| Round of 16 — Direct Qualification | ||||||||||
| 1 | Aston Villa | 6 | 5 | 1 | 0 | 23 | 5 | +18 | 16 | Direct |
| 2 | RFS | 6 | 5 | 1 | 0 | 13 | 4 | +9 | 16 | Direct |
| 3 | Panathinaikos 2 | 6 | 5 | 0 | 1 | 11 | 5 | +6 | 15 | Direct |
| 4 | Petrocub | 6 | 4 | 2 | 0 | 16 | 4 | +12 | 14 | Direct |
| 5 | Rennes 2 | 6 | 4 | 2 | 0 | 15 | 8 | +7 | 14 | Direct |
| 6 | Sivasspor | 6 | 4 | 1 | 1 | 17 | 6 | +11 | 13 | Direct |
| 7 | Gent 2 | 6 | 3 | 2 | 1 | 14 | 7 | +7 | 11 | Direct |
| 8 | Lyon 2 | 6 | 3 | 2 | 1 | 13 | 6 | +7 | 11 | Direct |
| Knockout Playoff Round | ||||||||||
| 9 | Coleraine | 6 | 3 | 1 | 2 | 18 | 11 | +7 | 10 | Playoff |
| 10 | Jagiellonia Bialystok | 6 | 3 | 1 | 2 | 15 | 12 | +3 | 10 | Playoff |
| 11 | Shamrock Rovers 2 | 6 | 3 | 1 | 2 | 17 | 16 | +1 | 10 | Playoff |
| 12 | Lech Poznan | 6 | 3 | 1 | 2 | 11 | 11 | 0 | 10 | Playoff |
| 13 | Rigas FS | 6 | 3 | 1 | 2 | 8 | 9 | -1 | 10 | Playoff |
| 14 | Torpedo Minsk | 6 | 3 | 0 | 3 | 12 | 11 | +1 | 9 | Playoff |
| 15 | Paide | 6 | 2 | 2 | 2 | 14 | 10 | +4 | 8 | Playoff |
| 16 | West Ham | 6 | 2 | 2 | 2 | 12 | 8 | +4 | 8 | Playoff |
| 17 | Vitoria SC | 6 | 2 | 2 | 2 | 13 | 13 | 0 | 8 | Playoff |
| 18 | Tre Fiori | 6 | 2 | 2 | 2 | 11 | 12 | -1 | 8 | Playoff |
| 19 | FC Andorra | 6 | 2 | 2 | 2 | 10 | 11 | -1 | 8 | Playoff |
| 20 | Anderlecht 2 | 6 | 2 | 2 | 2 | 9 | 12 | -3 | 8 | Playoff |
| 21 | Differdange | 6 | 2 | 1 | 3 | 13 | 12 | +1 | 7 | Playoff |
| 22 | Real Betis 2 | 6 | 2 | 1 | 3 | 10 | 10 | 0 | 7 | Playoff |
| 23 | Kayserispor | 6 | 2 | 1 | 3 | 9 | 13 | -4 | 7 | Playoff |
| 24 | PAOK 2 | 6 | 2 | 1 | 3 | 11 | 16 | -5 | 7 | Playoff |
| Eliminated | ||||||||||
| 25 | Aberdeen | 6 | 2 | 1 | 3 | 7 | 14 | -7 | 7 | Out |
| 26 | Fiorentina 2 | 6 | 1 | 3 | 2 | 8 | 12 | -4 | 6 | Out |
| 27 | Valletta | 6 | 1 | 2 | 3 | 14 | 19 | -5 | 5 | Out |
| 28 | Real Sociedad 2 | 6 | 1 | 2 | 3 | 11 | 19 | -8 | 5 | Out |
| 29 | SS Murata | 6 | 1 | 2 | 3 | 10 | 19 | -9 | 5 | Out |
| 30 | Utrecht | 6 | 1 | 2 | 3 | 8 | 18 | -10 | 5 | Out |
| 31 | Flora Tallinn | 6 | 1 | 1 | 4 | 8 | 12 | -4 | 4 | Out |
| 32 | Lazio 2 | 6 | 1 | 1 | 4 | 6 | 11 | -5 | 4 | Out |
| 33 | Levadia Tallinn 2 | 6 | 1 | 1 | 4 | 11 | 18 | -7 | 4 | Out |
| 34 | FK Suduva | 6 | 1 | 1 | 4 | 7 | 14 | -7 | 4 | Out |
| 35 | Vikingur Reykjavik | 6 | 1 | 1 | 4 | 9 | 18 | -9 | 4 | Out |
| 36 | Trans | 6 | 0 | 1 | 5 | 4 | 12 | -8 | 1 | Out |