The intention was that a large part of the mass murder of the Jews would be carried out by the local non-Jewish inhabitants by means of spontaneous pogroms. "The impression had to be created, that the local population had taken the first steps on their own initiative as a natural reaction to the long years of suppression by the Jews and the more recent terror by the communists", as Franz Walter Stahlecker stated in a report of October 1941. It would transpire however that such self-cleaning actions, as he called it, did not occurr very often and only very seldom spontaneously. Pogroms were almost always organized by the Einsatzgruppen after stirring up the local population first. Most acts of violence by civilians against Jews were of short duration. They started after the arrival of the Einsatzgruppen and usually ended when the Wehrmacht took control. The German military administration had no stomach for long-term local unrest. Within the Einsatzgruppen resistance also existed against the chaotic and bloody eruptions of violence by the local population as they preferred rigidly orchestrated executions. Nonetheless, an estimated 20.000 Jews were killed in pogroms during the first days of the German invasion.
In the Baltic states the Nazis counted on the fact that pogroms could easily be launched. The anti-Semitism had been fired up during the Soviet-occupation which had lasted for about a year before the German invasion. During that year members of the local elite and nationalists had fallen victim to Soviet-terror by arrests, deportations and executions. The Jewish minorities had been encouraged by the Soviet administration to contribute to the establishment of new Soviet states. The atheist Soviet government, contrary to earlier governments, did not distinguish between Jews and Christians; this made the Jews feel attracted to communism and thus they were well represented in the current Communist administration. After the German invasion, the entire Jewish population had to atone for this.
In Lithuania the pogroms were mainly the responsibility of a group of partisans commanded by the Lithuanian collaborator Algirdas Klimaitis. Earlier on, these partisans had taken up arms against the Red Army and were thereafter stimulated by Einsatzgruppe A to act against Jews which led to a large eruption of violence, especially in Kaunas/Kovno. "In the night of 25 to 26 June over 1,500 Jews were murdered by Lithuanian partisans, many synagogues were burned down or destroyed in other ways and a Jewish quarter of about 60 houses was set ablaze. During the next nights 2,300 more Jews were exterminated," Stahlecker reported. Elsewhere in Lithuania 1,200 Jews were killed by Klimaitis’ men in similar actions.
In Latvia Stahlecker experienced more difficulties in stimulating pogroms than in Lithuania. In his opinion, the reason was that all national leaders had been killed or deported by the Soviets and thus could not be used to incite the population to take action. Nevertheless, Einsatzgruppe A succeeded in inciting the Latvian auxiliary police to a pogrom, in the course of which all synagogues in Riga were destroyed and approximately 400 Jews killed. Under the direction of the Latvian nationalist Viktor Arajs, Jews were burned alive in a synagogue in Riga in early July 1941. In Estonia pogroms did not materialize; the nationalist Estonian militia, the Omakaitse did kill several Communists on its own initiative. The Estonian militia though was deployed by Sonderkommando 1a to carry out executions.
While in Byelorussia there were no pogroms either, in the border region of Poland and the Ukraine, especially in Galicia, several pogroms took place. In July 1941 in the small town of Jedwabne, which is approximately 43,50 miles north west of Bialystok, at least 340 Jews were slaughtered by fellow inhabitants of Polish descent. In Lviv/Lvov, the city in Galicia called Lemberg by the Germans and which is part of the Ukraine today, Einsatzgruppe C stimulated local Ukrainian collaborators to launch a pogrom against the Jews, which lasted several days. The Ukrainians were incited to this by the discovery of 2,500 dead prisoners in the prison of the NKVD, the secret service of the Soviet-Union. The victims, nationalists of Ukrainian and other descent had been executed by the secret service prior to the German invasion. The Jewish inhabitants were to atone for this, as they were accused of collaboration with the Soviet administration. In July thousands of Jews and also Poles fell victim to the violence in Lvov.
In the nearby town of Boryslaw/Boryslav a pogrom also took place in the same period, after corpses of young men, killed by the NKVD had been found. The commanding general of the Wehrmacht had the local inhabitants have their way for 24 hours with taking revenge on the Jews who allegedly had been involved in the murders by the Soviet secret service. With everything they could lay their hands on, like axes and hammers, the Jews were beaten to death. In Kremenets a similar action of revenge took place. The local Soviets had murdered 100 to 150 Ukrainians. A rumor circulated to the effect that some of them had been killed by throwing them in kettles with boiling water. Early July 1941, the Ukrainians took revenge by rounding up 130 Jews and bludgeoning them to death. In Tarnopol and Czortków/Chrotkiv pogroms took place as well. Einsatzgruppe C however was not satisfied with the willingness of the local people to use violence against Jews and reported: "The cautious way which was chosen at that time to stimulate pogroms against the Jews, was less successful as had been hoped for. […] A clear cut anti-Semitism based on racial or spiritual views however is foreign to these people".
Both in the Baltic States as in Byelorussia and the Ukraine local militia were deployed as auxiliary police forces. These played an important role in the arrests and executions. So-called Volksdeutschen, ethnic Germans who lived in the Soviet-Union, were also recruited for these supporting units. The exact number of locals collaborating with the Einsatzgruppen is unknown but runs into the thousands or tens of thousands. In numerous cases, especially in Byelorussia and the Ukraine, the number of local helpers supporting the mass murders even exceeded the number of German members of the Einsatzgruppen. These local collaborators had to their advantage that they were familiar with the language of the victims, they knew the environment well, they knew where the Jews lived and that they could better convince their countrymen to betray their neighbours. In addition, they were often used to carry out the dirty work, like participating in the firing squads. The local collaborators were not only motivated by anti-Semitism, but also by the hope that by collaborating with the Germans, their country would remain independent, which turned out to be an illusion.
The majority of the indigenous population however took a passive attitude towards the operations of the Einsatzgruppen. They feared they would be next to be murdered or did not dare to support the Germans as they feared that the Soviets would return and then it would be their turn to be punished for collaboration with the enemy. Although many did not show any interest in the fate of the Jews at all, there were in fact civilians in the occupied Soviet-Union who did help Jews to survive the war. In January 2012, for example, 2,402 non-Jewish Ukrainians were designated "Righteous among the Peoples" by Yad Vashem, the Israeli Holocaust Institute, an award for non-Jews for having rescued Jews during the Second World War.