| Tuesday 11th July 2006 | |||
| 1st Leg | |||
| Birkirkara | 0-3 | B36 Torshavn | |
| Elbasani | 1-0 | FK Ekranas Panevezys | |
| F91 Dudelange | 0-1 | Rabotnicki | |
| Linfield | 1-3 | HIT Gorica | |
| Pyunik Yerevan | 0-0 | Sheriff Tiraspol | |
| Sioni Bolnisi | 2-0 | FK Baku | |
| TVMK Tallinn | 2-3 | FH Hafnarfjordur | |
| Wednesday 12th July 2006 | |||
| 1st Leg | |||
| Cork City | 1-0 | Apollon Limassol | |
| Metalurgs Liepajas | 1-0 | FK Aktobe Lento | |
| MyPa-47 Anjalankoski | 1-0 | The New Saints | |
| Shakhter Soligorsk | 0-1 | NK Siroki Brijeg | |
| Tuesday 18th July 2006 | |||
| 2nd Leg | |||
| FK Baku | 1-0 | Sioni Bolnisi | (1-2) |
| FK Ekranas Panevezys | 3-0 | Elbasani | (3-1) |
| Rabotnicki | 0-0 | F91 Dudelange | (1-0) |
| Sheriff Tiraspol | 2-0 | Pyunik Yerevan | (2-0) |
| Wednesday 19th July 2006 | |||
| 2nd Leg | |||
| Apollon Limassol | 1-1 | Cork City | (1-2) |
| B36 Torshavn | 2-2 | Birkirkara | (5-2) |
| FH Hafnarfjordur | 1-1 | TVMK Tallinn | (4-3) |
| FK Aktobe Lento | 1-1 | Metalurgs Liepajas | (1-2) |
| HIT Gorica | 2-2 | Linfield | (5-3) |
| NK Siroki Brijeg | 1-0 | Shakhter Soligorsk | (2-0) |
| The New Saints | 0-1 | MyPa-47 Anjalankoski | (0-2) |
