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| U | Makedonija GP | - | BATE Borisov | 0:2 (0:1) | ||
| R | BATE Borisov | - | Makedonija GP | 2:0 (0:0) | ||
| U: 14.07.2009 17:00 | R: 21.07.2009 18:00 | Winnaars: BATE Borisov | ||||
| U | Pyunik FC | - | Dinamo Zagreb | 0:0 (0:0) | ||
| R | Dinamo Zagreb | - | Pyunik FC | 3:0 (1:0) | ||
| U: 14.07.2009 17:00 | R: 21.07.2009 20:30 | Winnaars: Dinamo Zagreb | ||||
| U | EB/Streymur | - | APOEL Nicosia | 0:2 (0:1) | ||
| R | APOEL Nicosia | - | EB/Streymur | 3:0 (1:0) | ||
| U: 14.07.2009 20:00 | R: 21.07.2009 19:00 | Winnaars: APOEL Nicosia | ||||
| U | FK Ekranas | - | FK Baku | 2:2 (0:0) | ||
| R | FK Baku | - | FK Ekranas | 4:2 (0:0) | ||
| U: 14.07.2009 20:00 | R: 21.07.2009 17:00 | Winnaars: FK Baku | ||||
| U | Rhyl FC | - | Partizan | 0:4 (0:3) | ||
| R | Partizan | - | Rhyl FC | 8:0 (4:0) | ||
| U: 14.07.2009 20:45 | R: 21.07.2009 20:45 | Winnaars: Partizan | ||||
| U | FK Ventspils | - | F91 Dudelange | 3:0 (0:0) | ||
| R | F91 Dudelange | - | FK Ventspils | 1:3 (1:1) | ||
| U: 15.07.2009 17:00 | R: 22.07.2009 18:00 | Winnaars: FK Ventspils | ||||
| U | Inter Turku | - | FC Sheriff | 0:1 (0:1) | ||
| R | FC Sheriff | - | Inter Turku | 1:0 (0:0) | ||
| U: 15.07.2009 17:30 | R: 21.07.2009 19:00 | Winnaars: FC Sheriff | ||||
| U | WIT Georgia | - | NK Maribor | 0:0 (0:0) | ||
| R | NK Maribor | - | WIT Georgia | 3:1 (2:1) | ||
| U: 15.07.2009 18:00 | R: 22.07.2009 20:45 | Winnaars: NK Maribor | ||||
| U | Levski Sofia | - | UE Sant Julià | 4:0 (0:0) | ||
| R | UE Sant Julià | - | Levski Sofia | 0:5 (0:3) | ||
| U: 15.07.2009 18:45 | R: 21.07.2009 18:45 | Winnaars: Levski Sofia | ||||
| U | Maccabi Haifa | - | Glentoran FC | 6:0 (1:0) | ||
| R | Glentoran FC | - | Maccabi Haifa | 0:4 (0:1) | ||
| U: 15.07.2009 19:50 | R: 22.07.2009 19:50 | Winnaars: Maccabi Haifa | ||||
| U | KF Tiranë | - | Stabæk IF | 1:1 (0:1) | ||
| R | Stabæk IF | - | KF Tiranë | 4:0 (3:0) | ||
| U: 15.07.2009 20:00 | R: 21.07.2009 20:45 | Winnaars: Stabæk IF | ||||
| U | Debreceni VSC | - | Kalmar FF | 2:0 (0:0) | ||
| R | Kalmar FF | - | Debreceni VSC | 3:1 (2:1) | ||
| U: 15.07.2009 20:00 | R: 22.07.2009 19:00 | Winnaars: Debreceni VSC | ||||
| U | FC Kopenhagen | - | FK Mogren Budva | 6:0 (3:0) | ||
| R | FK Mogren Budva | - | FC Kopenhagen | 0:6 (0:4) | ||
| U: 15.07.2009 20:15 | R: 22.07.2009 20:30 | Winnaars: FC Kopenhagen | ||||
| U | RB Salzburg | - | Bohemian FC | 1:1 (1:0) | ||
| R | Bohemian FC | - | RB Salzburg | 0:1 (0:0) | ||
| U: 15.07.2009 20:30 | R: 22.07.2009 20:30 | Winnaars: RB Salzburg | ||||
| U | Zrinjski Mostar | - | Slovan Bratislava | 1:0 (0:0) | ||
| R | Slovan Bratislava | - | Zrinjski Mostar | 4:0 (2:0) | ||
| U: 15.07.2009 20:30 | R: 21.07.2009 19:30 | Winnaars: Slovan Bratislava | ||||
| U | Wisła Kraków | - | FC Levadia | 1:1 (0:1) | ||
| R | FC Levadia | - | Wisła Kraków | 1:0 (0:0) | ||
| U: 15.07.2009 20:30 | R: 22.07.2009 18:00 | Winnaars: FC Levadia | ||||
| U | FH Hafnarfjörður | - | FK Aktobe | 0:4 (0:0) | ||
| R | FK Aktobe | - | FH Hafnarfjörður | 2:0 (1:0) | ||
| U: 15.07.2009 21:15 | R: 22.07.2009 18:00 | Winnaars: FK Aktobe | ||||
