2006 LFF Lyga 1 Lyga 1 Lyga

| Position_ | Club | Games_played | Wins | Draws | Loses | Goals_scored | Goals_conceded | Points |
|---|---|---|---|---|---|---|---|---|
| 10 | FC Vilnius-2 | 34 | 10 | 12 | 12 | 51 | 51 | 42 |
| 11 | Sūduva-2 Marijampolė | 34 | 12 | 5 | 17 | 44 | 65 | 41 |
| 12 | Banga Gargždai | 34 | 9 | 12 | 13 | 44 | 49 | 39 |
| 13 | KFK Šiauliai-2 | 34 | 11 | 6 | 17 | 51 | 69 | 39 |
| 14 | Vilkmergė Ukmergė | 34 | 10 | 8 | 16 | 40 | 51 | 38 |
| 15 | Lietava Jonava | 34 | 9 | 11 | 14 | 43 | 56 | 38 |
| 16 | Atletas Kaunas | 34 | 8 | 10 | 16 | 39 | 47 | 34 |
| 17 | Geležinis Vilkas Vilnius | 34 | 7 | 10 | 17 | 37 | 55 | 31 |