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In Tokyo, it is very popular to run around the Imperial Palace or the Akasaka Palace (home of visiting foreign dignitaries). Both places however are surrounded by busy streets which makes it almost unhealthy to run at any time except maybe very early morning. The best places in my mind are undoubtedly the many parks such as Ueno and Yoyogi, which are the two biggest. Ueno is particularly popular with Tokyo runners. Another place to consider would be Aoyama Cemetery. Nice and quiet place!