The kondō, located side-by-side to the Pagoda in Sai-in, is another one of the oldest wood buildings extant in the world. The hall measures 18.5 meters by 15.2 meters.[8] The hall is two storied, with roofs curved in the corners but only the first story has a double roof (裳階 mokoshi). This was added later in the Nara period with extra posts to hold up the original first roof because it extended more than four meters past the building.[11]
Due to a fire incident that broke out on January 26, 1949, severe damage was caused to the building, mainly its first floor, and the murals. As a result of the restoration (completed in 1954), it is estimated that about fifteen to twenty percent of the original seventh century Kondo materials is left in the current building, while the charred members were carefully removed and rebuilt to a separate fireproof warehouse for future research.[5][10][12]
Through a recent dendrochronological analysis carried out using the materials preserved during the restorations done in the 1950s, it has turned out that some of them were felled prior to 670, suggesting a possibility that the current kondō was already under construction when "the fire in 670", as recorded in the Nihon Shoki, burned the former Wakakusa-garan down.[13]
The hall holds the famous Shaka Triad, together with a bronze Yakushi and Amida Nyorai statues, and other national treasures. The wall paintings shown today in the Kondō are a reproduction from 1967.