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| U | FK Ekranas | - | Dinamo Zagreb | 1:4 (1:2) | ||
| R | Dinamo Zagreb | - | FK Ekranas | 5:2 (1:0) | ||
| U: 25.07.2006 17:00 | R: 02.08.2006 20:30 | Winnaars: Dinamo Zagreb | ||||
| U | FC Sheriff | - | Spartak Moskou | 1:1 (0:0) | ||
| R | Spartak Moskou | - | FC Sheriff | 0:0 (0:0) | ||
| U: 26.07.2006 19:00 | R: 02.08.2006 17:00 | Winnaars: Spartak Moskou | ||||
| U | FK Liepājas Metalurgs | - | Dinamo Kiev | 1:4 (0:3) | ||
| R | Dinamo Kiev | - | FK Liepājas Metalurgs | 4:0 (1:0) | ||
| U: 26.07.2006 19:00 | R: 02.08.2006 18:00 | Winnaars: Dinamo Kiev | ||||
| U | Levski Sofia | - | Sioni Bolnisi | 2:0 (1:0) | ||
| R | Sioni Bolnisi | - | Levski Sofia | 0:2 (0:1) | ||
| U: 26.07.2006 19:30 | R: 02.08.2006 17:00 | Winnaars: Levski Sofia | ||||
| U | Djurgårdens IF | - | MFK Ružomberok | 1:0 (0:0) | ||
| R | MFK Ružomberok | - | Djurgårdens IF | 3:1 (2:0) | ||
| U: 26.07.2006 20:00 | R: 02.08.2006 20:00 | Winnaars: MFK Ružomberok | ||||
| U | Fenerbahçe | - | B36 Tórshavn | 4:0 (2:0) | ||
| R | B36 Tórshavn | - | Fenerbahçe | 0:5 (0:1) | ||
| U: 26.07.2006 20:00 | R: 01.08.2006 19:30 | Winnaars: Fenerbahçe | ||||
| U | FC Zürich | - | RB Salzburg | 2:1 (2:1) | ||
| R | RB Salzburg | - | FC Zürich | 2:0 (1:0) | ||
| U: 26.07.2006 20:15 | R: 02.08.2006 20:15 | Winnaars: RB Salzburg | ||||
| U | FH Hafnarfjörður | - | Legia Warschau | 0:1 (0:0) | ||
| R | Legia Warschau | - | FH Hafnarfjörður | 2:0 (1:0) | ||
| U: 26.07.2006 20:30 | R: 02.08.2006 20:30 | Winnaars: Legia Warschau | ||||
| U | FK Mladá Boleslav | - | Vålerenga IF | 3:1 (3:0) | ||
| R | Vålerenga IF | - | FK Mladá Boleslav | 2:2 (0:1) | ||
| U: 26.07.2006 20:45 | R: 02.08.2006 20:45 | Winnaars: FK Mladá Boleslav | ||||
| U | Debreceni VSC | - | FK Rabotnički | 1:1 (0:1) | ||
| R | FK Rabotnički | - | Debreceni VSC | 4:1 (3:1) | ||
| U: 26.07.2006 20:45 | R: 02.08.2006 20:00 | Winnaars: FK Rabotnički | ||||
| U | Cork City | - | Rode Ster Belgrado | 0:1 (0:1) | ||
| R | Rode Ster Belgrado | - | Cork City | 3:0 (2:0) | ||
| U: 26.07.2006 20:45 | R: 02.08.2006 20:15 | Winnaars: Rode Ster Belgrado | ||||
| U | FC Kopenhagen | - | MyPa Anjalankoski | 2:0 (0:0) | ||
| R | MyPa Anjalankoski | - | FC Kopenhagen | 2:2 (1:1) | ||
| U: 26.07.2006 20:45 | R: 02.08.2006 19:00 | Winnaars: FC Kopenhagen | ||||
| U | Heart of Midlothian | - | Široki Brijeg | 3:0 (0:0) | ||
| R | Široki Brijeg | - | Heart of Midlothian | 0:0 (0:0) | ||
| U: 26.07.2006 20:45 | R: 02.08.2006 20:30 | Winnaars: Heart of Midlothian | ||||
| U | ND Gorica | - | FCSB | 0:2 (0:0) | ||
| R | FCSB | - | ND Gorica | 3:0 (1:0) | ||
| U: 26.07.2006 21:00 | R: 02.08.2006 19:30 | Winnaars: FCSB | ||||
