The main religions in Japan are Shintoism and Buddhism, and many Japanese consider themselves believers in both. Most Japanese, for example, will marry in a Shinto ceremony, but when they die, they'll have a Buddhist funeral.
A native religion of Japan, Shintoism is the worship of ancestors and national heroes, as well as of all natural things, both animate and inanimate. These natural things are thought to embody gods and can be anyone or anything -- mountains, trees, the moon, stars, rivers, seas, fires, animals, rocks, even vegetables. Shintoism also embraces much of Confucianism, which entered Japan in the 5th century and stressed the importance of family and loyalty. There are no scriptures in Shintoism, nor any ordained code of morals or ethics.
The place of worship in Shintoism is called a jinja, or shrine. The most obvious sign of a shrine is its torii, an entrance gate, usually of wood, consisting of two tall poles topped with either one or two crossbeams. Another feature common to shrines is a water trough with communal cups, where the Japanese will wash their hands and sometimes rinse out their mouths. Purification and cleanliness are important in Shintoism because they show respect to the gods. At the shrine, worshippers will throw a few coins into a money box, clap their hands twice to get the gods' attention, and then bow their heads and pray for whatever they wish -- good health, protection, the safe delivery of a child, or a prosperous year. The most famous shrine in Tokyo is Meiji Shrine.
Founded in India in the 5th century, Buddhism came to Japan in the 6th century via China and Korea, bringing with it the concept of eternal life, and, by the end of the 6th century, it had gained such popularity that it was declared the state religion. Of the various Buddhist sects in Japan today, Zen Buddhism is probably the most well known in the West. Considered the most Japanese form of Buddhism, Zen is the practice of meditation and a strictly disciplined lifestyle to rid yourself of desire so that you can achieve enlightenment. There are no rites in Zen Buddhism, no dogmas, no theological conceptions of divinity. You do not analyze rationally, but rather know things intuitively. The strict and simple lifestyle of Zen appealed greatly to Japan's samurai warrior class, and many of Japan's arts, including the tea ceremony, arose from the practice of Zen.
Whereas Shintoists have shrines, Buddhists have temples, called otera. Instead of torii, temples will often have an entrance gate with a raised doorsill and heavy doors. Temples may also have a cemetery on their grounds (which Shinto shrines never have) as well as a pagoda. Tokyo's most famous temple is Sensoji Temple in Asakusa.