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A great place to run in Tokyo is alongside the Tama River in Setagaya-ku. You can reach it by driving towards Setagaya by way of Meguro-dori which actually ends at the river or by train by taking the Shin-Tamagawa line to Futako Tamagawa Station. Once you are at the river you can run endless miles on both sides of it, without the hassle of cars and pollution. You actually feel in another world, sorrounded by nature and fresh air.