After German invasion of Lithuania Yacob Gens headed the Jewish hospital in Vilnius before the formation of the ghetto in September 1941. He was appointed chief of the ghetto police force and in July 1942 the Germans appointed him head of the ghetto Jewish government. Gens and his policemen helped Germans in rounding up the Jews for deportation and execution in Ponary in October–December 1941 and in liquidating several smaller ghettos from late 1942 to early 1943.
From late October to December 1941, the ghetto was subject to Aktions, selections of people for deportation and execution in Ponary. Gens was afraid that the actions of the Germans would result in a widespread massacre. He persuaded the Gestapo to let the Jewish police round up the deportees. Gens, backed by the Jewish police force, was responsible for deciding who was to be sent for resettlement and execution. In October, this brought him into conflict with the ghetto’s rabbis, who argued Gens was acting against Jewish law. Gens disagreed and considered it to be lawful to sacrifice some people to save others.