According to the Ribbentrop-Molotov treaty on the division of occupied Poland, the Russians occupied the Suwałki region, but after delineation of exact borders between Russia and Germany the Suwałki region fell into German hands. The retreating Russians allowed anyone who wanted to join them to move into their occupied territory, and many young people did leave the area together with the Russians. The Germans drove the remaining Jews out of their homes in Suwałki and its vicinity, robbed them of their possessions, then directed them to the Lithuanian border where they were left in dire poverty. The Lithuanians did not allow them to enter Lithuania and the Germans did not allow them to return. Thus, they stayed in this swampy area in cold and rain for several weeks until Jewish youths from the border villages smuggled them into Lithuania by various routes, with much risk to themselves. Altogether, about 2,400 refugees passed through the border or infiltrated on their own and were then dispersed in the Suwałki region. The Pilviškiai community accommodated and cared temporarily for 100 refugees.

In 1939 there were 2,905 people in Pilviškiai, including about 700 Jews (24%).

In June 1940 Lithuania was annexed to the Soviet Union and became a Soviet Republic. Following new rules, the bigger Jewish shops and workshops of Pilviškiai were nationalised and commissars were appointed to manage them. The supply of goods decreased and, as a result, prices soared. The middle class, mostly Jewish, bore most of the brunt and the standard of living dropped gradually. All Zionist parties and youth organizations were disbanded, the Hebrew school was closed and in its place a Yiddish school opened.

In the middle of June 1941 four Jewish families were exiled into Russia as ‘unreliable elements’ following the nationalisation of Jewish businesses in accordance with regulations. These were Yekutiel Fridman and his mother Tova (but they remained in town after the intervention of the workers committee of the fur factory which belonged to the Fridman family, where Mr Fridman was the specialist in this vocation), Leib Ushpitz and wife Tsilah, Moshe Markson and wife Freidl, Meir Shimberg and wife Sarah, sons Hirshl and Baruch. Most of them returned to Lithuania several years after the war.

On the 23rd of June 1941, one day after the war between Germany and the USSR began, the German army entered Pilviškiai. Immediately the Lithuanian police took over the rule of the town, the commander and his deputy were Germans. On the 28th of June an order was issued for Jews to wear a yellow ‘Magen David’ on their clothes, not to walk on side walks and not to be in the street after 8pm. It was also forbidden for Jews to buy goods in the market. One particular day the prominent Jews of the town, headed by Rabbi Avraham Reznik, were made to assemble in the market square where their beards were cut off and they were forced to do ‘exercises’.

At the beginning of July the men were separated from the women and children and concentrated in a barn in Antanavas Street, from where the Lithuanians would take them out for hard and humiliating labour. On their way back from work they were forced to go through the swamps, to do ‘exercises’ and to crawl for several kilometres. The German commander ordered the erection of a sewing shop and appointed Leibl Zeiberg as chief tailor. He also issued an order prohibiting Lithuanians to enter Jewish houses or to remove anything without his permission. Another order given stated that only men up to aged 50 and women up to aged 45 would be taken for work. The commander also forbade ‘exercises’ in the swamps and advised the Jews to create a Jewish committee whose were to contact him in order to defend the Jews. A committee of 4 persons was set up, headed by Yitskhak Ushpitz, with Yisrael-Ber Axel in charge of maintaining order. Among the local Jews there were a few who had escaped from Vilkaviškis, among them Rabbi Eliyahu-Aharon Grin.

On August 27th 1941, early in the morning, all men aged 14 to 70 years old were rounded up in the market square, the sick being brought on carts. They were kept under heavy guard by armed Lithuanians from the Pilviškiai Self-Defence Police Unit (White Stripers), who maltreated them during the day. At 9pm they were led back to the barn of a Jewish man named Kovenskis in the Pilviškiai township prior to their murder.

The next day, Thursday the 28th, at 3am before dawn, all the men were taken out of the barn. The 10 artisans were sent to the sewing shop, whereas 200 were given spades and told that they were being sent to Germany for digging peat. They were taken to land belonging to the large-scale farm of Jonas Lozoraitis in the Baltrušiai village (about 2 km from Pilviškiai) and ordered to dig two ditches. On Friday 29th about 300 to 350 Jewish men and several dozen Soviet activists (including a group of girls from the Communist Youth Organisation) were taken to the ditches. Before their murder, the victims were made to disrobe and were then taken in small groups to the edge of a ditch and shot. Germans and several Pilviškiai policemen did the shooting. There were about 10 to 15 shooters firing at the same time. Victims were shot in the back from approximately 10 metres away. German officers photographed the mass murder. Among the victims was Dr. Moshe Dembovsky, a reserve Colonel of the Lithuanian Army, who had fought during the Lithuanian independence war. Before he was shot he told the Lithuanian murderers that their crimes would not be forgotten and that the blood of the innocent victims would forever call for revenge, in response to which the Lithuanians cracked his head with the butts of their rifles. All the victims were piled into one of the ditches, the other was left empty. The Lithuanians took the valuables of the victims for themselves. The women and children were left in the town, as well as 10 men who worked for the German Kommandantur and 30 men who managed to hide. Among them were Rabbi Reznik and Rabbi Grin who were hidden in a cellar by the women.

On September 14th it was rumoured that something was about to happen. 70 women escaped and hid in surrounding villages. On the next day, September 15th, a bus with German soldiers from Vilkaviškis arrived, as did some local policemen from the local Self-Defence Squad, to murder the Jewish women, children, and elderly men. The women and children were ordered to leave their houses and for each to take a small parcel with them, having been told that they were going to be transferred to the Kovno Ghetto. They were brought to the market square and from there taken to the same field near Baltrušiai Village, where the shooting of August 29th had taken place. The 10 men who worked for the German Kommandantur and the rest of the men were also included. Among them was also the pharmacist Bolnik, who guessed what was going to happen and swallowed the poison he had prepared before. All, including the two Rabbis, were then led to the empty ditch. Before the shooting, the victims were told to sit down, strip to their underwear and to turn over their jewellery. They were then taken in small groups to the ditch and shot by the German soldiers from the Commander’s Office with submachine guns and by the Lithuanians with rifles. The children were thrown into the ditch alive. In the middle of the massacre, a bus with Vilkaviškis police arrived. They took over the shooting from the local police and from the White-Stripers squad. About 700-800 women, children and elderly men were murdered whilst Gestapo, in civilian dress, photographed the Lithuanian murderers at ‘work’. By evening the perpetrators returned to the town singing the Lithuanian anthem. The clothes and personal possessions of the victims were taken to storage and later distributed among the killers or sold to the local inhabitants.

According to various sources, between 750 to 1,000 people were murdered on that day. A Lithuanian source says that altogether 1,800 people were murdered in Pilviškiai.