After Rabbi Grodzinski's death in 1940, Rabbi Eigis was widely recognized as the senior rabbinic personality in Vilna and indeed in all of Lithuania. When the Second World War broke out, as a result of the Molotov–Ribbentrop Pact large numbers of yeshiva students streamed into Vilna from all corners of Lithuania. Rabbi Eigis worked tirelessly in support of these students, and many checks signed by him were sent by the "Joint". In 1941, at the age of 71, Rabbi Eigis was murdered by the Nazis. The date of his death in uncertain. There is testimony that he was killed on the 15th day of Elul (September 7); other reports state that he was killed 6 weeks earlier. The place of his death is also uncertain. Some reports indicate that he was killed in Vilna, while other reports indicate that he was first taken to Ponar, where he was killed by the Einsatzgruppen.