| Tuesday 29th July 2008 | |||
| 1st Leg | |||
| Drogheda United | 1-2 | Dinamo Kiev | |
| Inter Baku | 1-1 | Partizan Belgrade | |
| SK Brann | 1-0 | FK Ventspils | |
| Wednesday 30th July 2008 | |||
| 1st Leg | |||
| AaB Aalborg | 5-0 | Modrica | |
| Anderlecht | 1-2 | BATE Borisov | |
| Anorthosis Famagusta | 3-0 | Rapid Vienna | |
| Beitar Jerusalem | 2-1 | Wisla Krakow | |
| Fenerbahce | 2-0 | MTK Budapest | |
| IFK Gothenburg | 1-1 | Basle | |
| NK Domzale | 0-3 | Dinamo Zagreb | |
| Panathinaikos | 3-0 | Dinamo Tbilisi | |
| Rangers | 0-0 | FBK Kaunas | |
| Sheriff Tiraspol | 0-1 | Sparta Prague | |
| Tampere United | 1-3 | Artmedia Petrzalka | |
| Tuesday 5th August 2008 | |||
| 2nd Leg | |||
| FBK Kaunas | 2-1 | Rangers | (2-1) |
| FK Ventspils | 2-1 | SK Brann | (2-2) |
| (SK Brann won on away goals) | |||
| Wednesday 6th August 2008 | |||
| 2nd Leg | |||
| Artmedia Petrzalka | 4-2 | Tampere United | (7-3) |
| Basle | 4-2 | IFK Gothenburg | (5-3) |
| BATE Borisov | 2-2 | Anderlecht | (4-3) |
| Dinamo Kiev | 2-2 | Drogheda United | (4-3) |
| Dinamo Tbilisi | 0-0 | Panathinaikos | (0-3) |
| Dinamo Zagreb | 3-2 | NK Domzale | (6-2) |
| Modrica | 1-2 | AaB Aalborg | (1-7) |
| MTK Budapest | 0-5 | Fenerbahce | (0-7) |
| Partizan Belgrade | 2-0 | Inter Baku | (3-1) |
| Rapid Vienna | 3-1 | Anorthosis Famagusta | (3-4) |
| Sparta Prague | 2-0 | Sheriff Tiraspol | (3-0) |
| Wisla Krakow | 5-0 | Beitar Jerusalem | (6-2) |
