On arrival, Nyiszli volunteered himself as a doctor and was sent to work at number 12 barracks where he operated on and tried to help the ill with only the most basic medical supplies and tools. He was under the supervision of Josef Mengele, an SS officer and physician. Mengele decided after observing Nyiszli’s skills to move him to a specially built autopsy and operating theatre. The room had been built inside Crematorium 2 (Crematorium 1 being in Auschwitz Town camp), and Nyiszli, along with members of the 12th Sonderkommando, were housed there.
During Nyiszli’s time in the camp he witnessed many atrocities to which he refers in his book, Auschwitz: A Doctor’s Eyewitness Account. While imprisoned, Nyiszli was forced to carry out medical experiments and perform autopsies on dozens of bodies, particularly on dwarfs and twins. Mengele had done research into the causes of dwarfism and twinning, and used Nyiszli to gather more information for him. Nyiszli also carried out the autopsies of prisoners; specifically those suspected to have died from camp diseases. Mengele was also searching for evidence supporting the "inferiority of the Jewish race". At one point Nyiszli was forced to carry out medical experiments on a father-son pair, and after their murder, to prepare their skeletons for study at the Anthropological Museum in Berlin. “ [I] had to examine them with exact clinical methods before they died, and then perform the dissection on their still warm bodies. ”
One day, after the gassing of a new shipment of prisoners, Nyiszli was summoned by prisoners working in the gas chambers who had found a girl alive under a mass of bodies in a gas chamber. Nyiszli and his fellow prisoners did their best to help and care for the girl but she was eventually discovered by SS guards and shot. This incident was dramatized in the film The Grey Zone. Nyiszli was appalled by the disregard for human life and lack of sympathy for human suffering shown by the SS guards and officers; But like all in the camp his actions were dictated by his tormentors; he was forced to perform what for him were immoral acts. As he said (in obvious protest, under duress) : An event never before experienced in the history of medicine worldwide is realized here: Twins die at the same time, and there is the possibility of subjecting their corpses to an autopsy. Where in normal life is there the case, bordering on a miracle, that twins die at the same place at the same time? [...] A comparative autopsy is thus absolutely impossible under normal conditions. But in Auschwitz camp there are several hundred pairs of twins, and their deaths, in turn, present several hundred opportunities!"
During the roughly eight months he spent in Auschwitz, Nyiszli observed the murder of tens-of-thousands of people, including the slaughter of whole sub-camps at a time. These sub-camps held different ethnic, religious, national, and gender groups. For example, there was a Gypsy camp, several women’s camps, a Czech camp, and so on. Each sub-camp usually housed between 5,000–10,000 prisoners, and some had even higher populations. Nyiszli was often told which camps were to be exterminated next as it would signal that an increased workload was imminent.
When Nyiszli discovered that the women’s camp his wife and daughter lived in, Camp C, was to be liquidated, he bribed an SS officer to transfer his wife and daughter to a women’s work camp. Nyiszli remained in Auschwitz until shortly before its liberation by the Soviet army on January 27, 1945. On January 18 Nyiszli, along with an estimated 66,000 other prisoners, was forced on a death march that took the prisoners into various parts of the Third Reich’s territories including: Germany proper, Poland (which was part of Greater Germany) present-day Austria, Czechoslovakia, and further into various smaller concentration camps.
Nyiszli’s first major stop after the forced march out of Auschwitz was the Mauthausen concentration camp in northern Austria, near the city of Linz. After a three-day stay in a quarantine barracks at Mauthausen, he was sent to the Melk an der Donau concentration camp, about three hours away by train. After a total of 12 months of imprisonment, including two months in the Melk an der Donau camp, Nyiszli and his fellow prisoners were liberated on May 5, 1945, when U.S. troops reached the camp. Nyiszli's wife and daughter also survived Auschwitz and were liberated from Bergen Belsen. Nyiszli died of a heart attack on 5 May 1956. His daughter Susanna married in 1952 and had a daughter, Monica. She died on 8 January 1983. His wife Margareta died on 5 September 1985, aged 84.