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| U | MKT-Araz | - | FC Tiraspol | 1:0 (0:0) | ||
| R | FC Tiraspol | - | MKT-Araz | 2:0 (2:0, 2:0) n.v. | ||
| U: 17.06.2006 15:30 | R: 24.06.2006 19:00 | Winnaars: FC Tiraspol | ||||
| U | Tampere United | - | Carmarthen Town | 5:0 (3:0) | ||
| R | Carmarthen Town | - | Tampere United | 1:3 (1:2) | ||
| U: 17.06.2006 16:00 | R: 24.06.2006 15:30 | Winnaars: Tampere United | ||||
| U | Shakter Karaganda | - | MTZ-Ripo | 1:5 (0:0) | ||
| R | MTZ-Ripo | - | Shakter Karaganda | 1:3 (0:2) | ||
| U: 17.06.2006 16:30 | R: 25.06.2006 15:00 | Winnaars: MTZ-Ripo | ||||
| U | Ethnikos Achna | - | FK Partizani | 4:2 (2:0) | ||
| R | FK Partizani | - | Ethnikos Achna | 2:1 (1:1) | ||
| U: 17.06.2006 17:00 | R: 24.06.2006 18:00 | Winnaars: Ethnikos Achna | ||||
| U | JK Narva Trans | - | Kalmar FF | 1:6 (1:1) | ||
| R | Kalmar FF | - | JK Narva Trans | 2:0 (2:0) | ||
| U: 17.06.2006 17:00 | R: 25.06.2006 14:00 | Winnaars: Kalmar FF | ||||
| U | Zrinjski Mostar | - | Marsaxlokk FC | 3:0 (3:0) | ||
| R | Marsaxlokk FC | - | Zrinjski Mostar | 1:1 (1:0) | ||
| U: 17.06.2006 19:00 | R: 25.06.2006 10:00 | Winnaars: Zrinjski Mostar | ||||
| U | Keflavík ÍF | - | Dungannon Swifts | 4:1 (1:0) | ||
| R | Dungannon Swifts | - | Keflavík ÍF | 0:0 (0:0) | ||
| U: 17.06.2006 19:00 | R: 24.06.2006 16:00 | Winnaars: Keflavík ÍF | ||||
| U | UE Sant Julià | - | NK Maribor | 0:3 (0:0) | ||
| R | NK Maribor | - | UE Sant Julià | 5:0 (2:0) | ||
| U: 18.06.2006 12:00 | R: 24.06.2006 19:00 | Winnaars: NK Maribor | ||||
| U | FC Kilikia | - | Dinamo Tbilisi | 1:5 (1:2) | ||
| R | Dinamo Tbilisi | - | FC Kilikia | 3:0 (2:0) | ||
| U: 18.06.2006 16:00 | R: 24.06.2006 17:00 | Winnaars: Dinamo Tbilisi | ||||
| U | FC Nitra | - | CS Grevenmacher | 6:2 (3:0) | ||
| R | CS Grevenmacher | - | FC Nitra | 0:6 (0:2) | ||
| U: 18.06.2006 16:00 | R: 25.06.2006 17:00 | Winnaars: FC Nitra | ||||
| U | FC Dinaburg | - | HB Tórshavn | 1:1 (1:0) | ||
| R | HB Tórshavn | - | FC Dinaburg | 0:1 (0:0) | ||
| U: 18.06.2006 17:00 | R: 24.06.2006 19:00 | Winnaars: FC Dinaburg | ||||
| U | FK Vetra | - | Shelbourne FC | 0:1 (0:1) | ||
| R | Shelbourne FC | - | FK Vetra | 4:0 (1:0) | ||
| U: 18.06.2006 17:00 | R: 24.06.2006 20:00 | Winnaars: Shelbourne FC | ||||
| U | FK Pobeda | - | Farul Constanța | 2:2 (0:1) | ||
| R | Farul Constanța | - | FK Pobeda | 2:0 (1:0) | ||
| U: 18.06.2006 18:00 | R: 25.06.2006 18:00 | Winnaars: Farul Constanța | ||||
