This article traces changes in the theory of syncretic faith (shinbutsu shugo) in medieval Japan. The idea of gods have evolved with the penetration of the theory of "original substances and manifest traces" (honji suijaku) through the Middle Ages, but the biggest change was that it came to be thought that gods were in our hearts. It was thought that honji suijaku meant that Buddha appeared as inner gods, for example our essential evilness was considered to appear symbolically as the body of a snake. This indicates that Medieval Shinto was a positive faith offering relief from sin. However, the idea of inner evil gradually recedes in the latter period of the Middle Ages, and this leads to the foundation of early modern Shinto.