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| 01/05/1999 | 14:00 | FK Banga Gargždai | - | FK Žalgiris B | 1:1 | |
| 14:00 | Kauno Jegeriai | - | Inkaras Kaunas | 0:4 | ||
| 02/05/1999 | 13:00 | FK Kareda Siauliai | - | Lokomotyvas Kaunas | 7:0 | |
| 14:00 | FBK Kaunas | - | FK Ekranas | 2:1 | ||
| 15:00 | FK Nevėžis | - | FK Dainava Alytus | 0:1 | ||
| 15:00 | FK Zalgiris | - | FK Atlantas | 2:0 |
| » Tables | Home | Away | First round | Second round |
| # | Team | M. | W | D | L | goals | Dif. | Pt. | |
|---|---|---|---|---|---|---|---|---|---|
| 1 |
|
FK Zalgiris | 17 | 14 | 3 | 0 | 59:6 | 53 | 47 |
| 2 |
|
FBK Kaunas | 17 | 15 | 2 | 0 | 46:8 | 38 | 47 |
| 3 |
|
FK Kareda Siauliai | 17 | 14 | 3 | 0 | 56:7 | 49 | 45 |
| 4 |
|
FK Ekranas | 17 | 8 | 4 | 5 | 34:17 | 17 | 27 |
| 5 |
|
Inkaras Kaunas | 17 | 8 | 3 | 6 | 26:18 | 8 | 27 |
| 6 |
|
FK Atlantas | 17 | 6 | 3 | 8 | 24:24 | 0 | 21 |
| 7 |
|
FK Dainava Alytus | 17 | 6 | 1 | 10 | 18:41 | -23 | 19 |
| 8 |
|
FK Nevėžis | 17 | 5 | 3 | 9 | 13:28 | -15 | 18 |
| 9 |
|
FK Žalgiris B | 17 | 5 | 1 | 11 | 16:47 | -31 | 16 |
| 10 |
|
FK Banga Gargždai | 17 | 3 | 5 | 9 | 11:24 | -13 | 14 |
| 11 |
|
Kauno Jegeriai | 17 | 4 | 2 | 11 | 12:38 | -26 | 14 |
| 12 |
|
Lokomotyvas Kaunas | 17 | 4 | 0 | 13 | 10:31 | -21 | 12 |
| 13 |
|
Mastis Telšiai | 12 | 1 | 0 | 11 | 4:40 | -36 | 3 |
| 14 |
|
FK Panerys | 0 | 0 | 0 | 0 | 0:0 | 0 | 0 |
