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| 1st(1st leg) | FK Sezimovo Ústí | - | Sigma Olomouc | 1:4 (1:2) | ||
| 2nd (2nd leg) | Sigma Olomouc | - | FK Sezimovo Ústí | 1:0 (1:0) | ||
| 1st(1st leg): 21/09/2011 15:30 | 2nd (2nd leg): 19/10/2011 14:00 | Winner: Sigma Olomouc | ||||
| 1st(1st leg) | SK Převýšov | - | Slovan Liberec | 1:4 (0:3) | ||
| 2nd (2nd leg) | Slovan Liberec | - | SK Převýšov | 2:1 (0:0) | ||
| 1st(1st leg): 21/09/2011 15:30 | 2nd (2nd leg): 26/10/2011 16:30 | Winner: Slovan Liberec | ||||
| 1st(1st leg) | FK Teplice | - | MFK Karviná | 1:0 (1:0) | ||
| 2nd (2nd leg) | MFK Karviná | - | FK Teplice | 1:3 (0:2) | ||
| 1st(1st leg): 21/09/2011 16:30 | 2nd (2nd leg): 19/10/2011 14:30 | Winner: FK Teplice | ||||
| 1st(1st leg) | FK Baumit Jablonec | - | FK Dukla Praha | 1:0 (1:0) | ||
| 2nd (2nd leg) | FK Dukla Praha | - | FK Baumit Jablonec | 3:2 (1:2) | ||
| 1st(1st leg): 28/09/2011 14:00 | 2nd (2nd leg): 19/10/2011 14:30 | Winner: FK Baumit Jablonec | ||||
| 1st(1st leg) | 1. FC Slovácko | - | Baník Ostrava | 1:1 (1:0) | ||
| 2nd (2nd leg) | Baník Ostrava | - | 1. FC Slovácko | 0:0 (0:0) | ||
| 1st(1st leg): 28/09/2011 17:00 | 2nd (2nd leg): 18/10/2011 16:00 | Winner: Baník Ostrava | ||||
| 1st(1st leg) | Dynamo České Budějovice | - | Viktoria Žižkov | 1:0 (0:0) | ||
| 2nd (2nd leg) | Viktoria Žižkov | - | Dynamo České Budějovice | 1:1 (1:0) | ||
| 1st(1st leg): 06/10/2011 17:00 | 2nd (2nd leg): 26/10/2011 16:30 | Winner: Dynamo České Budějovice | ||||
| 1st(1st leg) | 1. SC Znojmo | - | AC Sparta Praha | 1:4 (0:2) | ||
| 2nd (2nd leg) | AC Sparta Praha | - | 1. SC Znojmo | 3:0 (1:0) | ||
| 1st(1st leg): 19/10/2011 14:30 | 2nd (2nd leg): 16/11/2011 17:00 | Winner: AC Sparta Praha | ||||
| 1st(1st leg) | Viktoria Plzeň | - | FK Mladá Boleslav | 1:1 (0:0) | ||
| 2nd (2nd leg) | FK Mladá Boleslav | - | Viktoria Plzeň | 2:0 (1:0) | ||
| 1st(1st leg): 07/03/2012 16:15 | 2nd (2nd leg): 14/03/2012 14:30 | Winner: FK Mladá Boleslav | ||||
