One theory says that originally the Chotei (Imperial Court) conducted hohei (offering a wand with hemp and paper streamers to a Shinto god) at the three shrines, namely Ise Jingu Shrine, Iwashimizu Hachiman-gu Shrine, and Kamo-jinja Shrine, which has spread to the general public as a custom to visit three shrines.
元々朝廷が伊勢神宮、石清水八幡宮、賀茂神社の三社に奉幣し、これが庶民にも三社詣でる風習として広まった、という説。