| Round of 16 — Direct Qualification | ||||||||||
| 1 | West Ham | 6 | 5 | 1 | 0 | 21 | 4 | +17 | 16 | Direct |
| 2 | Aston Villa | 6 | 4 | 2 | 0 | 13 | 2 | +11 | 14 | Direct |
| 3 | Zalgiris Vilnius | 6 | 4 | 1 | 1 | 10 | 3 | +7 | 13 | Direct |
| 4 | Lyon 2 | 6 | 4 | 0 | 2 | 18 | 9 | +9 | 12 | Direct |
| 5 | CSKA Sofia | 6 | 3 | 3 | 0 | 16 | 11 | +5 | 12 | Direct |
| 6 | Kayserispor | 6 | 4 | 0 | 2 | 13 | 8 | +5 | 12 | Direct |
| 7 | Kairat | 6 | 4 | 0 | 2 | 14 | 10 | +4 | 12 | Direct |
| 8 | Rigas FS | 6 | 3 | 2 | 1 | 19 | 13 | +6 | 11 | Direct |
| Knockout Playoff Round | ||||||||||
| 9 | Valletta | 6 | 3 | 1 | 2 | 17 | 12 | +5 | 10 | Playoff |
| 10 | Real Betis 2 | 6 | 3 | 1 | 2 | 17 | 13 | +4 | 10 | Playoff |
| 11 | OFK Beograd | 6 | 3 | 1 | 2 | 14 | 13 | +1 | 10 | Playoff |
| 12 | Portadown | 6 | 3 | 1 | 2 | 13 | 13 | 0 | 10 | Playoff |
| 13 | Sivasspor | 6 | 3 | 1 | 2 | 13 | 14 | -1 | 10 | Playoff |
| 14 | Sfintul Gheorghe | 6 | 3 | 1 | 2 | 11 | 12 | -1 | 10 | Playoff |
| 15 | Lech Poznan | 6 | 3 | 0 | 3 | 16 | 12 | +4 | 9 | Playoff |
| 16 | Lazio 2 | 6 | 2 | 3 | 1 | 11 | 9 | +2 | 9 | Playoff |
| 17 | Crusaders | 6 | 3 | 0 | 3 | 9 | 7 | +2 | 9 | Playoff |
| 18 | FC Andorra | 6 | 2 | 3 | 1 | 8 | 6 | +2 | 9 | Playoff |
| 19 | Skenderbeu | 6 | 3 | 0 | 3 | 15 | 18 | -3 | 9 | Playoff |
| 20 | Gent 2 | 6 | 2 | 2 | 2 | 12 | 10 | +2 | 8 | Playoff |
| 21 | Bohemian | 6 | 2 | 2 | 2 | 10 | 10 | 0 | 8 | Playoff |
| 22 | Rennes 2 | 6 | 2 | 2 | 2 | 10 | 11 | -1 | 8 | Playoff |
| 23 | PAOK | 6 | 2 | 2 | 2 | 12 | 16 | -4 | 8 | Playoff |
| 24 | Paide | 6 | 2 | 1 | 3 | 12 | 13 | -1 | 7 | Playoff |
| Eliminated | ||||||||||
| 25 | Jagiellonia Bialystok | 6 | 2 | 1 | 3 | 11 | 14 | -3 | 7 | Out |
| 26 | Flora Tallinn | 6 | 1 | 3 | 2 | 8 | 11 | -3 | 6 | Out |
| 27 | Waterford | 6 | 2 | 0 | 4 | 7 | 10 | -3 | 6 | Out |
| 28 | Brondby | 6 | 1 | 3 | 2 | 5 | 9 | -4 | 6 | Out |
| 29 | Anderlecht 2 | 6 | 2 | 0 | 4 | 14 | 21 | -7 | 6 | Out |
| 30 | Drogheda | 6 | 1 | 2 | 3 | 14 | 18 | -4 | 5 | Out |
| 31 | PAOK 2 | 6 | 1 | 2 | 3 | 8 | 13 | -5 | 5 | Out |
| 32 | Real Sociedad 2 | 6 | 1 | 2 | 3 | 8 | 14 | -6 | 5 | Out |
| 33 | Sparta Prague | 6 | 1 | 2 | 3 | 8 | 14 | -6 | 5 | Out |
| 34 | Fiorentina 2 | 6 | 1 | 1 | 4 | 7 | 18 | -11 | 4 | Out |
| 35 | Birkirkara 2 | 6 | 0 | 0 | 6 | 9 | 18 | -9 | 0 | Out |
| 36 | Panathinaikos 2 | 6 | 0 | 0 | 6 | 4 | 18 | -14 | 0 | Out |