One of the most horrific acts of genocide was the mass murder of Lithuanian Jews during the Nazi occupation. Approximately 190,000–200,000 of the roughly 210,000 Jews living in Lithuania in 1941 (95%) were killed. The killings were organized by the Nazi occupational administration, but some local residents and institutions were also involved in this crime. To persecute and exterminate the Jews, the Nazis employed Lithuanian administrative institutions that had been reestablished during and after the anti-Soviet uprising of June 1941, auxiliary police, and members of military–police formations. Initially, the Jews of Molėtai were isolated from Lithuanian population and ordered to relocate to a single quarter of the town. The ghetto was established on Dariaus ir Girėno Street and Kauno Street. It was guarded by members of the auxiliary police. Around July 1941, approximately 150 Jews from Molėtai were transported to Utena and placed in prison.
According to the report of Karl Jäger, leader of the German Security Police and SD (Sicherheitsdienst) in Lithuania, dated December 1, 1941, 3,782 Jews were shot (582 men, 1,731 women, 1,469 children) in Utena and Molėtai on August 29, 1941. According to the list compiled by G. Erslavaitė, on that day approximately 700 men, women and children were shot within a 1 km radius of Molėtai town center. Before the execution, the chief of Molėtai police station, Tomas Valionis, gathered about 30 workers and ordered them to dig a pit. On the eve of the execution, the Jews of Molėtai ghetto were driven into the synagogue. When the pits were ready, two German officers and a translator arrived. Members of the auxiliary police from Molėtai, Videniškis, and Bijutiškis, along with policemen, then escorted the Jews out of the synagogue and lined them up in columns. The condemned were marched to the execution site and shot. The execution was overseen by German officers and carried out by auxiliary police and policemen. Similar executions took place in Inturkė (Raša Manor), Joniškis, and Giedraičiai. The Jews of Balninkai were transported and shot in Pivonija Forest near Ukmergė.
Only a few managed to escape mass extermination - those who had been deported in June or had strong connections with local Lithuanians, or those brave enough to become rescuers of Jews.
