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| H | Mika FC | - | BSC Young Boys | 1:3 (0:1) | ||
| R | BSC Young Boys | - | Mika FC | 1:0 (0:0) | ||
| H: 13.07.2006 17:00 | R: 27.07.2006 19:30 | Sieger: BSC Young Boys | ||||
| H | FK Karvan | - | Spartak Trnava | 1:0 (0:0) | ||
| R | Spartak Trnava | - | FK Karvan | 0:1 (0:1) | ||
| H: 13.07.2006 17:00 | R: 27.07.2006 19:00 | Sieger: FK Karvan | ||||
| H | HNK Orašje | - | NK Domžale | 0:2 (0:2) | ||
| R | NK Domžale | - | HNK Orašje | 5:0 (3:0) | ||
| H: 13.07.2006 17:00 | R: 27.07.2006 20:15 | Sieger: NK Domžale | ||||
| H | FK Ventspils | - | GÍ Gøta | 2:1 (1:1) | ||
| R | GÍ Gøta | - | FK Ventspils | 0:2 (0:0) | ||
| H: 13.07.2006 17:30 | R: 27.07.2006 19:00 | Sieger: FK Ventspils | ||||
| H | FC Levadia | - | Haka Valkeakoski | 2:0 (2:0) | ||
| R | Haka Valkeakoski | - | FC Levadia | 1:0 (1:0) | ||
| H: 13.07.2006 17:30 | R: 27.07.2006 18:00 | Sieger: FC Levadia | ||||
| H | Zagłębie Lubin | - | Dinamo Minsk | 1:1 (0:0) | ||
| R | Dinamo Minsk | - | Zagłębie Lubin | 0:0 (0:0) | ||
| H: 13.07.2006 17:30 | R: 27.07.2006 17:30 | Sieger: Dinamo Minsk | ||||
| H | Dinamo Tiranë | - | CSKA Sofia | 0:1 (0:0) | ||
| R | CSKA Sofia | - | Dinamo Tiranë | 4:1 (1:1) | ||
| H: 13.07.2006 17:30 | R: 27.07.2006 19:00 | Sieger: CSKA Sofia | ||||
| H | HJK Helsinki | - | Drogheda United | 1:1 (0:1) | ||
| R | Drogheda United | - | HJK Helsinki | 3:1 (0:1, 1:1) n.V. | ||
| H: 13.07.2006 18:00 | R: 27.07.2006 20:45 | Sieger: Drogheda United | ||||
| H | Jeunesse Esch | - | Skonto FC | 0:2 (0:0) | ||
| R | Skonto FC | - | Jeunesse Esch | 3:0 (2:0) | ||
| H: 13.07.2006 18:00 | R: 27.07.2006 17:00 | Sieger: Skonto FC | ||||
| H | FC Ameri | - | FC Banants | 0:1 (0:1) | ||
| R | FC Banants | - | FC Ameri | 1:2 (1:0) | ||
| H: 13.07.2006 18:00 | R: 27.07.2006 16:00 | Sieger: FC Ameri | ||||
| H | BATE Borisov | - | Nistru Otaci | 2:0 (0:0) | ||
| R | Nistru Otaci | - | BATE Borisov | 0:1 (0:1) | ||
| H: 13.07.2006 18:00 | R: 27.07.2006 18:00 | Sieger: BATE Borisov | ||||
| H | FC Artmedia Bratislava | - | WIT Georgia | 2:0 (1:0) | ||
| R | WIT Georgia | - | FC Artmedia Bratislava | 2:1 (1:0) | ||
| H: 13.07.2006 18:00 | R: 27.07.2006 16:00 | Sieger: FC Artmedia Bratislava | ||||
| H | NK Varteks | - | KF Tiranë | 1:1 (0:1) | ||
| R | KF Tiranë | - | NK Varteks | 2:0 (1:0) | ||
| H: 13.07.2006 18:00 | R: 27.07.2006 17:00 | Sieger: KF Tiranë | ||||
| H | FK Sarajevo | - | FC Rànger's | 3:0 (3:0) | ||
| R | FC Rànger's | - | FK Sarajevo | 0:2 (0:2) | ||
| H: 13.07.2006 18:00 | R: 27.07.2006 18:00 | Sieger: FK Sarajevo | ||||
| H | Vardar Skopje | - | KSV Roeselare | 1:2 (1:2) | ||
| R | KSV Roeselare | - | Vardar Skopje | 5:1 (3:0) | ||
| H: 13.07.2006 18:00 | R: 27.07.2006 20:00 | Sieger: KSV Roeselare | ||||
| H | Gefle IF | - | Llanelli AFC | 1:2 (1:0) | ||
| R | Llanelli AFC | - | Gefle IF | 0:0 (0:0) | ||
| H: 13.07.2006 19:00 | R: 27.07.2006 20:30 | Sieger: Llanelli AFC | ||||
| H | Randers FC | - | ÍA Akranes | 1:0 (0:0) | ||
| R | ÍA Akranes | - | Randers FC | 2:1 (1:1) | ||
| H: 13.07.2006 19:00 | R: 27.07.2006 20:00 | Sieger: Randers FC | ||||
| H | Lyn Oslo | - | FC Flora | 1:1 (1:0) | ||
| R | FC Flora | - | Lyn Oslo | 0:0 (0:0) | ||
| H: 13.07.2006 19:00 | R: 27.07.2006 17:45 | Sieger: FC Flora | ||||
| H | IFK Göteborg | - | Derry City | 0:1 (0:0) | ||
| R | Derry City | - | IFK Göteborg | 1:0 (1:0) | ||
| H: 13.07.2006 19:00 | R: 27.07.2006 20:30 | Sieger: Derry City | ||||
| H | Újpest FC | - | FC Vaduz | 0:4 (0:2) | ||
| R | FC Vaduz | - | Újpest FC | 0:1 (0:0) | ||
| H: 13.07.2006 19:00 | R: 27.07.2006 19:30 | Sieger: FC Vaduz | ||||
| H | FC Zimbru | - | Qarabağ FK | 1:1 (0:0) | ||
| R | Qarabağ FK | - | FC Zimbru | 1:2 (1:0, 1:1) n.V. | ||
| H: 13.07.2006 19:00 | R: 27.07.2006 17:00 | Sieger: FC Zimbru | ||||
| H | APOEL Nikosia | - | SS Murata | 3:1 (1:0) | ||
| R | SS Murata | - | APOEL Nikosia | 0:4 (0:3) | ||
| H: 13.07.2006 19:00 | R: 27.07.2006 21:00 | Sieger: APOEL Nikosia | ||||
| H | Lokomotiv Sofia | - | Makedonija GP | 2:0 (0:0) | ||
| R | Makedonija GP | - | Lokomotiv Sofia | 1:1 (1:0) | ||
| H: 13.07.2006 19:30 | R: 27.07.2006 19:30 | Sieger: Lokomotiv Sofia | ||||
| H | Rapid Bucureşti | - | Sliema Wanderers | 5:0 (5:0) | ||
| R | Sliema Wanderers | - | Rapid Bucureşti | 0:1 (0:1) | ||
| H: 13.07.2006 19:30 | R: 27.07.2006 18:00 | Sieger: Rapid Bucureşti | ||||
| H | Åtvidabergs FF | - | Etzella Ettelbruck | 4:0 (2:0) | ||
| R | Etzella Ettelbruck | - | Åtvidabergs FF | 0:3 (0:0) | ||
| H: 13.07.2006 20:00 | R: 27.07.2006 18:00 | Sieger: Åtvidabergs FF | ||||
| H | Skála ÍF | - | IK Start | 0:1 (0:1) | ||
| R | IK Start | - | Skála ÍF | 3:0 (1:0) | ||
| H: 13.07.2006 20:00 | R: 27.07.2006 19:00 | Sieger: IK Start | ||||
| H | FC Fehérvár | - | FK Kairat | 1:0 (1:0) | ||
| R | FK Kairat | - | FC Fehérvár | 2:1 (0:1) | ||
| H: 13.07.2006 20:00 | R: 27.07.2006 15:30 | Sieger: FC Fehérvár | ||||
| H | FC Basel | - | Tobyl Kostanay | 3:1 (1:0) | ||
| R | Tobyl Kostanay | - | FC Basel | 0:0 (0:0) | ||
| H: 13.07.2006 20:00 | R: 27.07.2006 15:00 | Sieger: FC Basel | ||||
| H | FC Anet Koper | - | PFC Litex Lovech | 0:1 (0:1) | ||
| R | PFC Litex Lovech | - | FC Anet Koper | 5:0 (1:0) | ||
| H: 13.07.2006 20:00 | R: 27.07.2006 19:45 | Sieger: PFC Litex Lovech | ||||
| H | Glentoran FC | - | SK Brann | 0:1 (0:0) | ||
| R | SK Brann | - | Glentoran FC | 1:0 (0:0) | ||
| H: 13.07.2006 20:30 | R: 27.07.2006 19:30 | Sieger: SK Brann | ||||
| H | Portadown FC | - | FBK Kaunas | 1:3 (0:2) | ||
| R | FBK Kaunas | - | Portadown FC | 1:0 (1:0) | ||
| H: 13.07.2006 20:30 | R: 27.07.2006 19:00 | Sieger: FBK Kaunas | ||||
| H | Rhyl FC | - | FK Sūduva | 0:0 (0:0) | ||
| R | FK Sūduva | - | Rhyl FC | 2:1 (2:0) | ||
| H: 13.07.2006 20:30 | R: 27.07.2006 17:00 | Sieger: FK Sūduva | ||||
| H | Brøndby IF | - | Valur Reykjavík | 3:1 (3:0) | ||
| R | Valur Reykjavík | - | Brøndby IF | 0:0 (0:0) | ||
| H: 13.07.2006 20:45 | R: 27.07.2006 20:45 | Sieger: Brøndby IF | ||||
| H | HNK Rijeka | - | Omonia Nikosia | 2:2 (1:1) | ||
| R | Omonia Nikosia | - | HNK Rijeka | 2:1 (0:0) | ||
| H: 13.07.2006 20:45 | R: 27.07.2006 19:00 | Sieger: Omonia Nikosia | ||||
| H | Hibernians FC | - | Dinamo Bucureşti | 0:4 (0:1) | ||
| R | Dinamo Bucureşti | - | Hibernians FC | 5:1 (0:0) | ||
| H: 13.07.2006 21:00 | R: 27.07.2006 20:00 | Sieger: Dinamo Bucureşti | ||||
