After touring through June 2003, Shutoku commissioned friend and former Number Girl drummer Ahito Inazawa, and after former Art-School bassist Hidekazu Hinata and guitarist Sō Yoshikane (formerly of Kicking the Lion) joined, the first incarnation of Zazen Boys was formed.

Using Shutoku's experimental mindset, influenced by Buddhist chants, hip-hop, funk, punk, and improvisational jazz, Zazen Boys achieved unexpected success.

During this time, the band released the single "Hantōmei Shōjo Kankei" (半透明少女関係), as well as the acclaimed live album Matsuri Session 2.26.2004 Tokyo.

Zazen Boys III featured the improvisational and experimental elements prominent in live performances, and was met with more mixed reactions from fans and critics than their prior releases.

Yaji and Kita: The Midnight Pilgrims (真夜中の弥次さん喜多さん, Mayonaka no Yaji-san Kita-san) was mostly original Zazen Boys tracks, and an alternate version of "Jimonjitō" (自問自答) was featured on the soundtrack to Canary (カナリア, Kanaria).