The climate in Japan resembles that of the east coast of the United States, and the best time to visit Tokyo is spring and fall. Spring is beautiful and much celebrated. The first harbingers are plum blossoms in early March, followed by the sakura (cherry blossoms) in early April, and festivals celebrating springtime last until June. Fall has clear blue skies and glorious foliage. Occasionally a few typhoons occur in early fall, but the storms are usually harmless and are as quick to disappear as they are to appear, leaving behind crystal clear skies.
Summer in Tokyo can be unbearably hot in part due to the "heat island" effect, which occurs when exhausts from buildings in the crowded center affect the weather generally, raising the temperature and humidity to subtropical levels. It's also the rainy season, so avoid July and August if at all possible. Winter is gray and chilly. Western Japan receives plenty of snow, though Tokyo and other areas along the Pacific Coast don't get much at all.
For the most part, Japanese cannot choose when they want to take their vacations and tend to do so on the same holiday dates. So, to avoid stifling crowds and long waits, do not plan a trip to Tokyo for the few days before and after New Year's; Golden Week, which follows Greenery Day (April 29); and the Obon Festival (August 13 through 16). Airports, planes, trains, and hotels are usually booked far in advance for these dates and prices increase significantly. Also, many businesses, shops, and restaurants are closed during these holidays (except for tourist attractions outside the city).
