|A Lyga||1 Lyga||Farm team league|
|2 Lyga zone South||zone North||zone East||zone West|
This is a list of football (soccer) clubs in Lithuania that played in A Lyga (the highest league), Lyga 1 (second-tier league), or Lyga 2 (third-tier) from 2003 to 2007. In 2007 a separate league for Reserve teams and feeder teams was created.
|Club name||Location||Place (2003)||League (2003)||Place (2004)||League (2004)||Place (2005)||League (2005)||Place (2006)||League (2006)||Place (2007)||League (2007)||Notes|
|Akmenė-Šiauliai-3||Naujoji Akmenė||10||L2N||10||L2N||8||L2N||Akmenė became the second farm team of FK Šiauliai in 2006|
|Alytis||Alytus||1||L2S||14||L1||1||L1||2||L1||1||L1||Home stadium: Alytus Stadium|
|Alytis-2||Alytus||4||L2S||3||L2S||2||L2S||Feeder team for Alytis|
|Atlantas-2||Klaipėda||1||L2W||4||L2W||1||L2W||3||L1||8||FT||Feeder team for Atlantas|
|Atletas-2||Kaunas||6||L2S||Feeder team for Atletas|
|Babrungas-2||Plungė||8||L2W||8||L2N||12||L2W||Feeder team for Babrungas|
|Bangelė||Gargždai||7||L2W||6||L2N||Feeder team for Banga; also known as Banga-2|
|Ekranas-2||Panevėžys||10||L1||11||L1||2||L2N||1||L2N||5||FT||Feeder team for Ekranas|
|FBK Kaunas-2||Kaunas||4||FT||Feeder team for FBK Kaunas; also known as Žalgiris-2 Kaunas|
|FK Mažeikiai||Mažeikiai||1||L2N||6||L1||4||L2N||3||L2N||4||L2N||Before 2003 known as Nafta Mažeikiai|
|FK Prienai||Prienai||9||L2S||13||L2S||12||L2S||6||L2S||9||L2S||Before 2006 known as Valdima Prienai|
|FK Šiauliai||Šiauliai||8||LA||1||L1||9||LA||8||LA||8||LA||Known as Sakalas Šiauliai (2001-2003)|
|FK Šiauliai-2||Šiauliai||6||L2N||6||L1||13||L1||9||FT||Feeder team for FK Šiauliai|
|FK Šilutė-2||Šilutė||4||L2W||1||L2W||2||L2W||1||L2W||6||FT||Feeder team for FK Šilutė|
|FK Vilnius||Vilnius||7||LA||8||LA||5||LA||7||LA||7||LA||Before 2004 known as Šviesa Vilnius|
|FK Vilnius-2||Vilnius||1||L2E||17||L1||15||L1||10||L1||7||FT||Feeder team for FK Vilnius; also known as Šviesa-2|
|Glestum-2||Klaipėda||9||L2N||Feeder team for Glestrum|
|GMT-83||Gargždai||6||L2W||Merged with Banga|
|Interas-2||Visaginas||10||FT||Feeder team for Interas|
|Kareda||Kaunas||14||L1||Moved from Šiauliai to Kaunas in 2000; dissolved in 2003|
|Kauno Jėgeriai||Kaunas||7||L1||2||L1||2||L1||1||L1||8||L1||Former feeder team for FBK Kaunas|
|LKKA ir Teledema||Kaunas||12||L1||7||L1||6||L1||7||L1||Sponsored by Lithuanian Academy of Physical Education|
|Nevėžis-2||Kėdainiai||2||L2S||8||L2S||10||L2S||7||L2S||13||L2S||Feeder team for Nevėžis|
|Piritas||Klaipėda||4||L1||9||L1||18||L1||9||L2W||Until 2006 known as Rodovitas|
|Polonija||Vilnius||1||L1||5||L1||4||L1||Run by Polish minority in Lithuania|
|Polonija-2||Vilnius||3||L2E||Feeder team for Polonija|
|Šilas||Kazlų Rūda||5||L2S||14||L2S||9||L2S||Changed name to Kvintencija-Šilas in 2006|
|Sūduva-2||Marijampolė||4||L2S||1||L2S||8||L1||11||L1||3||FT||Farm team for Sūduva|
|Švyturys||Klaipėda||2||L2W||2||L2W||13||L1||4||L2W||Until 2006 known as Kuršiai Neringa|
|Tauras ERRA||Tauragė||18||L1||16||L1||17||L1||3||L2W||11||L1||Known as Tauras before 2005|
|Vėtra||Vilnius||3||LA||5||LA||4||LA||3||LA||5||LA||In 2004 moved from Rūdiškės to Vilnius|
|Vėtra-2||Vilnius||5||L1||10||L1||3||L1||7||L1||2||FT||In 2004 moved from Rūdiškės to Vilnius; feeder team for Vėtra|
|Vėtra-89||Vilnius||5||L2S||Youth team for Vėtra|
|VPU Šviesa||Vilnius||14||L2S||Sponsored by Vilnius Pedagogical University|
|Žalgiris-2||Vilnius||12||L1||9||L1||1||FT||Farm team for Žalgiris|
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