| Tuesday 15th July 2008 | |||
| 1st Leg | |||
| Anorthosis Famagusta | 1-0 | Pyunik Yerevan | |
| BATE Borisov | 2-0 | Valur Reykjavik | |
| Dinamo Tirana | 0-2 | Modrica | |
| F91 Dudelange | 0-1 | NK Domzale | |
| FC Santa Coloma | 1-4 | FBK Kaunas | |
| Inter Baku | 0-0 | Rabotnicki | |
| Llanelli | 1-0 | FK Ventspils | |
| Murata | 0-5 | IFK Gothenburg | |
| Tampere United | 2-1 | Buducnost Podgorica | |
| Valletta | 0-2 | Artmedia Petrzalka | |
| Wednesday 16th July 2008 | |||
| 1st Leg | |||
| Dinamo Tbilisi | 3-0 | NSI Runavik | |
| Drogheda United | 2-1 | Levadia Tallinn | |
| FK Aktobe Lento | 1-0 | Sheriff Tiraspol | |
| Linfield | 0-2 | Dinamo Zagreb | |
| Tuesday 22nd July 2008 | |||
| 2nd Leg | |||
| FBK Kaunas | 3-1 | FC Santa Coloma | (7-2) |
| FK Ventspils | 4-0 | Llanelli | (4-1) |
| NSI Runavik | 1-0 | Dinamo Tbilisi | (1-3) |
| Rabotnicki | 1-1 | Inter Baku | (1-1) |
| (Inter Baku won on away goals) | |||
| Sheriff Tiraspol | 4-0 | FK Aktobe Lento | (4-1) |
| Wednesday 23rd July 2008 | |||
| 2nd Leg | |||
| Artmedia Petrzalka | 1-0 | Valletta | (3-0) |
| Buducnost Podgorica | 1-1 | Tampere United | (2-3) |
| Dinamo Zagreb | 1-1 | Linfield | (3-1) |
| IFK Gothenburg | 4-0 | Murata | (9-0) |
| Levadia Tallinn | 0-1 | Drogheda United | (1-3) |
| Modrica | 2-1 | Dinamo Tirana | (4-1) |
| NK Domzale | 2-0 | F91 Dudelange | (3-0) |
| Pyunik Yerevan | 0-2 | Anorthosis Famagusta | (0-3) |
| Valur Reykjavik | 0-1 | BATE Borisov | (0-3) |
