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| 1st(1st leg) | MFK Košice | - | Zlaté Moravce | 1:1 | ||
| 2nd (2nd leg) | Zlaté Moravce | - | MFK Košice | 3:5 pso | ||
| 1st(1st leg): 21/10/2008 14:30 | 2nd (2nd leg): 04/11/2008 15:00 | Winner: MFK Košice | ||||
| 1st(1st leg) | MFK Dubnica | - | MFK Ružomberok | 0:1 | ||
| 2nd (2nd leg) | MFK Ružomberok | - | MFK Dubnica | 2:0 | ||
| 1st(1st leg): 21/10/2008 16:30 | 2nd (2nd leg): 04/11/2008 15:00 | Winner: MFK Ružomberok | ||||
| 1st(1st leg) | FC Artmedia Petržalka | - | FC DAC 1904 | 0:0 | ||
| 2nd (2nd leg) | FC DAC 1904 | - | FC Artmedia Petržalka | 1:1 | ||
| 1st(1st leg): 22/10/2008 13:00 | 2nd (2nd leg): 04/11/2008 12:30 | Winner: FC Artmedia Petržalka | ||||
| 1st(1st leg) | MŠK Žilina | - | Slovan Bratislava | 1:2 | ||
| 2nd (2nd leg) | Slovan Bratislava | - | MŠK Žilina | 0:0 | ||
| 1st(1st leg): 04/03/2009 16:30 | 2nd (2nd leg): 18/03/2009 16:00 | Winner: Slovan Bratislava | ||||
