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| H | MFK Košice | - | Zlaté Moravce | 1:1 | ||
| R | Zlaté Moravce | - | MFK Košice | 3:5 i.E. | ||
| H: 21.10.2008 15:30 | R: 04.11.2008 16:00 | Sieger: MFK Košice | ||||
| H | MFK Dubnica | - | MFK Ružomberok | 0:1 | ||
| R | MFK Ružomberok | - | MFK Dubnica | 2:0 | ||
| H: 21.10.2008 17:30 | R: 04.11.2008 16:00 | Sieger: MFK Ružomberok | ||||
| H | FC Artmedia Petržalka | - | FC DAC 1904 | 0:0 | ||
| R | FC DAC 1904 | - | FC Artmedia Petržalka | 1:1 | ||
| H: 22.10.2008 14:00 | R: 04.11.2008 13:30 | Sieger: FC Artmedia Petržalka | ||||
| H | MŠK Žilina | - | Slovan Bratislava | 1:2 | ||
| R | Slovan Bratislava | - | MŠK Žilina | 0:0 | ||
| H: 04.03.2009 17:30 | R: 18.03.2009 17:00 | Sieger: Slovan Bratislava | ||||
