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| 20/04/2013 | 09:15 | Bohemians Praha | - | 1. HFK Olomouc | 1:1 (0:0) | |
| 09:15 | FK Ústí nad Labem | - | FK Baník Sokolov | 1:2 (1:2) | ||
| 14:00 | FK MAS Táborsko | - | 1. SC Znojmo | 0:0 (0:0) | ||
| 15:30 | FK Baník Most | - | FK Pardubice | 1:2 (0:1) | ||
| 16:00 | FC Graffin Vlašim | - | Bohemians 1905 | 0:0 (0:0) | ||
| 21/04/2013 | 09:15 | Viktoria Žižkov | - | MFK Karviná | 3:1 (2:1) | |
| 16:00 | FK Čáslav | - | FC Fastav Zlín | 1:3 (1:2) | ||
| 16:00 | FK Varnsdorf | - | SFC Opava | 2:0 (2:0) |
| » Tables | Home | Away | First round | Second round |
| # | Team | M. | W | D | L | goals | Dif. | Pt. | |
|---|---|---|---|---|---|---|---|---|---|
| 1 |
|
Bohemians 1905 | 24 | 13 | 7 | 4 | 37:17 | 20 | 46 |
| 2 |
|
1. SC Znojmo | 24 | 13 | 6 | 5 | 35:20 | 15 | 45 |
| 3 |
|
FK Baník Sokolov | 24 | 12 | 7 | 5 | 32:20 | 12 | 43 |
| 4 |
|
FC Fastav Zlín | 24 | 12 | 4 | 8 | 41:29 | 12 | 40 |
| 5 |
|
FK Varnsdorf | 24 | 12 | 3 | 9 | 39:28 | 11 | 39 |
| 6 |
|
1. HFK Olomouc | 24 | 11 | 5 | 8 | 32:31 | 1 | 38 |
| 7 |
|
FK Pardubice | 24 | 11 | 3 | 10 | 36:26 | 10 | 36 |
| 8 |
|
Viktoria Žižkov | 24 | 10 | 6 | 8 | 29:23 | 6 | 36 |
| 9 |
|
FK Ústí nad Labem | 24 | 10 | 6 | 8 | 28:32 | -4 | 36 |
| 10 |
|
MFK Karviná | 24 | 7 | 8 | 9 | 30:38 | -8 | 29 |
| 11 |
|
Bohemians Praha | 24 | 4 | 15 | 5 | 21:21 | 0 | 27 |
| 12 |
|
FK MAS Táborsko | 24 | 5 | 9 | 10 | 21:31 | -10 | 24 |
| 13 |
|
FK Baník Most | 24 | 6 | 6 | 12 | 25:40 | -15 | 24 |
| 14 |
|
FC Graffin Vlašim | 24 | 6 | 6 | 12 | 29:45 | -16 | 24 |
| 15 |
|
FK Čáslav | 24 | 4 | 7 | 13 | 17:31 | -14 | 19 |
| 16 |
|
SFC Opava | 24 | 4 | 6 | 14 | 22:42 | -20 | 18 |
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