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| 1st(1st leg) | FK Ekranas | - | Dinamo Zagreb | 1:4 (1:2) | ||
| 2nd (2nd leg) | Dinamo Zagreb | - | FK Ekranas | 5:2 (1:0) | ||
| 1st(1st leg): 25/07/2006 16:00 | 2nd (2nd leg): 02/08/2006 19:30 | Winner: Dinamo Zagreb | ||||
| 1st(1st leg) | FC Sheriff | - | Spartak Moskva | 1:1 (0:0) | ||
| 2nd (2nd leg) | Spartak Moskva | - | FC Sheriff | 0:0 (0:0) | ||
| 1st(1st leg): 26/07/2006 18:00 | 2nd (2nd leg): 02/08/2006 16:00 | Winner: Spartak Moskva | ||||
| 1st(1st leg) | FK Liepājas Metalurgs | - | Dinamo Kiev | 1:4 (0:3) | ||
| 2nd (2nd leg) | Dinamo Kiev | - | FK Liepājas Metalurgs | 4:0 (1:0) | ||
| 1st(1st leg): 26/07/2006 18:00 | 2nd (2nd leg): 02/08/2006 17:00 | Winner: Dinamo Kiev | ||||
| 1st(1st leg) | Levski Sofia | - | Sioni Bolnisi | 2:0 (1:0) | ||
| 2nd (2nd leg) | Sioni Bolnisi | - | Levski Sofia | 0:2 (0:1) | ||
| 1st(1st leg): 26/07/2006 18:30 | 2nd (2nd leg): 02/08/2006 16:00 | Winner: Levski Sofia | ||||
| 1st(1st leg) | Djurgårdens IF | - | MFK Ružomberok | 1:0 (0:0) | ||
| 2nd (2nd leg) | MFK Ružomberok | - | Djurgårdens IF | 3:1 (2:0) | ||
| 1st(1st leg): 26/07/2006 19:00 | 2nd (2nd leg): 02/08/2006 19:00 | Winner: MFK Ružomberok | ||||
| 1st(1st leg) | Fenerbahçe | - | B36 Tórshavn | 4:0 (2:0) | ||
| 2nd (2nd leg) | B36 Tórshavn | - | Fenerbahçe | 0:5 (0:1) | ||
| 1st(1st leg): 26/07/2006 19:00 | 2nd (2nd leg): 01/08/2006 18:30 | Winner: Fenerbahçe | ||||
| 1st(1st leg) | FC Zürich | - | RB Salzburg | 2:1 (2:1) | ||
| 2nd (2nd leg) | RB Salzburg | - | FC Zürich | 2:0 (1:0) | ||
| 1st(1st leg): 26/07/2006 19:15 | 2nd (2nd leg): 02/08/2006 19:15 | Winner: RB Salzburg | ||||
| 1st(1st leg) | FH Hafnarfjörður | - | Legia Warszawa | 0:1 (0:0) | ||
| 2nd (2nd leg) | Legia Warszawa | - | FH Hafnarfjörður | 2:0 (1:0) | ||
| 1st(1st leg): 26/07/2006 19:30 | 2nd (2nd leg): 02/08/2006 19:30 | Winner: Legia Warszawa | ||||
| 1st(1st leg) | FK Mladá Boleslav | - | Vålerenga IF | 3:1 (3:0) | ||
| 2nd (2nd leg) | Vålerenga IF | - | FK Mladá Boleslav | 2:2 (0:1) | ||
| 1st(1st leg): 26/07/2006 19:45 | 2nd (2nd leg): 02/08/2006 19:45 | Winner: FK Mladá Boleslav | ||||
| 1st(1st leg) | Debreceni VSC | - | FK Rabotnički | 1:1 (0:1) | ||
| 2nd (2nd leg) | FK Rabotnički | - | Debreceni VSC | 4:1 (3:1) | ||
| 1st(1st leg): 26/07/2006 19:45 | 2nd (2nd leg): 02/08/2006 19:00 | Winner: FK Rabotnički | ||||
| 1st(1st leg) | Cork City | - | Crvena Zvezda | 0:1 (0:1) | ||
| 2nd (2nd leg) | Crvena Zvezda | - | Cork City | 3:0 (2:0) | ||
| 1st(1st leg): 26/07/2006 19:45 | 2nd (2nd leg): 02/08/2006 19:15 | Winner: Crvena Zvezda | ||||
| 1st(1st leg) | FC København | - | MyPa Anjalankoski | 2:0 (0:0) | ||
| 2nd (2nd leg) | MyPa Anjalankoski | - | FC København | 2:2 (1:1) | ||
| 1st(1st leg): 26/07/2006 19:45 | 2nd (2nd leg): 02/08/2006 18:00 | Winner: FC København | ||||
| 1st(1st leg) | Heart of Midlothian | - | Široki Brijeg | 3:0 (0:0) | ||
| 2nd (2nd leg) | Široki Brijeg | - | Heart of Midlothian | 0:0 (0:0) | ||
| 1st(1st leg): 26/07/2006 19:45 | 2nd (2nd leg): 02/08/2006 19:30 | Winner: Heart of Midlothian | ||||
| 1st(1st leg) | ND Gorica | - | FC Steaua Bucureşti | 0:2 (0:0) | ||
| 2nd (2nd leg) | FC Steaua Bucureşti | - | ND Gorica | 3:0 (1:0) | ||
| 1st(1st leg): 26/07/2006 20:00 | 2nd (2nd leg): 02/08/2006 18:30 | Winner: FC Steaua Bucureşti | ||||
