Japan Railways (JR) has a number of long-distance buses that are comfortable and inexpensive and also runs short-distance buses in some areas that have limited rail service. You can use Japan Rail Passes on some, but not all, of these buses. Japan Rail Passes are not accepted by private bus companies. Bus routes and schedules are constantly changing, but tourist information offices have up-to-date details. It's now possible to travel from Osaka to Tokyo for as little as ¥5,000 one way. Buses are generally modern and very comfortable, though overnight journeys are best avoided. Nearly all are now no-smoking. Daytime highway buses are often an excellent way to get to many interesting out-of-the-way destinations.

City buses, especially outside of Tokyo, are quite convenient, but be sure of your route and destination, because the bus driver probably won't speak English. Local buses usually have a set cost, anywhere from ¥100 to ¥200, depending on the route and municipality that operates them, in which case you typically board at the front of the bus and pay as you get on. On some buses cost is determined by the distance you travel. You take a ticket when you board at the rear door of the bus; it bears the number of the stop at which you boarded. Your fare depends on your destination and is indicated by a board at the front of the bus. Bus schedules can be hard to fathom if you don't read Japanese, however, so it's best to ask for help at a tourist information office. The Nihon Bus Association has information about routes and which companies have English Web information.

Reservations on long-distance routes are not always essential except at peak holiday times and on the most popular routes, like Tokyo–Osaka.

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