Josef Mengele had hoped to use the “research” he had garnered in Auschwitz in order to produce his Habilitation, a second, post-doctoral, dissertation required for admission to a university faculty as a professor in German-speaking lands. Instead, in January 1945, as the Soviet Army advanced through western Poland, Mengele fled Auschwitz. He spent the next few weeks at the Gross-Rosen concentration camp, until its evacuation. He then made his way west to evade capture by Soviet forces.

An Israeli historian Dina Porat claimed that the Final Solution, i.e.: "the systematic overall physical extermination of Jewish communities one after the other – began in Lithuania" during the massive German chase after the Red Army across the Baltic states in Reichskommissariat Ostland.[53] The subject of the Holocaust in Lithuania has been analysed by Konrad Kweit from USHMM who wrote: "Lithuanian Jews were among the first victims of the Holocaust [beyond the eastern borders of occupied Poland]. The Germans carried out the mass executions [...] signaling the beginning of the 'Final Solution'."[54] About 80,000 Jews were killed in Lithuania by October (including in formerly Polish Wilno) and about 175,000 by the end of 1941 according to official reports.[53]
The superior race was the "Aryans," the Germans. The word Aryan, "derived from the study of linguistics, which started in the eighteenth century and at some point determined that the Indo-Germanic (also known as Aryan) languages were superior in their structures, variety, and vocabulary to the Semitic languages that had evolved in the Near East. This judgment led to a certain conjecture about the character of the peoples who spoke these languages; the conclusion was that the 'Aryan' peoples were likewise superior to the 'Semitic' ones" (Leni Yahil, The Holocaust: The Fate of European Jewry, New York: Oxford University Press, 1990, p. 36).
Dr. Mengele was nicknamed the "Angel of Death" by the prisoners because he had the face of an angel, yet he callously made selections for the gas chambers at Birkenau. He was nice to the children in the camp, yet he experimented on them as though they were laboratory rats. He volunteered to do the selections at Birkenau, even when it wasn't his turn, because he wanted to find subjects for his medical research on genetic conditions and hereditary diseases, which he had already begun before the war. He particularly wanted to find twins for the research that he had started before he was posted to Birkenau.
He had a wide variety of other research interests. Among these was a fascination with heterochromia, a condition in which the irises of an individual's eyes differ in coloration. Throughout his stay in Auschwitz, Mengele collected the eyes of his murdered victims, in part to furnish “research material” to colleague Karin Magnussen, a KWI researcher of eye pigmentation. He himself also conducted several experiments in an attempt to unlock the secret of artificially changing eye color. He also zealously documented in camp inmates the progression of the disease Noma, a type of gangrene which destroys the mucous membrane of the mouth and other tissues.
According to a news article in the Quad-City Times, Yanina Cywinska survived the gas chamber at Auschwitz when she was 10 years old. Cywinska presented the Geifman Lecture in Holocaust Studies at the Augustana College in Rock Island, IL on April 11, 2005, sharing her firsthand account of the atrocities that she endured as a prisoner in Auschwitz and later at Dachau.

Entering conquered Soviet territories alongside the Wehrmacht (the German armed forces) were 3,000 men of the Einsatzgruppen (“Deployment Groups”), special mobile killing units. Their task was to murder Jews, Soviet commissars, and Roma in the areas conquered by the army. Alone or with the help of local police, native anti-Semitic populations, and accompanying Axis troops, the Einsatzgruppen would enter a town, round up their victims, herd them to the outskirts of the town, and shoot them. They killed Jews in family units. Just outside Kiev, Ukraine, in the ravine of Babi Yar, an Einsatzgruppe killed 33,771 Jews on September 28–29, 1941. In the Rumbula Forest outside the ghetto in Riga, Latvia, 25,000–28,000 Jews were shot on November 30 and December 8–9. Beginning in the summer of 1941, Einsatzgruppen murdered more than 70,000 Jews at Ponary, outside Vilna (now Vilnius) in Lithuania. They slaughtered 9,000 Jews, half of them children, at the Ninth Fort, adjacent to Kovno (now Kaunas), Lithuania, on October 28.

At Auschwitz, after the chambers were filled, the doors were shut and pellets of Zyklon-B were dropped into the chambers through vents,[293] releasing toxic prussic acid, or hydrogen cyanide.[294] Those inside died within 20 minutes; the speed of death depended on how close the inmate was standing to a gas vent, according to the commandant Rudolf Höss, who estimated that about one-third of the victims died immediately.[295] Johann Kremer, an SS doctor who oversaw the gassings, testified that: "Shouting and screaming of the victims could be heard through the opening and it was clear that they fought for their lives."[296] The gas was then pumped out, the bodies were removed, gold fillings in their teeth were extracted, and women's hair was cut.[297] The work was done by the Sonderkommando, work groups of mostly Jewish prisoners.[298] At Auschwitz, the bodies were at first buried in deep pits and covered with lime, but between September and November 1942, on the orders of Himmler, they were dug up and burned. In early 1943, new gas chambers and crematoria were built to accommodate the numbers.[299]
Italy introduced some antisemitic measures, but there was less antisemitism there than in Germany, and Italian-occupied countries were generally safer for Jews than German-occupied territories. In some areas, the Italian authorities even tried to protect Jews, such as in the Croatian areas of the Balkans. But while Italian forces in Russia were not as vicious towards Jews as the Germans, they did not try to stop German atrocities either. There were no deportations of Italian Jews to Germany while Italy remained an ally.[171] Several forced labor camps for Jews were established in Italian-controlled Libya. Almost 2,600 Libyan Jews were sent to camps, where 562 died.[172]

Before the war, Mengele had received doctorates in anthropology and medicine, and began a career as a researcher. He joined the Nazi Party in 1937 and the SS in 1938. He was assigned as a battalion medical officer at the start of World War II, then transferred to the Nazi concentration camps service in early 1943 and assigned to Auschwitz, where he saw the opportunity to conduct genetic research on human subjects. His subsequent experiments focused primarily on twins, with little regard for the health or safety of the victims.[2][3]