Raštikis married Elena Marija Smetonaitė, niece of Antanas Smetona, on 29 June 1929. She was a teacher and worked in Žiežmariai, Jonava, Kaunas. They had three daughters: Laima, Meilutė Marija, and Aldona. When Raštikis escaped to Germany in February 1941, he left his family behind. His wife was arrested on May 27 and interrogated in an attempt to find out his location. She was imprisoned in Kaunas Prison and awaited deportation to a gulag in Kazakhstan but was freed during the uprising of June 1941. Their daughters (at the time, ages 11, 4, and 1) and their maternal grandparents were deported to Kamen-na-Obi and Pavlovsk in Altai Krai during the June deportation. Other family members were deported as well, including two brothers of Smetonaitė and parents and three siblings of Raštikis, a total of 15 people. The youngest daughter Aldona and her grandfather died in exile.