For 60 hours the Jews were held in the stable and the synagogues, deprived of water and food and prevented from going outside to relieve themselves. Afterwards, all the Jews were taken to the horse market, where they were surrounded by Lithuanian policemen and SS men, and were forced to hand over all their valuables.
On September 24 the Nazis said that they needed strong young men to dig holes for a fence to surround the area where the Jews would be housed. A group of young men volunteered. The Germans took them to the local Jewish cemetery and ordered them to dig pits. Then the Jews were shot at the edge of the pits (according to another source, the pits were dug by Poles). When, on September 27 (according other sources, on September 26), 1941, the other Jews heard what had happened, they refused to move. The Germans threatened that if the Jews did not obey, they would be shot on the spot. To help carry out the execution reinforcements of Lithuanian police and German gendarmes were brought in. Then all the Jewish men were taken to the Jewish cemetery and shot at the pits.
The women, small children, the elderly, and the sick who were physically unable to walk to the murder site remained at the horse market. At night they were all taken to the pits, where they were also shot.
According to the Jaeger report, 3,446 Jews (989 men, 1,636 women, and 821 children) were executed by Einsatzkommando 3a in Ejszyszki on September 27, 1941.