Estimates of the death toll vary between locations; nearly 9,000 in the Ukrainian SSR, 20,000–30,000 in eastern Poland (now part of Western Ukraine), with the total number reaching approximately 100,000 victims of extrajudicial executions in the span of a few weeks.
The launch of Operation Barbarossa surprised the NKVD, whose jails and prisons in territories annexed by the Soviet Union in the aftermath of the Molotov–Ribbentrop Pact were crowded with political prisoners. In occupied eastern Poland, the NKVD was given the responsibility of evacuating and liquidating over 140,000 prisoners (NKVD evacuation order No. 00803). In Ukraine and Western Belarus 60,000 people were forced to evacuate on foot. By official Soviet count more than 9,800 were reportedly executed in the prisons, 1,443 were executed in the process of evacuation, 59 were killed for attempting to escape, 23 were killed by German bombs, and 1,057 died from other causes.
“It was not only the numbers of the executed,” historian Yuri Boshyk writes of the murders, “but also the manner in which they died that shocked the populace. When the families of the arrested rushed to the prisons after the Soviet evacuation, they were aghast to find bodies so badly mutilated that many could not be identified. It was evident that many of the prisoners had also been tortured before death; others were killed en masse.”
Approximately two thirds of the total number of 150,000 prisoners were murdered; most of the rest were transported into the interior of the Soviet Union, but some were abandoned inside the prisons if there was no time to execute them and others managed to escape.
The NKVD and the Red Army killed prisoners in many places from Poland to Crimea. Immediately after the start of the German invasion, the NKVD commenced the execution of large numbers of prisoners in most of their prisons, and the evacuation of the remainder in death marches. Most of them were political prisoners, imprisoned and executed without a trial. The massacres were later documented by the occupying German authorities and used in anti-Soviet and anti-Jewish propaganda. After the war and in recent years, the authorities of Germany, Poland, Belarus and Israel identified no fewer than 25 prisons whose prisoners were killed — and a much larger number of mass execution sites.
Litene massacre: On June 14, 1941, 120 Latvian Army officers were driven to the woods in the belief they were on a training mission. On arrival they were disarmed, tied up and executed by the NKVD. The remaining 500 or more officers of the 24th corps were arrested and deported to slave labour camp in Norilsk, including General Klavins.
"The Latvian soldiers and officers at Litene were unaware that Latvians throughout the country endured the same terror simultaneously. On the night of June 13–14 the NKVD struck at the civilian population as well, a nightmarish climax to the Year of Terror." – Valdis O. Lumans 
By 1941, a large part of the ethnically Polish population living under Soviet rule in the eastern half of Poland had already been deported to remote areas of the USSR. Others, including a large number of Polish civilians of other ethnicities (mostly Belarusians and Ukrainians), were held in provisional prisons in the towns of the region, where they awaited deportation either to NKVD prisons in Moscow or to the Gulag. It is estimated that out of 13 million people living in eastern Poland, roughly half a million were jailed, and more than 90% of them were men. Thus approximately 10% of adult males were imprisoned at the time of the German offensive. Many died in prisons from torture or neglect. Methods of torture included scalding victims in boiling water and cutting off ears, noses and fingers.Timothy Snyder estimates that the NKVD shot some 9,817 imprisoned Polish citizens following the German invasion of the USSR in 1941.
NKVD massacre sites in pre-war Poland are now in Lithuania (see above), Belarus and Ukraine (see below).
Hrodna (Grodno in pre-war Poland): on June 22, 1941, the NKVD executed several dozen people at the local prison. The mass execution of the remaining 1,700 prisoners was not possible due to the advance of the German army and hurried retreat of the NKVD executioners.
Hlybokaye (Berezwecz in pre-war Poland), near Vitebsk: on June 24, the NKVD executed approximately 800 prisoners, most of them Polish citizens. Several thousands more perished during a death march to Nikolaevo near Ulla.
Chervyen’ near Minsk: in late June, the NKVD started the evacuation of all prisons in Minsk. Between June 24 and June 27, several thousand people were killed in Cherven and during the death marches.
Vileyka (Wilejka in pre-war Poland): several dozen people, mostly political prisoners, sick, and wounded, were executed prior to the departure of the Soviet guards on June 24, 1941.
Ethnic Germans murdered at a TernopilGPU prison, as German troops approached, are being identified by their relatives on July 10, 1941
Berezhany (Brzeżany in pre-war Poland) near Ternopil (Tarnopol): between June 22 and July 1 the crew of the local NKVD prison executed approximately 300 Polish citizens, among them a large number of Ukrainians.
Dubno (in pre-war Poland): All the prisoners in Dubno's three-story prison, including women and children, were executed.
Ivano-Frankivsk (Stanisławów in pre-war Poland): Over 500 Polish prisoners (including 150 women with dozens of children) were shot by the NKVD and buried in several mass graves at Dem'ianiv Laz.
Lutsk (Łuck in pre-war Poland): After the prison was hit by German bombs, the Soviet authorities promised amnesty to all political prisoners, in order to prevent escapes. As they lined up outside they were machine-gunned by Soviet tanks. They were told: "Those still alive get up." Some 370 stood up and were forced to bury the dead, after which they were murdered as well. The Nazi foreign ministry claimed 1500 Ukrainians were killed while the SS and Nazi military intelligence claimed 4000.
Lviv (Lwów in pre-war Poland): the massacres in this city began immediately after German attack, on June 22 and continued until June 28, culminating in the Lviv pogroms. The NKVD executed several thousand inmates in a number of provisional prisons. Among the common methods of extermination were shooting the prisoners in their cells, killing them with grenades thrown into the cells or starving them to death in the cellars. Some were simply bayoneted to death. It is estimated that over 4000 people were murdered that way, while the number of survivors is estimated at approximately 270. A Ukrainian uprising briefly forced the NKVD to retreat, but it soon returned to kill the remaining prisoners in their cells. In the aftermath, medical students described the scene at one of the prisons: “From the courtyard, doors led to a large space, filled from top to bottom with corpses. The bottom ones were still warm. The victims were between 15 and 60 years old, but most were 20-35 years old. They laid in various poses, with open eyes and masks of terror on their faces. Among them were many women. On the left wall, three men were crucified, barely covered by clothing from their shoulders, with severed male organs. Underneath them on the floor in half-sitting, leaning positions – two nuns with those organs in their mouths. The victims of the NKVD’s sadism were killed with a shot in the mouth or the back of the head. But most were stabbed in the stomach with a bayonet. Some were naked or almost naked, others in decent street clothes. One man was in a tie, mostly likely just arrested.”
Sambir (Sambor in pre-war Poland): 570 killed.
^ abRichard Rhodes (2002). Masters of Death: The SS-Einsatzgruppen and the Invention of the Holocaust. New York: Alfred A. Knopf. ISBN0-375-40900-9. Barbarossa surprised the NKVD, whose jails and prisons in the annexed territories (despite earlier deportations) were crowded with political prisoners. Rather than releasing their prisoners as they hurriedly retreated during the first week of the war, the Soviet secret police killed most of them execution style. In the first week of Barbarossa NKVD prisoner executions totaled some ten thousand in western Ukraine and more than nine thousand in Vinnytsia, eastward toward Kiev. Comparable numbers of prisoners were executed in eastern Poland, Byelorussia, Lithuania, Latvia, and Estonia. The Soviet areas had already sustained losses numbering in the hundreds of thousands from the Stalinist purges of 1937-38. “It was not only the numbers of the executed,” historian Yuri Boshyk writes of the evacuation murders, “but also the manner in which they died that shocked the populace. When the families of the arrested rushed to the prisons after the Soviet evacuation, they were aghast to find bodies so badly mutilated that many could not be identified. It was evident that many of the prisoners had also been tortured before death; others were killed en masse.”