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| 22/05/1999 | 14:00 | FK Žalgiris B | - | FK Atlantas | 2:2 | |
| 16:00 | Kauno Jegeriai | - | FK Zalgiris | 0:1 | ||
| 16:30 | Lokomotyvas Kaunas | - | FK Nevėžis | 0:1 | ||
| 16:30 | FK Dainava Alytus | - | Inkaras Kaunas | 1:2 | ||
| 16:30 | FK Banga Gargždai | - | FBK Kaunas | 2:1 | ||
| 23/05/1999 | 13:00 | FK Kareda Siauliai | - | FK Ekranas | 1:1 |
| » Tables | Home | Away | First round | Second round |
| # | Team | M. | W | D | L | goals | Dif. | Pt. | |
|---|---|---|---|---|---|---|---|---|---|
| 1 |
|
FK Kareda Siauliai | 21 | 17 | 4 | 0 | 65:9 | 56 | 55 |
| 2 |
|
FK Zalgiris | 21 | 15 | 6 | 0 | 62:8 | 54 | 53 |
| 3 |
|
FBK Kaunas | 21 | 16 | 3 | 2 | 49:13 | 36 | 51 |
| 4 |
|
FK Ekranas | 21 | 10 | 6 | 5 | 40:19 | 21 | 35 |
| 5 |
|
Inkaras Kaunas | 21 | 9 | 4 | 8 | 30:26 | 4 | 31 |
| 6 |
|
FK Banga Gargždai | 21 | 7 | 5 | 9 | 18:26 | -8 | 26 |
| 7 |
|
FK Nevėžis | 21 | 7 | 4 | 10 | 17:31 | -14 | 25 |
| 8 |
|
FK Dainava Alytus | 21 | 8 | 1 | 12 | 23:45 | -22 | 25 |
| 9 |
|
FK Atlantas | 21 | 6 | 4 | 11 | 27:32 | -5 | 22 |
| 10 |
|
FK Žalgiris B | 21 | 6 | 3 | 12 | 23:53 | -30 | 21 |
| 11 |
|
Kauno Jegeriai | 21 | 5 | 2 | 14 | 18:45 | -27 | 17 |
| 12 |
|
Lokomotyvas Kaunas | 21 | 4 | 0 | 17 | 10:39 | -29 | 12 |
| 13 |
|
Mastis Telšiai | 12 | 1 | 0 | 11 | 4:40 | -36 | 3 |
| 14 |
|
FK Panerys | 0 | 0 | 0 | 0 | 0:0 | 0 | 0 |
