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| 1st(1st leg) | MKT-Araz | - | FC Tiraspol | 1:0 (0:0) | ||
| 2nd (2nd leg) | FC Tiraspol | - | MKT-Araz | 2:0 (2:0, 2:0) aet | ||
| 1st(1st leg): 17/06/2006 14:30 | 2nd (2nd leg): 24/06/2006 18:00 | Winner: FC Tiraspol | ||||
| 1st(1st leg) | Tampere United | - | Carmarthen Town | 5:0 (3:0) | ||
| 2nd (2nd leg) | Carmarthen Town | - | Tampere United | 1:3 (1:2) | ||
| 1st(1st leg): 17/06/2006 15:00 | 2nd (2nd leg): 24/06/2006 14:30 | Winner: Tampere United | ||||
| 1st(1st leg) | Shakter Karaganda | - | MTZ-Ripo | 1:5 (0:0) | ||
| 2nd (2nd leg) | MTZ-Ripo | - | Shakter Karaganda | 1:3 (0:2) | ||
| 1st(1st leg): 17/06/2006 15:30 | 2nd (2nd leg): 25/06/2006 14:00 | Winner: MTZ-Ripo | ||||
| 1st(1st leg) | Ethnikos Achna | - | FK Partizani | 4:2 (2:0) | ||
| 2nd (2nd leg) | FK Partizani | - | Ethnikos Achna | 2:1 (1:1) | ||
| 1st(1st leg): 17/06/2006 16:00 | 2nd (2nd leg): 24/06/2006 17:00 | Winner: Ethnikos Achna | ||||
| 1st(1st leg) | JK Narva Trans | - | Kalmar FF | 1:6 (1:1) | ||
| 2nd (2nd leg) | Kalmar FF | - | JK Narva Trans | 2:0 (2:0) | ||
| 1st(1st leg): 17/06/2006 16:00 | 2nd (2nd leg): 25/06/2006 13:00 | Winner: Kalmar FF | ||||
| 1st(1st leg) | Zrinjski Mostar | - | Marsaxlokk FC | 3:0 (3:0) | ||
| 2nd (2nd leg) | Marsaxlokk FC | - | Zrinjski Mostar | 1:1 (1:0) | ||
| 1st(1st leg): 17/06/2006 18:00 | 2nd (2nd leg): 25/06/2006 09:00 | Winner: Zrinjski Mostar | ||||
| 1st(1st leg) | Keflavík ÍF | - | Dungannon Swifts | 4:1 (1:0) | ||
| 2nd (2nd leg) | Dungannon Swifts | - | Keflavík ÍF | 0:0 (0:0) | ||
| 1st(1st leg): 17/06/2006 18:00 | 2nd (2nd leg): 24/06/2006 15:00 | Winner: Keflavík ÍF | ||||
| 1st(1st leg) | UE Sant Julià | - | NK Maribor | 0:3 (0:0) | ||
| 2nd (2nd leg) | NK Maribor | - | UE Sant Julià | 5:0 (2:0) | ||
| 1st(1st leg): 18/06/2006 11:00 | 2nd (2nd leg): 24/06/2006 18:00 | Winner: NK Maribor | ||||
| 1st(1st leg) | FC Kilikia | - | Dinamo Tbilisi | 1:5 (1:2) | ||
| 2nd (2nd leg) | Dinamo Tbilisi | - | FC Kilikia | 3:0 (2:0) | ||
| 1st(1st leg): 18/06/2006 15:00 | 2nd (2nd leg): 24/06/2006 16:00 | Winner: Dinamo Tbilisi | ||||
| 1st(1st leg) | FC Nitra | - | CS Grevenmacher | 6:2 (3:0) | ||
| 2nd (2nd leg) | CS Grevenmacher | - | FC Nitra | 0:6 (0:2) | ||
| 1st(1st leg): 18/06/2006 15:00 | 2nd (2nd leg): 25/06/2006 16:00 | Winner: FC Nitra | ||||
| 1st(1st leg) | FC Dinaburg | - | HB Tórshavn | 1:1 (1:0) | ||
| 2nd (2nd leg) | HB Tórshavn | - | FC Dinaburg | 0:1 (0:0) | ||
| 1st(1st leg): 18/06/2006 16:00 | 2nd (2nd leg): 24/06/2006 18:00 | Winner: FC Dinaburg | ||||
| 1st(1st leg) | FK Vetra | - | Shelbourne FC | 0:1 (0:1) | ||
| 2nd (2nd leg) | Shelbourne FC | - | FK Vetra | 4:0 (1:0) | ||
| 1st(1st leg): 18/06/2006 16:00 | 2nd (2nd leg): 24/06/2006 19:00 | Winner: Shelbourne FC | ||||
| 1st(1st leg) | FK Pobeda | - | Farul Constanța | 2:2 (0:1) | ||
| 2nd (2nd leg) | Farul Constanța | - | FK Pobeda | 2:0 (1:0) | ||
| 1st(1st leg): 18/06/2006 17:00 | 2nd (2nd leg): 25/06/2006 17:00 | Winner: Farul Constanța | ||||
