The JR "Premium Dream" highway bus at Tokyo Station.
Willer Express highway buses are known for their distinctive pink colors.
Long-distance highway buses (高速バス kōsoku basu; ハイウェイバス haiwei basu) serve many of the inter-city routes covered by trains at significantly lower prices, but take much longer than the Shinkansen. Especially on the route between Tokyo and Kyoto-Osaka-Kobe triangle the high competition broke down the prices: as low as ¥3500 one-way. There is a multitude of operators, including Star Express and Willer Express, Kansai Bus, as well as companies of the JR group.
Note that your JR Rail Pass may be valid for JR buses (although choosing the bus instead of the Shinkansen or any Express train for the same trip would be a very awkward choice in terms of comfort and speed).
Many of these are overnight runs (夜行バス yakō basu), which allows you to save on a night's accommodation. It may be worth it to pay a premium to get a better seat; remember that it is less fun to sightsee after a sleepless night. Look out for ３列シート sanretsu shiito, meaning there are only three seats per row instead of four. Intercity buses usually have significantly less legroom than intercity trains, so passengers over about 175 cm may be uncomfortable.
A few buses offer more luxurious Premium Seating. These seats are bigger, offer more legroom, and are exclusive, with only a few seats allocated to an entire bus. Examples include the first floor seating on JR Bus' Premium Dream service, and Cocoon seats on Willer Express services. Expect to pay around �10000 for such a seat on an overnight service between Tokyo and Kansai.
Like their railroad counterparts, a few overnight buses can be used only by women (an example is the Ladies Dream Osaka bus service between Tokyo and Osaka).
The Most Frequently Asked Travel Questions about Japan
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Japan Travel Guide from Wikitravel. Many thanks to all Wikitravel contributors. Text is available under Creative Commons Attribution-ShareAlike 3.0, images are available under various licenses, see each image for details.
