Born in Kōjimachi, Chiyoda, Tokyo Saneatsu was the eighth son of Viscount Mushanokōji Saneyo, who died when Saneatsu was age two.
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In 1918, Mushanokōji took the next step in the development of his philosophy by moving to the mountains of Kijō, Miyazaki in Kyūshū, and establishing a quasi-socialistic utopian commune, Atarashiki-mura (New Village) along vaguely Tolstoyan lines.
While Shiga was at the Gakushuin he became friends with Saneatsu Mushanokōji and Kinoshita Rigen.