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| 06.04.2013 | 10:15 | FK Ústí nad Labem | - | FK Pardubice | 1:0 (0:0) | |
| 15:00 | FK MAS Táborsko | - | MFK Karviná | 1:3 (0:0) | ||
| 16:00 | FK Baník Most | - | Bohemians Praha | 1:0 (0:0) | ||
| 16:30 | FC Graffin Vlašim | - | FC Fastav Zlín | 2:2 (0:1) | ||
| 07.04.2013 | 10:15 | Viktoria Žižkov | - | FK Baník Sokolov | 1:2 (0:2) | |
| 16:30 | FK Varnsdorf | - | Bohemians 1905 | 0:2 (0:2) | ||
| 16:30 | FK Čáslav | - | 1. HFK Olomouc | 3:0 (1:0) | ||
| 24.04.2013 | 18:00 | SFC Opava | - | 1. SC Znojmo | 0:1 (0:0) |
| » Classement | équipe recevante | à l'extérieur | Premier tour | Second tour |
| # | Équipe | M. | G. | N. | P. | Buts | Diff. | Pts. | |
|---|---|---|---|---|---|---|---|---|---|
| 1 |
|
Bohemians 1905 | 22 | 12 | 6 | 4 | 34:17 | 17 | 42 |
| 2 |
|
1. SC Znojmo | 22 | 12 | 5 | 5 | 29:19 | 10 | 41 |
| 3 |
|
FK Baník Sokolov | 22 | 10 | 7 | 5 | 28:19 | 9 | 37 |
| 4 |
|
1. HFK Olomouc | 22 | 11 | 4 | 7 | 30:27 | 3 | 37 |
| 5 |
|
FK Varnsdorf | 22 | 11 | 3 | 8 | 37:25 | 12 | 36 |
| 6 |
|
FC Fastav Zlín | 22 | 10 | 4 | 8 | 35:28 | 7 | 34 |
| 7 |
|
FK Pardubice | 22 | 10 | 3 | 9 | 34:24 | 10 | 33 |
| 8 |
|
Viktoria Žižkov | 22 | 9 | 6 | 7 | 26:20 | 6 | 33 |
| 9 |
|
FK Ústí nad Labem | 22 | 9 | 6 | 7 | 24:29 | -5 | 33 |
| 10 |
|
MFK Karviná | 22 | 6 | 8 | 8 | 24:33 | -9 | 26 |
| 11 |
|
FK Baník Most | 22 | 6 | 6 | 10 | 24:36 | -12 | 24 |
| 12 |
|
Bohemians Praha | 22 | 3 | 14 | 5 | 18:20 | -2 | 23 |
| 13 |
|
FC Graffin Vlašim | 22 | 6 | 5 | 11 | 28:39 | -11 | 23 |
| 14 |
|
FK MAS Táborsko | 22 | 4 | 8 | 10 | 20:31 | -11 | 20 |
| 15 |
|
FK Čáslav | 22 | 4 | 7 | 11 | 16:25 | -9 | 19 |
| 16 |
|
SFC Opava | 22 | 4 | 6 | 12 | 20:35 | -15 | 18 |
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