Above is a photo of the latest shinkansen bullet train which whizzes from Tokyo Station south to Osaka and sometimes all the way to Kyushu, the southern island. The shinkansen has all the conveniences of  travel by plane (hostesses, beer, meals--although you'd do better to buy a bento box lunch on from a stand on the platform-- 

--or even better from a stand in the basement of a department store). The shinkansen also goes north, and a tunnel to Hokkaido, the northern island, is now under construction. 

The latest shinkansen can hit 300 kph but the experimental maglev (magnetic levitation) variation, which cannot be bothered to make physical contact with the tracks, has hit 580 kph on test runs. The construction of the maglev is due to begin in 2014. 

Looking at a map of Japan's rail system, you would think the busiest train station would be Tokyo's Shinjuku Station, because Shinjuku is the starting point for trains funneling out all over the country not just north and south, just as Chicago is the busiest station in the US, but no, Tokyo Station is the busiest just because it is where the shinkansen starts. A 16-car Shinkansen train (inevitably, with all seats taken) leaves Tokyo Station every six minutes. As you can imagine, a certain discipline on the part of passengers is required for this schedule to work: when a soon-to-depart train opens its doors, its seats are all taken in, say, thirty seconds.