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| H | Pyunik FC | - | FC Sheriff | 0:0 (0:0) | ||
| R | FC Sheriff | - | Pyunik FC | 2:0 (1:0) | ||
| H: 11.07.2006 16:00 | R: 18.07.2006 19:00 | Sieger: FC Sheriff | ||||
| H | FC TVMK | - | FH Hafnarfjörður | 2:3 (0:1) | ||
| R | FH Hafnarfjörður | - | FC TVMK | 1:1 (0:0) | ||
| H: 11.07.2006 17:00 | R: 19.07.2006 21:15 | Sieger: FH Hafnarfjörður | ||||
| H | Sioni Bolnisi | - | FK Baku | 2:0 (0:0) | ||
| R | FK Baku | - | Sioni Bolnisi | 1:0 (0:0) | ||
| H: 11.07.2006 17:00 | R: 18.07.2006 16:00 | Sieger: Sioni Bolnisi | ||||
| H | KF Elbasani | - | FK Ekranas | 1:0 (0:0) | ||
| R | FK Ekranas | - | KF Elbasani | 3:0 (1:0) | ||
| H: 11.07.2006 17:30 | R: 18.07.2006 17:00 | Sieger: FK Ekranas | ||||
| H | Birkirkara FC | - | B36 Tórshavn | 0:3 (0:2) | ||
| R | B36 Tórshavn | - | Birkirkara FC | 2:2 (1:0) | ||
| H: 11.07.2006 18:30 | R: 19.07.2006 20:00 | Sieger: B36 Tórshavn | ||||
| H | F91 Dudelange | - | FK Rabotnički | 0:1 (0:0) | ||
| R | FK Rabotnički | - | F91 Dudelange | 0:0 (0:0) | ||
| H: 11.07.2006 19:00 | R: 18.07.2006 20:00 | Sieger: FK Rabotnički | ||||
| H | Linfield FC | - | ND Gorica | 1:3 (0:2) | ||
| R | ND Gorica | - | Linfield FC | 2:2 (1:1) | ||
| H: 11.07.2006 19:00 | R: 19.07.2006 20:05 | Sieger: ND Gorica | ||||
| H | MyPa Anjalankoski | - | The New Saints | 1:0 (0:0) | ||
| R | The New Saints | - | MyPa Anjalankoski | 0:1 (0:1) | ||
| H: 12.07.2006 18:00 | R: 19.07.2006 20:30 | Sieger: MyPa Anjalankoski | ||||
| H | FK Liepājas Metalurgs | - | FK Aktobe | 1:0 (1:0) | ||
| R | FK Aktobe | - | FK Liepājas Metalurgs | 1:1 (1:0) | ||
| H: 12.07.2006 19:00 | R: 19.07.2006 17:00 | Sieger: FK Liepājas Metalurgs | ||||
| H | Shakhter Soligorsk | - | Široki Brijeg | 0:1 (0:1) | ||
| R | Široki Brijeg | - | Shakhter Soligorsk | 1:0 (1:0) | ||
| H: 12.07.2006 19:00 | R: 19.07.2006 20:30 | Sieger: Široki Brijeg | ||||
| H | Cork City | - | Apollon Limassol | 1:0 (0:0) | ||
| R | Apollon Limassol | - | Cork City | 1:1 (0:0) | ||
| H: 12.07.2006 20:30 | R: 19.07.2006 20:00 | Sieger: Cork City | ||||
