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| 18.04.1999 | 16:30 | FC Boby-sport Brno | - | Sigma Olomouc | 0:0 (0:0) | |
| 16:30 | FC Dukla Pribram | - | FK Jablonec 97 | 1:1 (1:1) | ||
| 16:30 | SFC Opava | - | FC Petra Drnovice | 4:0 (0:0) | ||
| 16:30 | Slovan Liberec | - | FC Karviná | 3:1 (2:1) | ||
| 16:30 | FK Teplice | - | SK Hradec Králové | 4:0 (3:0) | ||
| 19.04.1999 | 16:25 | Chmel Blsany | - | Sparta Praga | 1:1 (1:0) | |
| 19:00 | Baník Ostrava | - | Viktoria Žižkov | 2:1 (0:0) | ||
| 19:00 | Slavia Praga | - | Viktoria Plzeň | 1:1 (1:1) |
| » Clasificación | En casa | Fuera de casa | 1.ª vuelta | 2.ª vuelta | 1.ª parte | 2.ª parte |
| # | Equipo | P | V | E | D | Goles | DG | Pun. | |
|---|---|---|---|---|---|---|---|---|---|
| 1 |
|
Sparta Praga | 23 | 13 | 8 | 2 | 44:15 | 29 | 47 |
| 2 |
|
FK Teplice | 23 | 11 | 6 | 6 | 42:27 | 15 | 39 |
| 3 |
|
Slavia Praga | 23 | 10 | 9 | 4 | 33:24 | 9 | 39 |
| 4 |
|
Sigma Olomouc | 23 | 9 | 9 | 5 | 29:25 | 4 | 36 |
| 5 |
|
FC Petra Drnovice | 23 | 9 | 8 | 6 | 31:30 | 1 | 35 |
| 6 |
|
Chmel Blsany | 23 | 10 | 3 | 10 | 35:32 | 3 | 33 |
| 7 |
|
Baník Ostrava | 23 | 6 | 13 | 4 | 28:21 | 7 | 31 |
| 8 |
|
FC Boby-sport Brno | 23 | 8 | 7 | 8 | 27:24 | 3 | 31 |
| 9 |
|
SFC Opava | 23 | 8 | 6 | 9 | 37:38 | -1 | 30 |
| 10 |
|
Slovan Liberec | 23 | 7 | 9 | 7 | 25:26 | -1 | 30 |
| 11 |
|
SK Hradec Králové | 23 | 8 | 5 | 10 | 28:31 | -3 | 29 |
| 12 |
|
FK Jablonec 97 | 23 | 7 | 7 | 9 | 28:32 | -4 | 28 |
| 13 |
|
Viktoria Žižkov | 23 | 7 | 4 | 12 | 22:38 | -16 | 25 |
| 14 |
|
FC Dukla Pribram | 23 | 5 | 8 | 10 | 19:29 | -10 | 23 |
| 15 |
|
Viktoria Plzeň | 23 | 5 | 6 | 12 | 18:35 | -17 | 21 |
| 16 |
|
FC Karviná | 23 | 5 | 4 | 14 | 20:39 | -19 | 19 |
