In the medieval period, various schools such as Ise Shinto and Yoshida Shinto established a complicated framework of theories such as Han honji suijaku setsu (the theory of converse origin and traces.)
中世には伊勢神道をはじめとして吉田神道などの諸派が反本地垂迹説など複雑な教理の大系をつくりあげてゆく。