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| H | Inter Baku | - | Partizan | 1:1 (0:1) | ||
| R | Partizan | - | Inter Baku | 2:0 (0:0) | ||
| H: 29.07.2008 16:00 | R: 06.08.2008 20:45 | Sieger: Partizan | ||||
| H | SK Brann | - | FK Ventspils | 1:0 (0:0) | ||
| R | FK Ventspils | - | SK Brann | 2:1 (2:0) | ||
| H: 29.07.2008 20:45 | R: 05.08.2008 17:00 | Sieger: SK Brann | ||||
| H | Drogheda United | - | Dinamo Kiev | 1:2 (0:1) | ||
| R | Dinamo Kiev | - | Drogheda United | 2:2 (1:1) | ||
| H: 29.07.2008 20:45 | R: 06.08.2008 18:00 | Sieger: Dinamo Kiev | ||||
| H | Tampere United | - | FC Artmedia Petržalka | 1:3 (1:2) | ||
| R | FC Artmedia Petržalka | - | Tampere United | 4:2 (3:0) | ||
| H: 30.07.2008 18:00 | R: 06.08.2008 20:15 | Sieger: FC Artmedia Petržalka | ||||
| H | FC Sheriff | - | AC Sparta Praha | 0:1 (0:0) | ||
| R | AC Sparta Praha | - | FC Sheriff | 2:0 (1:0) | ||
| H: 30.07.2008 19:00 | R: 06.08.2008 20:15 | Sieger: AC Sparta Praha | ||||
| H | Beitar Jerusalem | - | Wisła Kraków | 2:1 (0:1) | ||
| R | Wisła Kraków | - | Beitar Jerusalem | 5:0 (3:0) | ||
| H: 30.07.2008 20:00 | R: 06.08.2008 20:45 | Sieger: Wisła Kraków | ||||
| H | Fenerbahçe | - | MTK Budapest | 2:0 (1:0) | ||
| R | MTK Budapest | - | Fenerbahçe | 0:5 (0:1) | ||
| H: 30.07.2008 20:00 | R: 06.08.2008 20:45 | Sieger: Fenerbahçe | ||||
| H | Aalborg BK | - | FK Modriča | 5:0 (3:0) | ||
| R | FK Modriča | - | Aalborg BK | 1:2 (0:1) | ||
| H: 30.07.2008 20:00 | R: 06.08.2008 20:00 | Sieger: Aalborg BK | ||||
| H | IFK Göteborg | - | FC Basel | 1:1 (1:1) | ||
| R | FC Basel | - | IFK Göteborg | 4:2 (1:1) | ||
| H: 30.07.2008 20:15 | R: 06.08.2008 20:15 | Sieger: FC Basel | ||||
| H | Anorthosis Famagusta | - | Rapid Wien | 3:0 (1:0) | ||
| R | Rapid Wien | - | Anorthosis Famagusta | 3:1 (1:1) | ||
| H: 30.07.2008 20:30 | R: 06.08.2008 19:30 | Sieger: Anorthosis Famagusta | ||||
| H | RSC Anderlecht | - | BATE Borisov | 1:2 (0:0) | ||
| R | BATE Borisov | - | RSC Anderlecht | 2:2 (1:1) | ||
| H: 30.07.2008 20:30 | R: 06.08.2008 18:00 | Sieger: BATE Borisov | ||||
| H | Rangers FC | - | FBK Kaunas | 0:0 (0:0) | ||
| R | FBK Kaunas | - | Rangers FC | 2:1 (1:1) | ||
| H: 30.07.2008 20:45 | R: 05.08.2008 19:05 | Sieger: FBK Kaunas | ||||
| H | NK Domžale | - | Dinamo Zagreb | 0:3 (0:3) | ||
| R | Dinamo Zagreb | - | NK Domžale | 3:2 (1:1) | ||
| H: 30.07.2008 20:45 | R: 06.08.2008 20:45 | Sieger: Dinamo Zagreb | ||||
| H | Panathinaikos | - | Dinamo Tbilisi | 3:0 (2:0) | ||
| R | Dinamo Tbilisi | - | Panathinaikos | 0:0 (0:0) | ||
| H: 30.07.2008 20:45 | R: 06.08.2008 18:00 | Sieger: Panathinaikos | ||||
