The prison became more notorious during the Nazi occupation of Lithuania, when it was used by the Gestapo and Lithuanian Saugumas as a holding cell for thousands of Jews from the Vilna Ghetto and Poles, picked up in "łapankas" (roundups) in reprisals for actions by the Polish resistance. The majority were taken to the outskirts of Vilnius and executed at Ponary (Paneriai). When Soviets reoccupied the territory in 1944, the prison was returned to the NKVD who detained thousands of Polish activists and partisans of Armia Krajowa.