| Round of 16 — Direct Qualification | ||||||||||
| 1 | Aston Villa | 6 | 6 | 0 | 0 | 19 | 2 | +17 | 18 | Direct |
| 2 | Maccabi Tel Aviv | 6 | 4 | 1 | 1 | 16 | 10 | +6 | 13 | Direct |
| 3 | Panathinaikos 2 | 6 | 4 | 1 | 1 | 14 | 11 | +3 | 13 | Direct |
| 4 | FK Zalgiris | 6 | 3 | 3 | 0 | 16 | 9 | +7 | 12 | Direct |
| 5 | Rennes 2 | 6 | 4 | 0 | 2 | 12 | 7 | +5 | 12 | Direct |
| 6 | Riteriai | 6 | 4 | 0 | 2 | 20 | 18 | +2 | 12 | Direct |
| 7 | Rapid Wien | 6 | 4 | 0 | 2 | 18 | 17 | +1 | 12 | Direct |
| 8 | Wisla Krakow | 6 | 3 | 2 | 1 | 16 | 9 | +7 | 11 | Direct |
| Knockout Playoff Round | ||||||||||
| 9 | Glenavon | 6 | 3 | 2 | 1 | 13 | 11 | +2 | 11 | Playoff |
| 10 | West Ham | 6 | 3 | 1 | 2 | 17 | 8 | +9 | 10 | Playoff |
| 11 | Real Sociedad 2 | 6 | 3 | 1 | 2 | 17 | 12 | +5 | 10 | Playoff |
| 12 | Lyon 2 | 6 | 3 | 1 | 2 | 16 | 11 | +5 | 10 | Playoff |
| 13 | Sligo Rovers | 6 | 3 | 1 | 2 | 15 | 11 | +4 | 10 | Playoff |
| 14 | Glentoran | 6 | 3 | 1 | 2 | 14 | 11 | +3 | 10 | Playoff |
| 15 | Breidablik | 6 | 3 | 1 | 2 | 10 | 9 | +1 | 10 | Playoff |
| 16 | Sivasspor | 6 | 3 | 0 | 3 | 12 | 13 | -1 | 9 | Playoff |
| 17 | Kayserispor | 6 | 3 | 0 | 3 | 10 | 11 | -1 | 9 | Playoff |
| 18 | Aktobe | 6 | 3 | 0 | 3 | 10 | 15 | -5 | 9 | Playoff |
| 19 | FK Valmiera | 6 | 3 | 0 | 3 | 12 | 19 | -7 | 9 | Playoff |
| 20 | AZ Alkmaar | 6 | 2 | 2 | 2 | 12 | 13 | -1 | 8 | Playoff |
| 21 | Waterford | 6 | 2 | 1 | 3 | 12 | 11 | +1 | 7 | Playoff |
| 22 | PAOK 2 | 6 | 2 | 1 | 3 | 14 | 14 | 0 | 7 | Playoff |
| 23 | Anderlecht 2 | 6 | 1 | 4 | 1 | 13 | 14 | -1 | 7 | Playoff |
| 24 | Vikingur Reykjavik | 6 | 2 | 1 | 3 | 12 | 13 | -1 | 7 | Playoff |
| Eliminated | ||||||||||
| 25 | Vojvodina | 6 | 2 | 1 | 3 | 12 | 14 | -2 | 7 | Out |
| 26 | Lazio 2 | 6 | 2 | 1 | 3 | 9 | 13 | -4 | 7 | Out |
| 27 | Jagiellonia Bialystok | 6 | 2 | 0 | 4 | 6 | 12 | -6 | 6 | Out |
| 28 | Besiktas | 6 | 1 | 2 | 3 | 10 | 11 | -1 | 5 | Out |
| 29 | Banik Ostrava | 6 | 1 | 2 | 3 | 11 | 15 | -4 | 5 | Out |
| 30 | Gent 2 | 6 | 1 | 2 | 3 | 11 | 15 | -4 | 5 | Out |
| 31 | Lech Poznan | 6 | 1 | 2 | 3 | 8 | 12 | -4 | 5 | Out |
| 32 | Real Betis 2 | 6 | 1 | 2 | 3 | 10 | 17 | -7 | 5 | Out |
| 33 | Valletta | 6 | 1 | 1 | 4 | 12 | 17 | -5 | 4 | Out |
| 34 | Sheriff | 6 | 0 | 3 | 3 | 12 | 18 | -6 | 3 | Out |
| 35 | Gent | 6 | 1 | 0 | 5 | 7 | 14 | -7 | 3 | Out |
| 36 | Fiorentina 2 | 6 | 1 | 0 | 5 | 9 | 20 | -11 | 3 | Out |