Mitsukuri and his wife Mitsu (a daughter of 進十六) had two sons and three daughters: the first son, Shukichi MITSUKURI, was a chemist with a Doctorate of Science, and also was a composer; the second son, Yosuke, was known as an industrial technician.
みつ夫人（進十六の娘）との間に2男3女をもうけ、長男・箕作秋吉は理学博士号を持つ化学者であると同時に作曲家としても活躍し、次男・洋輔は工業技術家として知られた。