| Round of 16 — Direct Qualification | ||||||||||
| 1 | Aston Villa | 6 | 6 | 0 | 0 | 15 | 2 | +13 | 18 | Direct |
| 2 | West Ham | 6 | 5 | 1 | 0 | 14 | 3 | +11 | 16 | Direct |
| 3 | Vojvodina | 6 | 5 | 1 | 0 | 15 | 6 | +9 | 16 | Direct |
| 4 | Slovan Bratislava | 6 | 4 | 1 | 1 | 17 | 10 | +7 | 13 | Direct |
| 5 | FCSB | 6 | 4 | 1 | 1 | 15 | 10 | +5 | 13 | Direct |
| 6 | PAOK 2 | 6 | 4 | 1 | 1 | 14 | 10 | +4 | 13 | Direct |
| 7 | Lyon 2 | 6 | 4 | 1 | 1 | 16 | 14 | +2 | 13 | Direct |
| 8 | Jagiellonia Bialystok | 6 | 4 | 0 | 2 | 17 | 9 | +8 | 12 | Direct |
| Knockout Playoff Round | ||||||||||
| 9 | Lazio 2 | 6 | 4 | 0 | 2 | 19 | 12 | +7 | 12 | Playoff |
| 10 | Panathinaikos 2 | 6 | 4 | 0 | 2 | 18 | 16 | +2 | 12 | Playoff |
| 11 | Sfintul Gheorghe | 6 | 4 | 0 | 2 | 8 | 10 | -2 | 12 | Playoff |
| 12 | Real Betis 2 | 6 | 3 | 1 | 2 | 12 | 7 | +5 | 10 | Playoff |
| 13 | Real Sociedad 2 | 6 | 3 | 1 | 2 | 11 | 10 | +1 | 10 | Playoff |
| 14 | Utrecht | 6 | 3 | 1 | 2 | 7 | 9 | -2 | 10 | Playoff |
| 15 | SS Murata | 6 | 2 | 3 | 1 | 16 | 12 | +4 | 9 | Playoff |
| 16 | Gent 2 | 6 | 2 | 3 | 1 | 11 | 10 | +1 | 9 | Playoff |
| 17 | Lech Poznan | 6 | 3 | 0 | 3 | 10 | 11 | -1 | 9 | Playoff |
| 18 | Fiorentina 2 | 6 | 2 | 2 | 2 | 13 | 11 | +2 | 8 | Playoff |
| 19 | KR Reykjavik | 6 | 2 | 2 | 2 | 11 | 9 | +2 | 8 | Playoff |
| 20 | Sivasspor | 6 | 2 | 2 | 2 | 11 | 13 | -2 | 8 | Playoff |
| 21 | Nomme Kalju | 6 | 2 | 1 | 3 | 14 | 16 | -2 | 7 | Playoff |
| 22 | Paide | 6 | 2 | 1 | 3 | 9 | 13 | -4 | 7 | Playoff |
| 23 | Tre Penne | 6 | 2 | 1 | 3 | 10 | 15 | -5 | 7 | Playoff |
| 24 | Tre Fiori | 6 | 2 | 0 | 4 | 10 | 10 | 0 | 6 | Playoff |
| Eliminated | ||||||||||
| 25 | Kukes | 6 | 2 | 0 | 4 | 9 | 12 | -3 | 6 | Out |
| 26 | Partizan | 6 | 2 | 0 | 4 | 9 | 12 | -3 | 6 | Out |
| 27 | Panevezys | 6 | 1 | 2 | 3 | 10 | 14 | -4 | 5 | Out |
| 28 | Hearts | 6 | 1 | 2 | 3 | 7 | 11 | -4 | 5 | Out |
| 29 | Portadown | 6 | 1 | 2 | 3 | 6 | 12 | -6 | 5 | Out |
| 30 | Kayserispor | 6 | 1 | 1 | 4 | 7 | 12 | -5 | 4 | Out |
| 31 | Anderlecht 2 | 6 | 1 | 1 | 4 | 6 | 13 | -7 | 4 | Out |
| 32 | Rennes 2 | 6 | 0 | 3 | 3 | 6 | 10 | -4 | 3 | Out |
| 33 | Maccabi Tel Aviv | 6 | 0 | 2 | 4 | 7 | 12 | -5 | 2 | Out |
| 34 | Buducnost | 6 | 0 | 2 | 4 | 5 | 12 | -7 | 2 | Out |
| 35 | Zalgiris Vilnius | 6 | 0 | 2 | 4 | 8 | 17 | -9 | 2 | Out |
| 36 | FK Liepaja | 6 | 0 | 1 | 5 | 5 | 13 | -8 | 1 | Out |