The present invention has been made to provide a technique capable of easily preventing the third party from misusing the data related to an individual physical feature in the case where individual authentication is performed based on the physical feature. An individual authentication system that authenticates an individual based on his or her physical feature comprises an authentication information acquisition section that acquires, at the time of authentication of an individual, information related to a state in which predetermined processing has applied to predetermined physical feature of the individual as authentication information for authentication determination; a registration information acquisition section that acquires the previously registered information related to a state in which predetermined processing has applied to predetermined individual physical feature as registration information for authentication; and an authentication determination section that determines authentication of the authentication information acquired by the authentication information acquisition section based on the registration information acquired by the registration information acquisition section.