The defining features of a shrine are the kami it enshrines and the shintai (or go-shintai if the honorific prefix go- is used) that houses it. While the name literally means "body of a kami", shintai are physical objects worshiped at or near Shinto shrines because a kami is believed to reside in them. In spite of what their name may suggest, shintai are not themselves part of kami, but rather just symbolic repositories which make them accessible to human beings for worship. It is said therefore that the kami inhabits them. Shintai are also of necessity yorishiro, that is objects by their very nature capable of attracting kami.
The most common shintai are man-made objects like mirrors, swords, jewels (for example comma-shaped stones called magatama), gohei (wands used during religious rites), and sculptures of kami called shinzō (神像?), but they can be also natural objects such as rocks, mountains, trees and waterfalls. Mountains were among the first, and are still among the most important, shintai, and are worshiped at several famous shrines. A mountain believed to house a kami, as for example Mount Fuji or Mount Miwa, is called a shintai-zan (ja:神体山?). In the case of a man-made shintai, a kami must be invited to reside in it (see the next subsection, Kanjō).
The founding of a new shrine requires the presence of either a pre-existing, naturally occurring shintai (for example a rock or waterfall housing a local kami), or of an artificial one, which must therefore be procured or made to the purpose. An example of the first case are the Nachi Falls, worshiped at Hiryū Shrine near Kumano Nachi Taisha and believed to be inhabited by a kami called Hiryū Gongen.
The first duty of a shrine is to house and protect its shintai and the kami which inhabits it. If a shrine has more than one building, the one containing the shintai is called honden; because it is meant for the exclusive use of the kami, it is always closed to the public and is not used for prayer or religious ceremonies. The shintai leaves the honden only during festivals (matsuri), when it is put in portable shrines (mikoshi) and carried around the streets among the faithful. The portable shrine is used to physically protect the shintai and to hide it from sight.
Read more about this topic: Shinto Shrines