| Tuesday 31st July 2012 | |||
| 1st Leg | |||
| Dinamo Kiev | 2-1 | Feyenoord | |
| Motherwell | 0-2 | Panathinaikos | |
| Wednesday 1st August 2012 | |||
| 1st Leg | |||
| AEL Limassol | 1-0 | Partizan Belgrade | |
| Anderlecht | 5-0 | FK Ekranas Panevezys | |
| BATE Borisov | 1-1 | Debreceni VSC | |
| Celtic | 2-1 | HJK Helsinki | |
| CFR Cluj-Napoca | 1-0 | Slovan Liberec | |
| FC Copenhagen | 0-0 | Club Brugge | |
| Fenerbahce | 1-1 | Vaslui | |
| Hapoel Ironi KS | 4-0 | Neftchi Baku | |
| Molde | 0-1 | Basel | |
| NK Maribor | 4-1 | F91 Dudelange | |
| Sheriff Tiraspol | 0-1 | Dinamo Zagreb | |
| Slask Wroclaw | 0-3 | Helsingborgs | |
| Tuesday 7th August 2012 | |||
| 2nd Leg | |||
| Debreceni VSC | 0-2 | BATE Borisov | (1-3) |
| Feyenoord | 0-1 | Dinamo Kiev | (1-3) |
| Wednesday 8th August 2012 | |||
| 2nd Leg | |||
| Basel | 1-1 | Molde | (2-1) |
| Club Brugge | 2-3 | FC Copenhagen | (2-3) |
| Dinamo Zagreb | 4-0 | Sheriff Tiraspol | (5-0) |
| F91 Dudelange | 0-1 | NK Maribor | (1-5) |
| FK Ekranas Panevezys | 0-6 | Anderlecht | (0-11) |
| Helsingborgs | 3-1 | Slask Wroclaw | (6-1) |
| HJK Helsinki | 0-2 | Celtic | (1-4) |
| Neftchi Baku | 2-2 | Hapoel Ironi KS | (2-6) |
| Panathinaikos | 3-0 | Motherwell | (5-0) |
| Partizan Belgrade | 0-1 | AEL Limassol | (0-2) |
| Slovan Liberec | 1-2 | CFR Cluj-Napoca | (1-3) |
| Vaslui | 1-4 | Fenerbahce | (2-5) |
