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| H | FK Moskva | - | MTZ-Ripo | 2:0 (0:0) | ||
| R | MTZ-Ripo | - | FK Moskva | 0:1 (0:0) | ||
| H: 01.07.2006 15:30 | R: 09.07.2006 16:00 | Sieger: FK Moskva | ||||
| H | Lillestrøm SK | - | Keflavík ÍF | 4:1 (2:1) | ||
| R | Keflavík ÍF | - | Lillestrøm SK | 2:2 (0:2) | ||
| H: 01.07.2006 16:00 | R: 09.07.2006 16:00 | Sieger: Lillestrøm SK | ||||
| H | Maccabi Petach-Tikva | - | Zrinjski Mostar | 1:1 (0:0) | ||
| R | Zrinjski Mostar | - | Maccabi Petach-Tikva | 1:3 (1:1) | ||
| H: 01.07.2006 16:30 | R: 08.07.2006 19:00 | Sieger: Maccabi Petach-Tikva | ||||
| H | FC Sopron | - | Kayserispor | 3:3 (0:2) | ||
| R | Kayserispor | - | FC Sopron | 1:0 (0:0) | ||
| H: 01.07.2006 19:00 | R: 08.07.2006 19:00 | Sieger: Kayserispor | ||||
| H | Farul Constanța | - | Lokomotiv Plovdiv | 2:1 (1:1) | ||
| R | Lokomotiv Plovdiv | - | Farul Constanța | 1:1 (1:0) | ||
| H: 01.07.2006 19:00 | R: 08.07.2006 19:30 | Sieger: Farul Constanța | ||||
| H | SV Ried | - | Dinamo Tbilisi | 3:1 (1:1) | ||
| R | Dinamo Tbilisi | - | SV Ried | 0:1 (0:0) | ||
| H: 01.07.2006 19:00 | R: 09.07.2006 17:00 | Sieger: SV Ried | ||||
| H | FC Tiraspol | - | Lech Poznań | 1:0 (1:0) | ||
| R | Lech Poznań | - | FC Tiraspol | 1:3 (0:1) | ||
| H: 01.07.2006 19:00 | R: 08.07.2006 18:00 | Sieger: FC Tiraspol | ||||
| H | Odense BK | - | Shelbourne FC | 3:0 (2:0) | ||
| R | Shelbourne FC | - | Odense BK | 1:0 (1:0) | ||
| H: 02.07.2006 15:00 | R: 09.07.2006 16:00 | Sieger: Odense BK | ||||
| H | Hibernian FC | - | FC Dinaburg | 5:0 (1:0) | ||
| R | FC Dinaburg | - | Hibernian FC | 0:3 (0:1) | ||
| H: 02.07.2006 16:00 | R: 08.07.2006 17:00 | Sieger: Hibernian FC | ||||
| H | FC Nitra | - | Dnipro Dnipropetrovsk | 2:1 (2:1) | ||
| R | Dnipro Dnipropetrovsk | - | FC Nitra | 2:0 (1:0) | ||
| H: 02.07.2006 17:00 | R: 08.07.2006 18:00 | Sieger: Dnipro Dnipropetrovsk | ||||
| H | FK Zeta | - | NK Maribor | 1:2 (0:0) | ||
| R | NK Maribor | - | FK Zeta | 2:0 (0:0) | ||
| H: 02.07.2006 17:30 | R: 08.07.2006 18:00 | Sieger: NK Maribor | ||||
| H | Tampere United | - | Kalmar FF | 1:2 (0:1) | ||
| R | Kalmar FF | - | Tampere United | 3:2 (1:1) | ||
| H: 02.07.2006 17:30 | R: 08.07.2006 17:00 | Sieger: Kalmar FF | ||||
| H | NK Osijek | - | Ethnikos Achna | 2:2 (0:1) | ||
| R | Ethnikos Achna | - | NK Osijek | 0:0 (0:0) | ||
| H: 02.07.2006 18:00 | R: 08.07.2006 17:00 | Sieger: Ethnikos Achna | ||||
| H | Grasshopper Club Zürich | - | FK Teplice | 2:0 (0:0) | ||
| R | FK Teplice | - | Grasshopper Club Zürich | 0:2 (0:0) | ||
| H: 02.07.2006 18:00 | R: 09.07.2006 16:30 | Sieger: Grasshopper Club Zürich | ||||
