Building pagodas within the precincts of shrines was a common style of construction and the syncretic idea was accepted through the Middle ages down to the Meiji Restoration. Many of those pagodas, however, have been destroyed since then and up to the present day there remain only so pagodas affiliated with shrines. They are regarded as the evidence of the combination of Shintoism and Buddhism. Among them some were relocated from shrines to temples and others of which main idols were changed or even removed under the policy of the separation. There fore, they are now far from their original style of construction in those days. This paper assembles a lot of historical and religious facts and idols written about pagodas. Its aim is to try to frame an explanation about their idiosyncrasies by the comparison with the ones belonging to temples.