | 5 | +8 | 17 | Direct |
| 8 | Lyon | 8 | 5 | 1 | 2 | 25 | 12 | +13 | 16 | Direct |
| Knockout Playoff Round | ||||||||||
| 9 | Tottenham | 8 | 5 | 1 | 2 | 15 | 7 | +8 | 16 | Playoff |
| 10 | Panathinaikos | 8 | 5 | 0 | 3 | 16 | 10 | +6 | 15 | Playoff |
| 11 | Panevezys | 8 | 3 | 5 | 0 | 17 | 12 | +5 | 14 | Playoff |
| 12 | Nomme Kalju | 8 | 4 | 2 | 2 | 14 | 11 | +3 | 14 | Playoff |
| 13 | Portadown | 8 | 3 | 4 | 1 | 13 | 9 | +4 | 13 | Playoff |
| 14 | Hibernians | 8 | 4 | 1 | 3 | 19 | 16 | +3 | 13 | Playoff |
| 15 | Maccabi Tel Aviv | 8 | 4 | 1 | 3 | 17 | 19 | -2 | 13 | Playoff |
| 16 | Slavia Prague 2 | 8 | 4 | 0 | 4 | 14 | 11 | +3 | 12 | Playoff |
| 17 | Real Betis | 8 | 3 | 3 | 2 | 15 | 19 | -4 | 12 | Playoff |
| 18 | Rennes | 8 | 2 | 5 | 1 | 15 | 9 | +6 | 11 | Playoff |
| 19 | Basel | 8 | 3 | 2 | 3 | 17 | 19 | -2 | 11 | Playoff |
| 20 | Rapid Wien 2 | 8 | 3 | 1 | 4 | 13 | 14 | -1 | 10 | Playoff |
| 21 | Club Brugge 2 | 8 | 3 | 0 | 5 | 14 | 14 | 0 | 9 | Playoff |
| 22 | Eintracht Frankfurt | 8 | 2 | 3 | 3 | 14 | 14 | 0 | 9 | Playoff |
| 23 | FC Santa Coloma | 8 | 2 | 3 | 3 | 14 | 21 | -7 | 9 | Playoff |
| 24 | Ludogorets | 8 | 1 | 5 | 2 | 15 | 16 | -1 | 8 | Playoff |
| Eliminated | ||||||||||
| 25 | AS Roma | 8 | 2 | 2 | 4 | 12 | 18 | -6 | 8 | Out |
| 26 | Banik Ostrava | 8 | 2 | 2 | 4 | 10 | 19 | -9 | 8 | Out |
| 27 | Sparta Prague 2 | 8 | 2 | 1 | 5 | 10 | 15 | -5 | 7 | Out |
| 28 | Ajax 2 | 8 | 2 | 1 | 5 | 12 | 19 | -7 | 7 | Out |
| 29 | Vitesse | 8 | 2 | 1 | 5 | 11 | 21 | -10 | 7 | Out |
| 30 | Manchester United | 8 | 1 | 2 | 5 | 10 | 21 | -11 | 5 | Out |
| 31 | Brondby | 8 | 1 | 1 | 6 | 8 | 18 | -10 | 4 | Out |
| 32 | Sliema Wanderers | 8 | 1 | 1 | 6 | 7 | 21 | -14 | 4 | Out |
| 33 | Rigas FS | 8 | 1 | 0 | 7 | 11 | 21 | -10 | 3 | Out |
| 34 | Twente | 8 | 0 | 3 | 5 | 7 | 19 | -12 | 3 | Out |
| 35 | Lincoln Red Imps | 8 | 1 | 0 | 7 | 6 | 25 | -19 | 3 | Out |
| 36 | Tre Fiori | 8 | 0 | 2 | 6 | 7 | 24 | -17 | 2 | Out |