Before World War II, 135,000 Jews lived in Slovakia. Some emigrated before the war, but most were killed in deportation. After the Slovakia Republic proclaimed its independence in March 1939 under the protection of Nazi Germany, Slovakia began a series of measures aimed against the Jews in the country, first excluding them from the military and government positions. The Hlinka's Guard began to attack Jews, and the "Jewish Code" was passed in September 1941. Resembling the Nuremberg Laws, the Code required that Jews wear a yellow armband, and were banned from intermarriage and many jobs.

The pro-Nazi regime of President Jozef Tiso, a Catholic priest, agreed to deport its Jews as part of the Nazi Final Solution. In October 1941, the Jews were to be expelled from Bratislava. The Slovak capital had a Jewish population of about 15,000, but only 10,000 Jews were subject to expulsion. The remaining 5,000 comprising holders of work permits, government employees, entrepreneurs, and professionals (with their families) were permitted to stay. All others were scheduled for deportation to provincial towns, labor camps, and labor centers.  On October 28, 1941, the first transport of 238 Jews left Bratislava, and during the next three months approximately half of the capital’s Jews were deported.

Originally, the Slovak government tried to make a deal with Germany in October 1941 to deport its Jews as a substitute for providing Slovak workers to help the war effort. After the Wannsee Conference, the Germans agreed to the Slovak proposal, and a deal was reached where the Slovak Republic would pay for each Jew deported, and, in return, Germany promised that the Jews would never return to the republic. The initial terms were for "20,000 young, strong Jews", but the Slovak government quickly agreed to a German proposal to deport the entire population for "evacuation to territories in the east".

The deportations of Jews from Slovakia started on 25 March 1942, but halted on 20 October 1942 after a group of Jewish citizens, led by Gisi Fleischmann and Rabbi Michael Ber Weissmandl, built a coalition of concerned officials from the Vatican and the government, and, through a mix of bribery and negotiation, was able to stop the process. By then, however, about 58,000 Jews had already been deported. According to a final tally by the Slovak Transport Ministry, fifty-seven transports had left from March to October 1942 with 57,752 Jews. Of this number, 18,746 were deported to Auschwitz and 39,006 to the Lublin district. In the Lublin district, about 9,000 mainly young men were sent to Majdanek camp, and 30,000 mostly older people or families with children were distributed in small towns and villages from which Polish Jews had already been deported. A total of 24,378 of these 30,000 were moved to Sobibor for gassing. Around this time, about 6,000 Jews fled to Hungary and at the end 24,000 remained in Slovakia.

Jewish deportations resumed on 30 September 1944, when the Soviet army reached the Slovak border, and the Slovak National Uprising took place. As a result of these events, Germany decided to occupy all of Slovakia and the country lost its independence. Approximately 13,000 to 14,000 Jews were caught in the roundups. Of these victims, 7,936 were transported to Auschwitz, 4,370 ended up in the Theresienstadt ghetto, and many others were shot in Slovakia itself. A few thousands Jews were able to hide. Deportations continued until 31 March 1945. In all, German and Slovak authorities deported about 70,000 Jews from Slovakia; about 65,000 of them were murdered or died in concentration camps. The overall figures are inexact, partly because many Jews did not identify themselves, but one 2006 estimate is that approximately 105,000 Slovak Jews, or 77% of their prewar population, died during the war.

After the war, the number of Jews in Slovakia was estimated to 25,000. Most of them decided to emigrate.  Today only 6,000 Jews live in Slovakia, predominantly in Bratislava.