The first arrests of Zagreb's Jews began already in mid-April 1941. At the end of May of the same year, mass arrests began. At that time, 165 youths between the ages of 18 and 21 were arrested. They were deported to Danica near Koprivnica, from where they were deported to Jadovno near Gospić at the beginning of July, where 155 youths were killed. The next wave of arrests took place at the end of June, and Maccabi athletes, members of the left-wing trade union SBOTIČ, students, and younger members of the municipality were arrested. In the following days, entire families were also arrested. The place of internment was the Zagreb Fair. After two months, the place of internment was transferred to Zavrtnica. From these transit camps, the Jews were deported to Danica, then to the Gospić – Velebit – island of Pag camp system, and finally to the Jasenovac camp system. About 2,500 Jews from Zagreb and from other parts of the NDH passed through the Zagreb Choir. These trains passed through the Central Station, and between 800 and 1,000 Jews from Zagreb, and those mostly from northern Croatia, passed through Zavrtnica (the former “Kristalum” factory). At the end of September 1941, a wave of deportations began (about 1,500 Jews), also from Zavrtnica. Women and children were deported to Stara Gradiška and later to Đakovo, and men to the Jasenovac camp system (Stara Gradiška and Jasenovac). In Zagreb, by the end of September 1941, more than 3,000 Jews were killed, deported or murdered.
A new wave of mass arrests and deportations began in January 1942. The transit camps were the prison in Savska and the Zagreb Choir. Around 1,500 Jews were deported to Stara Gradiška and Đakovo (women) and Jasenovac (men). After this wave, about half of Zagreb's Jews had been deported.
The final destination of the two waves of deportations – in August 1942 and May 1943 – was the Auschwitz-Birkenau camp system. In August, about 1,200 Jews were arrested, and they were interned in the eastern part of the school building in Križanićeva, and a number in the prison on Savska cesta. 800 of them were deported from the Central Station.
In May 1943, the last wave of mass deportations from Zagreb took place, when around 1,700 Jews from Zagreb and around 300 Jews from the territory of the NDH were arrested. They were interned in the municipal building at 9 Trenkova Street and in the prison on Savska cesta and other locations. They were deported from the West Station. In these deportations, elderly people were also taken from several Jewish nursing homes located around Zagreb, and the one in Stenjevac was spared thanks to Zagreb Archbishop Alojzije Stepinac.