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| H | Rubin Kazan | - | Parma FC | 0:1 (0:0) | ||
| R | Parma FC | - | Rubin Kazan | 1:0 (0:0) | ||
| H: 14.09.2006 15:30 | R: 28.09.2006 18:30 | Sieger: Parma FC | ||||
| H | FC Levadia | - | Newcastle United | 0:1 (0:1) | ||
| R | Newcastle United | - | FC Levadia | 2:1 (0:0) | ||
| H: 14.09.2006 16:55 | R: 28.09.2006 20:30 | Sieger: Newcastle United | ||||
| H | Hertha BSC | - | Odense BK | 2:2 (1:1) | ||
| R | Odense BK | - | Hertha BSC | 1:0 (0:0) | ||
| H: 14.09.2006 17:00 | R: 28.09.2006 15:30 | Sieger: Odense BK | ||||
| H | Legia Warszawa | - | Austria Wien | 1:1 (1:1) | ||
| R | Austria Wien | - | Legia Warszawa | 1:0 (0:0) | ||
| H: 14.09.2006 17:30 | R: 28.09.2006 20:45 | Sieger: Austria Wien | ||||
| H | Slovan Liberec | - | Crvena Zvezda | 2:0 (1:0) | ||
| R | Crvena Zvezda | - | Slovan Liberec | 1:2 (1:1) | ||
| H: 14.09.2006 17:30 | R: 28.09.2006 20:00 | Sieger: Slovan Liberec | ||||
| H | Chernomorets Odessa | - | Hapoel Tel Aviv | 0:1 (0:0) | ||
| R | Hapoel Tel Aviv | - | Chernomorets Odessa | 3:1 (1:0) | ||
| H: 14.09.2006 18:00 | R: 28.09.2006 18:30 | Sieger: Hapoel Tel Aviv | ||||
| H | Ethnikos Achna | - | RC Lens | 0:0 (0:0) | ||
| R | RC Lens | - | Ethnikos Achna | 3:1 (1:0) | ||
| H: 14.09.2006 18:00 | R: 28.09.2006 18:00 | Sieger: RC Lens | ||||
| H | Skoda Xanthi | - | Dinamo Bucureşti | 3:4 (2:3) | ||
| R | Dinamo Bucureşti | - | Skoda Xanthi | 4:1 (1:0) | ||
| H: 14.09.2006 18:00 | R: 28.09.2006 19:00 | Sieger: Dinamo Bucureşti | ||||
| H | Lokomotiv Moskva | - | SV Zulte Waregem | 2:1 (1:0) | ||
| R | SV Zulte Waregem | - | Lokomotiv Moskva | 2:0 (0:0) | ||
| H: 14.09.2006 18:15 | R: 28.09.2006 19:00 | Sieger: SV Zulte Waregem | ||||
| H | IK Start | - | AFC Ajax | 2:5 (1:2) | ||
| R | AFC Ajax | - | IK Start | 4:0 (3:0) | ||
| H: 14.09.2006 18:15 | R: 28.09.2006 20:45 | Sieger: AFC Ajax | ||||
| H | Beşiktaş | - | CSKA Sofia | 2:0 (0:0) | ||
| R | CSKA Sofia | - | Beşiktaş | 2:2 (0:0, 2:0) n.V. | ||
| H: 14.09.2006 18:45 | R: 28.09.2006 18:30 | Sieger: Beşiktaş | ||||
| H | FC Artmedia Bratislava | - | Espanyol Barcelona | 2:2 (2:1) | ||
| R | Espanyol Barcelona | - | FC Artmedia Bratislava | 3:1 (1:1) | ||
| H: 14.09.2006 18:45 | R: 28.09.2006 21:30 | Sieger: Espanyol Barcelona | ||||
| H | FC Schalke 04 | - | AS Nancy Lorraine | 1:0 (0:0) | ||
| R | AS Nancy Lorraine | - | FC Schalke 04 | 3:1 (2:0) | ||
| H: 14.09.2006 19:00 | R: 28.09.2006 18:00 | Sieger: AS Nancy Lorraine | ||||
| H | Rapid Bucureşti | - | CD Nacional | 1:0 (1:0) | ||
| R | CD Nacional | - | Rapid Bucureşti | 1:2 (1:0, 1:1) n.V. | ||
| H: 14.09.2006 19:00 | R: 28.09.2006 21:00 | Sieger: Rapid Bucureşti | ||||
| H | Trabzonspor | - | CA Osasuna | 2:2 (0:1) | ||
| R | CA Osasuna | - | Trabzonspor | 0:0 (0:0) | ||
| H: 14.09.2006 19:00 | R: 28.09.2006 20:45 | Sieger: CA Osasuna | ||||
| H | Partizan | - | FC Groningen | 4:2 (3:0) | ||
| R | FC Groningen | - | Partizan | 1:0 (0:0) | ||
| H: 14.09.2006 19:00 | R: 28.09.2006 20:00 | Sieger: Partizan | ||||
| H | Åtvidabergs FF | - | Grasshopper Club Zürich | 0:3 (0:2) | ||
| R | Grasshopper Club Zürich | - | Åtvidabergs FF | 5:0 (2:0) | ||
| H: 14.09.2006 19:30 | R: 28.09.2006 19:30 | Sieger: Grasshopper Club Zürich | ||||
| H | Sporting Braga | - | Chievo Verona | 2:0 (1:0) | ||
| R | Chievo Verona | - | Sporting Braga | 2:1 (1:0, 2:0) n.V. | ||
| H: 14.09.2006 20:00 | R: 28.09.2006 20:45 | Sieger: Sporting Braga | ||||
| H | Derry City | - | Paris Saint-Germain | 0:0 (0:0) | ||
| R | Paris Saint-Germain | - | Derry City | 2:0 (2:0) | ||
| H: 14.09.2006 20:00 | R: 28.09.2006 21:00 | Sieger: Paris Saint-Germain | ||||
| H | AZ Alkmaar | - | Kayserispor | 3:2 (2:1) | ||
| R | Kayserispor | - | AZ Alkmaar | 1:1 (1:0) | ||
| H: 14.09.2006 20:00 | R: 28.09.2006 19:00 | Sieger: AZ Alkmaar | ||||
| H | FC Basel | - | FK Rabotnički | 6:2 (4:0) | ||
| R | FK Rabotnički | - | FC Basel | 0:1 (0:0) | ||
| H: 14.09.2006 20:00 | R: 28.09.2006 19:30 | Sieger: FC Basel | ||||
| H | Slavia Praha | - | Tottenham Hotspur | 0:1 (0:1) | ||
| R | Tottenham Hotspur | - | Slavia Praha | 1:0 (0:0) | ||
| H: 14.09.2006 20:00 | R: 28.09.2006 21:00 | Sieger: Tottenham Hotspur | ||||
| H | Molde FK | - | Rangers FC | 0:0 (0:0) | ||
| R | Rangers FC | - | Molde FK | 2:0 (2:0) | ||
| H: 14.09.2006 20:05 | R: 28.09.2006 20:45 | Sieger: Rangers FC | ||||
| H | Lokomotiv Sofia | - | Feyenoord | 2:2 (2:1) | ||
| R | Feyenoord | - | Lokomotiv Sofia | 0:0 (0:0) | ||
| H: 14.09.2006 20:15 | R: 28.09.2006 19:45 | Sieger: Feyenoord | ||||
| H | Dinamo Zagreb | - | AJ Auxerre | 1:2 (0:1) | ||
| R | AJ Auxerre | - | Dinamo Zagreb | 3:1 (2:0) | ||
| H: 14.09.2006 20:15 | R: 28.09.2006 19:30 | Sieger: AJ Auxerre | ||||
| H | Standard Liège | - | RC Celta | 0:1 (0:1) | ||
| R | RC Celta | - | Standard Liège | 3:0 (1:0) | ||
| H: 14.09.2006 20:30 | R: 28.09.2006 21:00 | Sieger: RC Celta | ||||
| H | Maccabi Haifa | - | PFC Litex Lovech | 1:1 (1:0) | ||
| R | PFC Litex Lovech | - | Maccabi Haifa | 1:3 (1:2) | ||
| H: 14.09.2006 20:30 | R: 28.09.2006 20:00 | Sieger: Maccabi Haifa | ||||
| H | FC Sion | - | Bayer Leverkusen | 0:0 (0:0) | ||
| R | Bayer Leverkusen | - | FC Sion | 3:1 (0:0) | ||
| H: 14.09.2006 20:30 | R: 28.09.2006 20:30 | Sieger: Bayer Leverkusen | ||||
| H | Wisła Kraków | - | Iraklis Saloniki | 0:1 (0:1) | ||
| R | Iraklis Saloniki | - | Wisła Kraków | 0:2 (0:0, 0:1) n.V. | ||
| H: 14.09.2006 20:30 | R: 28.09.2006 19:30 | Sieger: Wisła Kraków | ||||
| H | Panathinaikos | - | Metalurg Zaporizhya | 1:1 (1:0) | ||
| R | Metalurg Zaporizhya | - | Panathinaikos | 0:1 (0:1) | ||
| H: 14.09.2006 20:45 | R: 28.09.2006 19:00 | Sieger: Panathinaikos | ||||
| H | Heart of Midlothian | - | AC Sparta Praha | 0:2 (0:1) | ||
| R | AC Sparta Praha | - | Heart of Midlothian | 0:0 (0:0) | ||
| H: 14.09.2006 20:45 | R: 28.09.2006 21:00 | Sieger: AC Sparta Praha | ||||
| H | Fenerbahçe | - | Randers FC | 2:1 (1:1) | ||
| R | Randers FC | - | Fenerbahçe | 0:3 (0:0) | ||
| H: 14.09.2006 20:45 | R: 28.09.2006 20:30 | Sieger: Fenerbahçe | ||||
| H | RB Salzburg | - | Blackburn Rovers | 2:2 (1:2) | ||
| R | Blackburn Rovers | - | RB Salzburg | 2:0 (1:0) | ||
| H: 14.09.2006 20:45 | R: 28.09.2006 20:45 | Sieger: Blackburn Rovers | ||||
| H | Eintracht Frankfurt | - | Brøndby IF | 4:0 (0:0) | ||
| R | Brøndby IF | - | Eintracht Frankfurt | 2:2 (1:1) | ||
| H: 14.09.2006 20:45 | R: 28.09.2006 18:05 | Sieger: Eintracht Frankfurt | ||||
| H | Olympique Marseille | - | FK Mladá Boleslav | 1:0 (1:0) | ||
| R | FK Mladá Boleslav | - | Olympique Marseille | 4:2 (1:1) | ||
| H: 14.09.2006 20:45 | R: 28.09.2006 17:30 | Sieger: FK Mladá Boleslav | ||||
| H | MFK Ružomberok | - | Club Brugge KV | 0:1 (0:1) | ||
| R | Club Brugge KV | - | MFK Ružomberok | 1:1 (0:1) | ||
| H: 14.09.2006 20:45 | R: 28.09.2006 20:30 | Sieger: Club Brugge KV | ||||
| H | AS Livorno | - | FC Superfund | 2:0 (1:0) | ||
| R | FC Superfund | - | AS Livorno | 0:1 (0:0) | ||
| H: 14.09.2006 20:45 | R: 28.09.2006 18:30 | Sieger: AS Livorno | ||||
| H | Atromitos | - | Sevilla FC | 1:2 (0:2) | ||
| R | Sevilla FC | - | Atromitos | 4:0 (3:0) | ||
| H: 14.09.2006 21:00 | R: 28.09.2006 21:30 | Sieger: Sevilla FC | ||||
| H | West Ham United | - | US Palermo | 0:1 (0:1) | ||
| R | US Palermo | - | West Ham United | 3:0 (1:0) | ||
| H: 14.09.2006 21:00 | R: 28.09.2006 20:45 | Sieger: US Palermo | ||||
| H | Vitória Setúbal | - | sc Heerenveen | 0:3 (0:0) | ||
| R | sc Heerenveen | - | Vitória Setúbal | 0:0 (0:0) | ||
| H: 14.09.2006 22:00 | R: 28.09.2006 18:45 | Sieger: sc Heerenveen | ||||
