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| 1st(1st leg) | FK Moskva | - | MTZ-Ripo | 2:0 (0:0) | ||
| 2nd (2nd leg) | MTZ-Ripo | - | FK Moskva | 0:1 (0:0) | ||
| 1st(1st leg): 01/07/2006 14:30 | 2nd (2nd leg): 09/07/2006 15:00 | Winner: FK Moskva | ||||
| 1st(1st leg) | Lillestrøm SK | - | Keflavík ÍF | 4:1 (2:1) | ||
| 2nd (2nd leg) | Keflavík ÍF | - | Lillestrøm SK | 2:2 (0:2) | ||
| 1st(1st leg): 01/07/2006 15:00 | 2nd (2nd leg): 09/07/2006 15:00 | Winner: Lillestrøm SK | ||||
| 1st(1st leg) | Maccabi Petach-Tikva | - | Zrinjski Mostar | 1:1 (0:0) | ||
| 2nd (2nd leg) | Zrinjski Mostar | - | Maccabi Petach-Tikva | 1:3 (1:1) | ||
| 1st(1st leg): 01/07/2006 15:30 | 2nd (2nd leg): 08/07/2006 18:00 | Winner: Maccabi Petach-Tikva | ||||
| 1st(1st leg) | FC Sopron | - | Kayserispor | 3:3 (0:2) | ||
| 2nd (2nd leg) | Kayserispor | - | FC Sopron | 1:0 (0:0) | ||
| 1st(1st leg): 01/07/2006 18:00 | 2nd (2nd leg): 08/07/2006 18:00 | Winner: Kayserispor | ||||
| 1st(1st leg) | Farul Constanța | - | Lokomotiv Plovdiv | 2:1 (1:1) | ||
| 2nd (2nd leg) | Lokomotiv Plovdiv | - | Farul Constanța | 1:1 (1:0) | ||
| 1st(1st leg): 01/07/2006 18:00 | 2nd (2nd leg): 08/07/2006 18:30 | Winner: Farul Constanța | ||||
| 1st(1st leg) | SV Ried | - | Dinamo Tbilisi | 3:1 (1:1) | ||
| 2nd (2nd leg) | Dinamo Tbilisi | - | SV Ried | 0:1 (0:0) | ||
| 1st(1st leg): 01/07/2006 18:00 | 2nd (2nd leg): 09/07/2006 16:00 | Winner: SV Ried | ||||
| 1st(1st leg) | FC Tiraspol | - | Lech Poznań | 1:0 (1:0) | ||
| 2nd (2nd leg) | Lech Poznań | - | FC Tiraspol | 1:3 (0:1) | ||
| 1st(1st leg): 01/07/2006 18:00 | 2nd (2nd leg): 08/07/2006 17:00 | Winner: FC Tiraspol | ||||
| 1st(1st leg) | Odense BK | - | Shelbourne FC | 3:0 (2:0) | ||
| 2nd (2nd leg) | Shelbourne FC | - | Odense BK | 1:0 (1:0) | ||
| 1st(1st leg): 02/07/2006 14:00 | 2nd (2nd leg): 09/07/2006 15:00 | Winner: Odense BK | ||||
| 1st(1st leg) | Hibernian FC | - | FC Dinaburg | 5:0 (1:0) | ||
| 2nd (2nd leg) | FC Dinaburg | - | Hibernian FC | 0:3 (0:1) | ||
| 1st(1st leg): 02/07/2006 15:00 | 2nd (2nd leg): 08/07/2006 16:00 | Winner: Hibernian FC | ||||
| 1st(1st leg) | FC Nitra | - | Dnipro Dnipropetrovsk | 2:1 (2:1) | ||
| 2nd (2nd leg) | Dnipro Dnipropetrovsk | - | FC Nitra | 2:0 (1:0) | ||
| 1st(1st leg): 02/07/2006 16:00 | 2nd (2nd leg): 08/07/2006 17:00 | Winner: Dnipro Dnipropetrovsk | ||||
| 1st(1st leg) | FK Zeta | - | NK Maribor | 1:2 (0:0) | ||
| 2nd (2nd leg) | NK Maribor | - | FK Zeta | 2:0 (0:0) | ||
| 1st(1st leg): 02/07/2006 16:30 | 2nd (2nd leg): 08/07/2006 17:00 | Winner: NK Maribor | ||||
| 1st(1st leg) | Tampere United | - | Kalmar FF | 1:2 (0:1) | ||
| 2nd (2nd leg) | Kalmar FF | - | Tampere United | 3:2 (1:1) | ||
| 1st(1st leg): 02/07/2006 16:30 | 2nd (2nd leg): 08/07/2006 16:00 | Winner: Kalmar FF | ||||
| 1st(1st leg) | NK Osijek | - | Ethnikos Achna | 2:2 (0:1) | ||
| 2nd (2nd leg) | Ethnikos Achna | - | NK Osijek | 0:0 (0:0) | ||
| 1st(1st leg): 02/07/2006 17:00 | 2nd (2nd leg): 08/07/2006 16:00 | Winner: Ethnikos Achna | ||||
| 1st(1st leg) | Grasshopper Club Zürich | - | FK Teplice | 2:0 (0:0) | ||
| 2nd (2nd leg) | FK Teplice | - | Grasshopper Club Zürich | 0:2 (0:0) | ||
| 1st(1st leg): 02/07/2006 17:00 | 2nd (2nd leg): 09/07/2006 15:30 | Winner: Grasshopper Club Zürich | ||||
