The Honzon of Enryaku-ji Temple is Yakushinyorai for Konpon Chu-do, the east tower of Enryaku-ji Temple, Shakanyorai for Tenhorin-do (Shaka-do) for the west tower and Kannon Bosatsu for the Yokokawa Chu-do in Enryaku-ji Temple Yokokawa.
延暦寺の本尊は、延暦寺東塔の根本中堂が薬師如来、延暦寺西塔の転法輪堂（釈迦堂）が釈迦如来、延暦寺横川の横川中堂は観音菩薩である。