 Iltis fathered four sons, Frank and Michael by his first wife, Grace Schaffel, and David and John by his second wife, Carolyn Merchant.He and his third wife, Sharyn Wisniewski (1950–2013), endowed a fund at the University of Wisconsin–Madison Department of Botany to support graduate student fieldwork in plant systematics.He remained active up to his death in Madison at age 91 from complications of vascular disease.