The honden main shrine is the most sacred building in the Meiji Jingu shrine. The inner sanctum is at the heart of the main shrine, and is where the kami deities are enshrined. Many rituals are carried out daily inside the inner sanctum, including the offering of sacred food and prayers known as onikkusai, which is held at 8 a.m. and 2 p.m. every day.
The honden and the buildings around it are of Japanese cypress wood, while the roofs are clad with copper. The timber used is mainly from Kiso in Nagano Prefecture, a district famous for the cultivation of large Japanese cypress trees.
The main shrine is built in the nagare zukuri style, which is a popular style of shrine architecture found throughout Japan. In this style of architecture, the roof at the front of the shrine is much longer than at the back, as the front roof is extended to cover the steps up to the shrine building.
The structures of the honden include the noritoden or Shinto prayer recital hall, the naihaiden, inner shrine hall, and the gehaiden, or outer shrine hall. The gehaiden is at the front of the shrine, and is where visitors pray.
The main shrine building was originally completed in 1920, but was burnt down during the air raids at the end of World War II. The present building was completed in 1958. For reasons of fire proofing, copper was used for the roofs of the new buildings rather than the tree bark which had been used for the original buildings.