The Honden is treated as the most sacred place in Toshogu Shrine. The Honden consists of three rooms such as Gejin (Outer room), Naijin (Inner room) and Nainaijin (Inner room of the Naijin). Divine spirit is enshrined in the Nainaijin.

Sculpture of tapir is put on the door of the Honden. That door opens only in the festival. According to a Chinese poem, tapir eats iron and copper, which can be weapon. Therefore, the tapir was considered as a symbol of peace. 54 of 78 sculptures of tapirs are put on the Honden.