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What's the best website to find apartments for rent in Tokyo?

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1. That depends on your level of Japanese. When I was looking for apartments I liked yahoo Japan's apartment search feature. http://rent.realestate.yahoo.co.jp/05/ This link is to the apartment search. I find it best to search by area then by train station. You can say how far from the station you want your apartment to be. (Closer is more expensive of course) If you press on the second tab you will see areas of Kanto. Click on the area within Kanto you wish to look for apartments then you can look by stations(in Japanese, but it isn't too hard to find out the station your looking for over the internet) i.e. Ofuna equals 大船 If you want to look at another area outside of the Kanto area you have to know that area by its name and by its Kanji and click on the blue hyper link. Ex. Kansai equals 近畿 (This is the Kinki name for Kansai which is displayed for this website) Heres a list of areas of Japan click on that to find their Kanji names: http://en.wikipedia.org/wiki/Regions_of_Japan gaijinpot.com is foreigner friendly. But the selection is much more limited and much more expensive it seems. Gambatte mas!
2. There are many websites to look for an apartment in Japan. But if you can't read Japanese, you would have limited choice. You can use the site below. http://www.best-estate.jp/En/