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| 23/09/2008 | 15:30 | Fotbal Fulnek | - | Viktoria Plzeň | 0:2 | |
| 24/09/2008 | 15:30 | FK Ústí nad Labem | - | SK Kladno | 1:2 | |
| 15:30 | SK Uničov | - | FK Baumit Jablonec | 0:2 | ||
| 15:30 | FK Mutenice | - | Dynamo České Budějovice | 4:0 | ||
| 15:30 | SFC Opava | - | Slovan Liberec | 3:5 pso | ||
| 15:30 | MFK Karviná | - | Sigma Olomouc | 0:2 | ||
| 15:30 | Nobica Boskovice | - | Baník Ostrava | 0:7 | ||
| 15:30 | Olympia Hradec Králové | - | Bohemians Praha | 1:5 | ||
| 15:30 | FK Sezimovo Ústí | - | FK Baník Sokolov | 2:0 | ||
| 15:45 | FC Velim | - | SK Hlavice | 2:4 pso | ||
| 25/09/2008 | 15:30 | SK Votice | - | Slavia Praha | 1:2 | |
| 15:30 | Fotbal Frýdek-Místek | - | AC Sparta Praha | 1:4 pso | ||
| 30/09/2008 | 15:30 | Slavoj Vyšehrad | - | FC Hradec Králové | 0:2 | |
| 01/10/2008 | 15:00 | FC Písek | - | FK Teplice | 1:4 | |
| 17:00 | 1. FC Slovácko | - | 1. FC Brno | 4:3 pso | ||
| 07/10/2008 | 16:00 | Vysočina Jihlava | - | Tescoma Zlín | 2:4 pso |
