Intelligent Systems grew out of Nintendo's R&D1;, Nintendo's first internal game development studio. Intelligent Systems team members worked on such beloved classics as Metroid, Fire Emblem, ExciteBike and Kid Icarus, as well as soft- and hardware tools like the Wide Boy.

Headed up by Gumpei Yokoi, the division also created and developed for the Game Boy. In 1986, members of R&D1; formed Intelligent Systems. Whereas R&D1; (which later merged into EAD) concentrated on Game Boy development, Intelligent Systems went on to create the Super Famicom (SNES) hit series Fire Emblem.

During the SNES days, Intelligent Systems was internally split into different teams: Team Deer Force, responsible for Super Metroid's programming, Team Battle Clash (Super Scope Titles), Team Emblem (Fire Emblem) and Team Shikamaru (Mario Paint).

After working on Paper Mario (N64), Intelligent Systems branched out to Game Boy Advance and GameCube development.