By Train
Japan's railroads belong to JR (Japan Railways, a group of 6 nationwide companies) and other companies functioning in most megapolises. JR's service features renowned punctuality.
JR Shinkansen's most prestigious service is Japan's Bullet Train. It goes to Tokaido (Tokyo-Osaka), Sanyo (Fukuoka), Tohoku (Sendai) and Dzyoetsu (Niigata). Speed and comfort divide japan's trains into express (Hikari), semi-express (Kodama) and super express (Nozomi). Note that during transfers platform crossings can be very long and with several stair-wells. The rule of a thumb here is traveling light as there're no porters.
Ticket booking is not expensive but do it beforehand - around a month. The train fee depends on the distance and service option. In cities you can buy tickets for local lines in special slot machines at every station.
Train ticket
Kid Discount
Kids under 6 travel free, 6 to 11 - half-priced.
Tourist Discount
2 types of passes save on transport a lot - the nationwide Japan Rail Pass and Regional Railroad Passes only for regional lines.