When Germany invaded Lithuania, 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. He attempted to secure better conditions in the ghetto and believed that it was possible to save some Jews by working for the Germans. 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. His policies, including the attempt to save some Jews by surrendering others for deportation or execution, continue to be a subject of debate and controversy.