| Round of 16 — Direct Qualification | ||||||||||
| 1 | Aston Villa | 6 | 5 | 1 | 0 | 14 | 3 | +11 | 16 | Direct |
| 2 | Slovan Bratislava | 6 | 5 | 0 | 1 | 17 | 7 | +10 | 15 | Direct |
| 3 | Lazio 2 | 6 | 4 | 1 | 1 | 15 | 11 | +4 | 13 | Direct |
| 4 | PAOK 2 | 6 | 4 | 1 | 1 | 14 | 10 | +4 | 13 | Direct |
| 5 | Rennes 2 | 6 | 4 | 1 | 1 | 16 | 13 | +3 | 13 | Direct |
| 6 | Anderlecht 2 | 6 | 4 | 1 | 1 | 16 | 15 | +1 | 13 | Direct |
| 7 | Twente | 6 | 3 | 3 | 0 | 15 | 9 | +6 | 12 | Direct |
| 8 | Real Betis 2 | 6 | 4 | 0 | 2 | 18 | 13 | +5 | 12 | Direct |
| Knockout Playoff Round | ||||||||||
| 9 | West Ham | 6 | 3 | 1 | 2 | 13 | 10 | +3 | 10 | Playoff |
| 10 | Gent 2 | 6 | 3 | 1 | 2 | 14 | 12 | +2 | 10 | Playoff |
| 11 | Lyon 2 | 6 | 3 | 0 | 3 | 17 | 10 | +7 | 9 | Playoff |
| 12 | Trans | 6 | 3 | 0 | 3 | 17 | 14 | +3 | 9 | Playoff |
| 13 | Slavia Prague | 6 | 3 | 0 | 3 | 14 | 14 | 0 | 9 | Playoff |
| 14 | Kayserispor | 6 | 2 | 3 | 1 | 12 | 12 | 0 | 9 | Playoff |
| 15 | FK Liepaja | 6 | 3 | 0 | 3 | 13 | 14 | -1 | 9 | Playoff |
| 16 | Utrecht | 6 | 3 | 0 | 3 | 10 | 11 | -1 | 9 | Playoff |
| 17 | Wisla Krakow | 6 | 2 | 2 | 2 | 14 | 12 | +2 | 8 | Playoff |
| 18 | Panathinaikos 2 | 6 | 2 | 2 | 2 | 14 | 13 | +1 | 8 | Playoff |
| 19 | Tobol | 6 | 2 | 2 | 2 | 12 | 11 | +1 | 8 | Playoff |
| 20 | Rosenborg | 6 | 2 | 2 | 2 | 15 | 16 | -1 | 8 | Playoff |
| 21 | Suduva 2 | 6 | 2 | 2 | 2 | 13 | 16 | -3 | 8 | Playoff |
| 22 | Torpedo Minsk | 6 | 2 | 2 | 2 | 10 | 14 | -4 | 8 | Playoff |
| 23 | Teuta | 6 | 1 | 4 | 1 | 13 | 10 | +3 | 7 | Playoff |
| 24 | Waterford | 6 | 2 | 1 | 3 | 13 | 13 | 0 | 7 | Playoff |
| Eliminated | ||||||||||
| 25 | Rio Ave | 6 | 2 | 1 | 3 | 14 | 15 | -1 | 7 | Out |
| 26 | CFR Cluj | 6 | 2 | 1 | 3 | 13 | 16 | -3 | 7 | Out |
| 27 | Sivasspor | 6 | 2 | 0 | 4 | 9 | 11 | -2 | 6 | Out |
| 28 | Qarabag | 6 | 2 | 0 | 4 | 11 | 14 | -3 | 6 | Out |
| 29 | Lech Poznan | 6 | 2 | 0 | 4 | 10 | 15 | -5 | 6 | Out |
| 30 | Real Sociedad 2 | 6 | 1 | 2 | 3 | 7 | 12 | -5 | 5 | Out |
| 31 | Jagiellonia Bialystok | 6 | 1 | 2 | 3 | 7 | 13 | -6 | 5 | Out |
| 32 | Fiorentina 2 | 6 | 1 | 2 | 3 | 12 | 19 | -7 | 5 | Out |
| 33 | Linfield | 6 | 1 | 1 | 4 | 12 | 16 | -4 | 4 | Out |
| 34 | Zalgiris Vilnius | 6 | 1 | 1 | 4 | 10 | 14 | -4 | 4 | Out |
| 35 | Hajduk Split | 6 | 1 | 1 | 4 | 10 | 17 | -7 | 4 | Out |
| 36 | FK Zalgiris | 6 | 0 | 1 | 5 | 4 | 13 | -9 | 1 | Out |