Japan is extremely fortunate to have an excellent high-speed train network - the shinkansen or 'bullet train' - which links all major regions and provides the visitor with fast affordable travel between each of the islands.
There is also an extensive inter-regional rail network which will take you through some of Japan's most stunning scenery at a more gentle pace. The rail network Japan Rail (JR) has now been split into seven regional networks - tickets fortunately are still valid throught all seven networks. The vast majority of all routes in Japan are owned by JR although some smaller ones operate local services in the major cities. Best value for those planning on travelling quite extensively through the country would be the excellent value Japan Rail Pass which can only be purchased by visitors.