| Round of 16 — Direct Qualification | ||||||||||
| 1 | KR Reykjavik | 6 | 6 | 0 | 0 | 22 | 4 | +18 | 18 | Direct |
| 2 | Aston Villa | 6 | 6 | 0 | 0 | 16 | 4 | +12 | 18 | Direct |
| 3 | West Ham | 6 | 5 | 1 | 0 | 12 | 5 | +7 | 16 | Direct |
| 4 | Gent 2 | 6 | 4 | 1 | 1 | 18 | 9 | +9 | 13 | Direct |
| 5 | Molde | 6 | 4 | 1 | 1 | 13 | 4 | +9 | 13 | Direct |
| 6 | Lazio 2 | 6 | 3 | 3 | 0 | 17 | 10 | +7 | 12 | Direct |
| 7 | Rennes 2 | 6 | 4 | 0 | 2 | 19 | 13 | +6 | 12 | Direct |
| 8 | Real Betis 2 | 6 | 4 | 0 | 2 | 11 | 8 | +3 | 12 | Direct |
| Knockout Playoff Round | ||||||||||
| 9 | SS Murata | 6 | 3 | 2 | 1 | 9 | 5 | +4 | 11 | Playoff |
| 10 | Lech Poznan | 6 | 3 | 2 | 1 | 13 | 11 | +2 | 11 | Playoff |
| 11 | Red Star | 6 | 3 | 1 | 2 | 14 | 7 | +7 | 10 | Playoff |
| 12 | Fiorentina 2 | 6 | 3 | 1 | 2 | 14 | 11 | +3 | 10 | Playoff |
| 13 | Drogheda | 6 | 3 | 1 | 2 | 9 | 11 | -2 | 10 | Playoff |
| 14 | Lyon 2 | 6 | 3 | 0 | 3 | 21 | 17 | +4 | 9 | Playoff |
| 15 | CSKA Sofia | 6 | 3 | 0 | 3 | 15 | 12 | +3 | 9 | Playoff |
| 16 | FCSB | 6 | 3 | 0 | 3 | 14 | 13 | +1 | 9 | Playoff |
| 17 | PAOK 2 | 6 | 3 | 0 | 3 | 15 | 15 | 0 | 9 | Playoff |
| 18 | Kayserispor | 6 | 2 | 2 | 2 | 15 | 12 | +3 | 8 | Playoff |
| 19 | Panathinaikos 2 | 6 | 2 | 2 | 2 | 10 | 15 | -5 | 8 | Playoff |
| 20 | Teuta | 6 | 2 | 1 | 3 | 11 | 12 | -1 | 7 | Playoff |
| 21 | Europa FC | 6 | 2 | 1 | 3 | 9 | 15 | -6 | 7 | Playoff |
| 22 | F91 Dudelange | 6 | 1 | 3 | 2 | 15 | 17 | -2 | 6 | Playoff |
| 23 | Sturm Graz | 6 | 1 | 3 | 2 | 9 | 11 | -2 | 6 | Playoff |
| 24 | Riteriai | 6 | 2 | 0 | 4 | 16 | 20 | -4 | 6 | Playoff |
| Eliminated | ||||||||||
| 25 | Skenderbeu | 6 | 1 | 3 | 2 | 14 | 18 | -4 | 6 | Out |
| 26 | FC Santa Coloma | 6 | 2 | 0 | 4 | 13 | 17 | -4 | 6 | Out |
| 27 | Jagiellonia Bialystok | 6 | 2 | 0 | 4 | 7 | 12 | -5 | 6 | Out |
| 28 | Anderlecht 2 | 6 | 2 | 0 | 4 | 9 | 16 | -7 | 6 | Out |
| 29 | Metta LU | 6 | 1 | 2 | 3 | 12 | 15 | -3 | 5 | Out |
| 30 | Differdange | 6 | 1 | 2 | 3 | 6 | 10 | -4 | 5 | Out |
| 31 | Real Sociedad 2 | 6 | 1 | 2 | 3 | 5 | 11 | -6 | 5 | Out |
| 32 | Sutjeska | 6 | 1 | 2 | 3 | 10 | 17 | -7 | 5 | Out |
| 33 | Sivasspor | 6 | 1 | 1 | 4 | 9 | 15 | -6 | 4 | Out |
| 34 | OFK Beograd | 6 | 1 | 1 | 4 | 11 | 18 | -7 | 4 | Out |
| 35 | Panevezys | 6 | 1 | 0 | 5 | 6 | 11 | -5 | 3 | Out |
| 36 | Qarabag | 6 | 0 | 0 | 6 | 6 | 24 | -18 | 0 | Out |