Prior to World War II, 4,500 Jews lived in Estonia half in the capital of Tallinn and the rest primarily in Tartu, Valga, Parnu, Narva, Giljandi, Rakevere, Voru and Nomme. In June 1940, the country was occupied by the Soviets who in mid-June 1941 deported some ten thousand Estonians, among them close to 500 Jews, to Siberia.

The Nazis invaded the Baltics in late June 1941, but by the time they reached Estonia several weeks later, most of the Jews had managed to flee the country, leaving approximately between nine hundred and fifty and one thousand Jews living in Estonia under the Nazi occupation. During the initial weeks of German rule, the Jews were immediately subjected to discriminatory measures and their property was confiscated. Shortly thereafter, executions of Jews were carried out by Sonderkommando 1A/ a subdivision of Einsatzgruppe A), headed by Dr. Martin Sandberger with the active assistance of Estonian Omakaitse (nationalist vigilantes) units and the Estonian Political Police. By the end of 1941 over 900 Jews had been murdered and Estonia was declared as the first Judenfrei (country free of Jews) at the infamous Wannsee conference held in Berlin on January 20, 1942 to discuss the implementation of the Final Solution.

Starting in the fall of 1942, tens to thousands of Jews from all over Europe were deported to concentration and forced labor camps in Estonia. Thus, for example, in 1942, several thousand Jews were sent from Theresienstadt to Jagala, a camp commanded by the Estonian Aleksander Laak. Three thousand of them, who were considered unfit for work, were then taken to Kalevi-Liiva, where they were murdered. When the Jagala camp was closed down in the spring of 1943, most of its inmates were killed.

In the fall of 1943 following the liquidation of the ghettos of Vilnius and Kaunas, several thousand Lithuanian Jews were sent to various forced labor camps in Estonia, the largest of which was at Vaivara. The inmates of these camps were forced to mine oil shale, dig anti-tank ditches, build bunkers and perform other military tasks. Those who became weak and could no longer work were executed; others died of hunger and disease.