Dowbor-Muśnicki had two sons, Giedymin and Olgierd, and two daughters, Janina and Agnieszka. Olgierd committed suicide before World War II, Giedymin emigrated to France in the 1930s, while both daughters were executed during World War II. Agnieszka, who was an active member of the Polish resistance, was arrested by the German occupiers, tortured in the Pawiak prison in Warsaw and then executed in the Palmiry mass murder site, while Janina Lewandowska was the only woman murdered by the Soviet NKVD during the Katyn massacre.