Validity of the Japan Rail Pass:
With a national Japan Rail Pass you can use all the trains on the JR railway network as well as JR Kyushu, JR Shikoku, JR West, JR Center, JR East and JR Hokkaido. Of course, you will have access to local and express trains but also to the fast bullet trains, 'Shinkansen', that connect most of the main cities in Japan.
The Japan Rail Pass is also valid for:
JR Bus: local JR Bus on a large number of lines
JR Ferry: JR Miyajima Ferry (Please note that the JR Hakata-Pusan ferry to Korea is not included)
Monorails: Tokyo Monorail connecting Haneda Airport to Hamamatsucho Station
The Japan Rail Pass is not valid for:
Private Rail Lines: With the Japan Rail Pass you do not, however, have access to other private rail lines apart from the JR line.If you wish, for instance, to take the Odakyu trains in the Kanto region or the Kintetsu trains in the Kansai region, you will have to buy regular tickets.
Super Express only shinkansen: You will not have access to the "Nozomi" and "Mizuho" Shinkansen that are the fastest ones on the Tokaido and Sanyo lines. Instead you will be able to take the 'Hikari' or 'Sakura' Shinkansen that serve the same routes even if they stop at more stations and take a little longer. However, there is not a very big difference; when travelling from Tokyo to Kyoto for instance there is only a 20 minutes difference between a "Hikari" and a "Nozomi" Shinkansen.
The Japan Rail Pass does not allow you to ride on subways or trams within cities. However most big cities have a few JR lines that you can use to go around (Osaka Loop or Kanjo line, Tokyo Yamanote line, etc…)
It is possible to take a night train with the Japan Rail Pass but the ticket is not valid for the sleeper wagon, private wagons in night trains, and special compartments for which you will have to pay an extra fee.
If, during your journey, your JR train uses another company’s tracks, and even if you hold a pass, you will have to pay a part of the trip. Payment can be made before boarding the train or on board. For instance, to go from Shinjuku or Ikebukuro to Nikko, there is a train that links these JR stations in Tokyo to the Tobu station in Nikko.
The train leaves the JR tracks at Kurihashi to use Tobu tracks. The trip itself cost 3 900 yen, but the Japan Rail Pass holders will only have to pay the portion between Kurihashi and Nikko, that is to say 1 560 yen.