There were about 3,200 Jews living in Topoľčany before World War II, of which 550 survived the Holocaust and returned to the town after the war ended. Anti-semitism was widespread at that time due to both Slovak state official policy and also the strong economic position of Jews, which contrasted with a lack of basic commodities among the majority population.
According to the protocol of county police boss Zidor, rumors began to spread in the town two days before the pogrom that Jews were about to overtake a local Catholic school, run by nuns. Also, there were rumors that Jews had already created a separate classroom for Jewish children, in which they desecrated a crucifix. Further, the Jews were said to had overtaken a school in the nearby village of Bojná, run by Catholic monks. Local women wanted to protest against the rumored actions, but local authorities refused them. A group of people, mostly women, then entered the school. Coincidentally, a Jewish doctor was at the time vaccinating children against smallpox in one of the school's classrooms. Some of the vaccinated children cried, which gave base for a new rumor to spread among the angry crowd: that a Jewish doctor was poisoning Slovak children. The mob then attacked and beat the doctor. As new rumors spread to the streets, many more Jews were beaten both in the streets and in their homes, and many of their houses were looted.
Nehemiah Robinson (1956). European Jewry Ten Years After the War: An Account of the Development and Present Status of the Decimated Jewish Communities of Europe. New York: Institute of Jewish Affairs of the World Jewish Congress. p. 100.