| Tuesday 17th July 2007 | |||
| 1st Leg | |||
| Apoel Nicosia | 2-0 | BATE Borisov | |
| FK Khazar Lankaran | 1-1 | Dinamo Zagreb | |
| Linfield | 0-0 | Elfsborg | |
| Murata | 1-2 | Tampere United | |
| Olimpi Rustavi | 0-0 | Zhenis Astana | |
| The New Saints | 3-2 | FK Ventspils | |
| Zeta | 3-1 | FBK Kaunas | |
| Wednesday 18th July 2007 | |||
| 1st Leg | |||
| Derry City | 0-0 | Pyunik Yerevan | |
| F91 Dudelange | 1-2 | MSK Zilina | |
| FH Hafnarfjordur | 4-1 | HB Torshavn | |
| FK Pobeda Prilep | 0-1 | Levadia Tallinn | |
| Marsaxlokk FC | 0-6 | FK Sarajevo | |
| NK Domzale | 1-0 | SK Tirana | |
| Sheriff Tiraspol | 2-0 | Ranger's FC Venecia | |
| Tuesday 24th July 2007 | |||
| 2nd Leg | |||
| BATE Borisov | 3-0 | Apoel Nicosia | aet (3-2) |
| Dinamo Zagreb | 3-1 | FK Khazar Lankaran | aet (4-2) |
| FBK Kaunas | 3-2 | Zeta | (4-5) |
| FK Sarajevo | 3-1 | Marsaxlokk FC | (9-1) |
| Ranger's FC Venecia | 0-3 | Sheriff Tiraspol | (0-5) |
| Zhenis Astana | 3-0 | Olimpi Rustavi | (3-0) |
| Wednesday 25th July 2007 | |||
| 2nd Leg | |||
| Elfsborg | 1-0 | Linfield | (1-0) |
| FK Ventspils | 2-1 | The New Saints | (4-4) |
| (FK Ventspils won on away goals) | |||
| HB Torshavn | 0-0 | FH Hafnarfjordur | (1-4) |
| Levadia Tallinn | 0-0 | FK Pobeda Prilep | (1-0) |
| MSK Zilina | 5-4 | F91 Dudelange | (7-5) |
| Pyunik Yerevan | 2-0 | Derry City | (2-0) |
| SK Tirana | 1-2 | NK Domzale | (1-3) |
| Tampere United | 2-0 | Murata | (4-1) |
