2006 LFF Lyga 1 Lyga 1 Lyga

| Position_ | Club | Games_played | Wins | Draws | Loses | Goals_scored | Goals_conceded | Points |
|---|---|---|---|---|---|---|---|---|
| 1 | Kauno Jėgeriai | 34 | 23 | 7 | 4 | 75 | 28 | 76 |
| 2 | Alytis Alytus | 34 | 22 | 7 | 5 | 69 | 23 | 73 |
| 3 | Atlantas-2 Klaipėda | 34 | 19 | 8 | 7 | 70 | 35 | 65 |
| 4 | Kruoja Pakruojis | 34 | 17 | 9 | 8 | 71 | 36 | 60 |
| 5 | Rodiklis Kaunas | 34 | 17 | 7 | 10 | 70 | 44 | 58 |
| 6 | Vėtra-2 Vilnius | 34 | 15 | 7 | 12 | 64 | 40 | 52 |
| 7 | Interas Visaginas | 34 | 15 | 7 | 12 | 59 | 47 | 52 |
| 8 | LKKA ir Teledema Kaunas | 34 | 15 | 7 | 12 | 50 | 53 | 52 |
| 9 | Žalgiris-2 Vilnius | 34 | 13 | 7 | 14 | 42 | 42 | 46 |