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| 29/05/1999 | 16:30 | FBK Kaunas | - | FK Žalgiris B | 5:1 | |
| 30/05/1999 | 14:00 | Kauno Jegeriai | - | Lokomotyvas Kaunas | 3:1 | |
| 16:30 | FK Nevėžis | - | FK Atlantas | 0:2 | ||
| 16:30 | Inkaras Kaunas | - | FK Banga Gargždai | 2:0 | ||
| 16:30 | FK Ekranas | - | FK Dainava Alytus | 3:1 | ||
| 16:30 | FK Zalgiris | - | FK Kareda Siauliai | 1:0 |
| » Tables | Home | Away | First round | Second round |
| # | Team | M. | W | D | L | goals | Dif. | Pt. | |
|---|---|---|---|---|---|---|---|---|---|
| 1 |
|
FK Zalgiris | 22 | 16 | 6 | 0 | 63:8 | 55 | 56 |
| 2 |
|
FK Kareda Siauliai | 22 | 17 | 4 | 1 | 65:10 | 55 | 55 |
| 3 |
|
FBK Kaunas | 22 | 17 | 3 | 2 | 54:14 | 40 | 54 |
| 4 |
|
FK Ekranas | 22 | 11 | 6 | 5 | 43:20 | 23 | 38 |
| 5 |
|
Inkaras Kaunas | 22 | 10 | 4 | 8 | 32:26 | 6 | 34 |
| 6 |
|
FK Banga Gargždai | 22 | 7 | 5 | 10 | 18:28 | -10 | 26 |
| 7 |
|
FK Atlantas | 22 | 7 | 4 | 11 | 29:32 | -3 | 25 |
| 8 |
|
FK Nevėžis | 22 | 7 | 4 | 11 | 17:33 | -16 | 25 |
| 9 |
|
FK Dainava Alytus | 22 | 8 | 1 | 13 | 24:48 | -24 | 25 |
| 10 |
|
FK Žalgiris B | 22 | 6 | 3 | 13 | 24:58 | -34 | 21 |
| 11 |
|
Kauno Jegeriai | 22 | 6 | 2 | 14 | 21:46 | -25 | 20 |
| 12 |
|
Lokomotyvas Kaunas | 22 | 4 | 0 | 18 | 11:42 | -31 | 12 |
| 13 |
|
Mastis Telšiai | 12 | 1 | 0 | 11 | 4:40 | -36 | 3 |
| 14 |
|
FK Panerys | 0 | 0 | 0 | 0 | 0:0 | 0 | 0 |
