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| U | OFK Beograd | - | AJ Auxerre | 1:0 (1:0) | ||
| R | AJ Auxerre | - | OFK Beograd | 5:1 (2:1) | ||
| U: 08.08.2006 17:00 | R: 24.08.2006 20:00 | Winnaars: AJ Auxerre | ||||
| U | Omonia Nikosia | - | PFC Litex Lovech | 0:0 (0:0) | ||
| R | PFC Litex Lovech | - | Omonia Nikosia | 2:1 (2:1) | ||
| U: 08.08.2006 18:00 | R: 24.08.2006 20:45 | Winnaars: PFC Litex Lovech | ||||
| U | FC Artmedia Bratislava | - | Dinamo Minsk | 2:1 (0:1) | ||
| R | Dinamo Minsk | - | FC Artmedia Bratislava | 2:3 (0:2) | ||
| U: 10.08.2006 17:00 | R: 24.08.2006 18:00 | Winnaars: FC Artmedia Bratislava | ||||
| U | FK Karvan | - | Slavia Praag | 0:2 (0:1) | ||
| R | Slavia Praag | - | FK Karvan | 0:0 (0:0) | ||
| U: 10.08.2006 17:00 | R: 24.08.2006 20:45 | Winnaars: Slavia Praag | ||||
| U | Chernomorets Odessa | - | Wisła Płock | 0:0 (0:0) | ||
| R | Wisła Płock | - | Chernomorets Odessa | 1:1 (0:1) | ||
| U: 10.08.2006 17:00 | R: 24.08.2006 17:30 | Winnaars: Chernomorets Odessa | ||||
| U | Rubin Kazan | - | BATE Borisov | 3:0 (1:0) | ||
| R | BATE Borisov | - | Rubin Kazan | 0:2 (0:2) | ||
| U: 10.08.2006 17:00 | R: 24.08.2006 18:30 | Winnaars: Rubin Kazan | ||||
| U | KF Tiranë | - | Kayserispor | 0:2 (0:2) | ||
| R | Kayserispor | - | KF Tiranë | 3:1 (1:0) | ||
| U: 10.08.2006 17:30 | R: 24.08.2006 18:00 | Winnaars: Kayserispor | ||||
| U | KSV Roeselare | - | Ethnikos Achna | 2:1 (1:0) | ||
| R | Ethnikos Achna | - | KSV Roeselare | 5:0 (2:0) | ||
| U: 10.08.2006 18:00 | R: 24.08.2006 17:00 | Winnaars: Ethnikos Achna | ||||
| U | Bnei Yehuda Tel Aviv | - | Lokomotiv Sofia | 0:2 (0:1) | ||
| R | Lokomotiv Sofia | - | Bnei Yehuda Tel Aviv | 4:0 (2:0) | ||
| U: 10.08.2006 18:00 | R: 24.08.2006 19:30 | Winnaars: Lokomotiv Sofia | ||||
| U | CSKA Sofia | - | Hajduk Rodić | 0:0 (0:0) | ||
| R | Hajduk Rodić | - | CSKA Sofia | 1:1 (0:0, 0:0) n.v. | ||
| U: 10.08.2006 18:30 | R: 24.08.2006 20:30 | Winnaars: CSKA Sofia | ||||
| U | SV Ried | - | FC Sion | 0:0 (0:0) | ||
| R | FC Sion | - | SV Ried | 1:0 (1:0) | ||
| U: 10.08.2006 18:30 | R: 24.08.2006 20:00 | Winnaars: FC Sion | ||||
| U | Hapoel Tel Aviv | - | NK Domžale | 1:2 (1:0) | ||
| R | NK Domžale | - | Hapoel Tel Aviv | 0:3 (0:0) | ||
| U: 10.08.2006 19:00 | R: 24.08.2006 18:30 | Winnaars: Hapoel Tel Aviv | ||||
| U | FC Zimbru | - | Metalurg Zaporizhya | 0:0 (0:0) | ||
| R | Metalurg Zaporizhya | - | FC Zimbru | 3:0 (1:0) | ||
| U: 10.08.2006 19:00 | R: 24.08.2006 19:00 | Winnaars: Metalurg Zaporizhya | ||||
| U | Hertha BSC | - | FC Ameri | 1:0 (0:0) | ||
| R | FC Ameri | - | Hertha BSC | 2:2 (1:1) | ||
| U: 10.08.2006 19:00 | R: 24.08.2006 19:00 | Winnaars: Hertha BSC | ||||
| U | IK Start | - | Drogheda United | 1:0 (0:0) | ||
| R | Drogheda United | - | IK Start | 11:12 (0:0, 1:0, 1:0) d.p. | ||
| U: 10.08.2006 19:00 | R: 24.08.2006 20:45 | Winnaars: IK Start | ||||
| U | Odense BK | - | Llanelli AFC | 1:0 (1:0) | ||
| R | Llanelli AFC | - | Odense BK | 1:5 (1:2) | ||
| U: 10.08.2006 19:00 | R: 24.08.2006 20:45 | Winnaars: Odense BK | ||||
| U | Randers FC | - | FBK Kaunas | 3:1 (0:0) | ||
| R | FBK Kaunas | - | Randers FC | 1:0 (0:0) | ||
| U: 10.08.2006 19:00 | R: 24.08.2006 18:00 | Winnaars: Randers FC | ||||
| U | SK Brann | - | Åtvidabergs FF | 3:3 (2:1) | ||
| R | Åtvidabergs FF | - | SK Brann | 1:1 (1:0) | ||
| U: 10.08.2006 19:00 | R: 24.08.2006 19:30 | Winnaars: Åtvidabergs FF | ||||
| U | Molde FK | - | Skonto FC | 0:0 (0:0) | ||
| R | Skonto FC | - | Molde FK | 1:2 (0:1) | ||
| U: 10.08.2006 19:00 | R: 24.08.2006 18:00 | Winnaars: Molde FK | ||||
| U | BSC Young Boys | - | Olympique Marseille | 3:3 (1:2) | ||
| R | Olympique Marseille | - | BSC Young Boys | 0:0 (0:0) | ||
| U: 10.08.2006 19:30 | R: 24.08.2006 20:45 | Winnaars: Olympique Marseille | ||||
| U | FC Twente | - | FC Levadia | 1:1 (0:1) | ||
| R | FC Levadia | - | FC Twente | 1:0 (1:0) | ||
| U: 10.08.2006 19:30 | R: 24.08.2006 20:00 | Winnaars: FC Levadia | ||||
| U | FK Ventspils | - | Newcastle United | 0:1 (0:0) | ||
| R | Newcastle United | - | FK Ventspils | 0:0 (0:0) | ||
| U: 10.08.2006 19:50 | R: 24.08.2006 20:45 | Winnaars: Newcastle United | ||||
| U | APOEL Nicosia | - | Trabzonspor | 1:1 (1:0) | ||
| R | Trabzonspor | - | APOEL Nicosia | 1:0 (0:0) | ||
| U: 10.08.2006 20:00 | R: 24.08.2006 19:45 | Winnaars: Trabzonspor | ||||
| U | Dinamo Boekarest | - | Beitar Jerusalem | 1:0 (0:0) | ||
| R | Beitar Jerusalem | - | Dinamo Boekarest | 1:1 (1:1) | ||
| U: 10.08.2006 20:00 | R: 24.08.2006 20:00 | Winnaars: Dinamo Boekarest | ||||
| U | Partizan | - | NK Maribor | 2:1 (2:0) | ||
| R | NK Maribor | - | Partizan | 1:1 (0:1) | ||
| U: 10.08.2006 20:00 | R: 24.08.2006 21:00 | Winnaars: Partizan | ||||
| U | FK Sarajevo | - | Rapid Bucureşti | 1:0 (0:0) | ||
| R | Rapid Bucureşti | - | FK Sarajevo | 2:0 (1:0) | ||
| U: 10.08.2006 20:00 | R: 24.08.2006 18:30 | Winnaars: Rapid Bucureşti | ||||
| U | FC Fehérvár | - | Grasshopper Club Zürich | 1:1 (0:0) | ||
| R | Grasshopper Club Zürich | - | FC Fehérvár | 2:0 (2:0) | ||
| U: 10.08.2006 20:00 | R: 24.08.2006 19:30 | Winnaars: Grasshopper Club Zürich | ||||
| U | FC Basel | - | FC Vaduz | 1:0 (0:0) | ||
| R | FC Vaduz | - | FC Basel | 2:1 (0:0) | ||
| U: 10.08.2006 20:00 | R: 24.08.2006 19:30 | Winnaars: FC Basel | ||||
| U | FC Flora | - | Brøndby IF | 0:0 (0:0) | ||
| R | Brøndby IF | - | FC Flora | 4:0 (0:0) | ||
| U: 10.08.2006 20:00 | R: 24.08.2006 20:45 | Winnaars: Brøndby IF | ||||
| U | FK Sūduva | - | Club Brugge KV | 0:2 (0:1) | ||
| R | Club Brugge KV | - | FK Sūduva | 5:2 (2:0) | ||
| U: 10.08.2006 20:00 | R: 24.08.2006 20:30 | Winnaars: Club Brugge KV | ||||
| U | SV Mattersburg | - | Wisła Kraków | 1:1 (1:1) | ||
| R | Wisła Kraków | - | SV Mattersburg | 1:0 (1:0) | ||
| U: 10.08.2006 20:45 | R: 24.08.2006 20:30 | Winnaars: Wisła Kraków | ||||
| U | Gretna FC | - | Derry City | 1:5 (1:1) | ||
| R | Derry City | - | Gretna FC | 2:2 (1:1) | ||
| U: 10.08.2006 20:45 | R: 24.08.2006 20:30 | Winnaars: Derry City | ||||
