By the end of September, the SS had started to develop plans to deport Jews to newly invaded Poland: the first steps towards the systematic murder that would follow. In Poland itself, thousands of Poles and Jews were rounded up and shot, early indications of the systematic murder that would follow. Alongside this, Hitler approved a new programme of euthanasia to exterminate the handicapped and mentally ill.

Mengele's health had been steadily deteriorating since 1972. He suffered a stroke in 1976,[99] and he also had high blood pressure and an ear infection that affected his balance. On 7 February 1979, while visiting his friends Wolfram and Liselotte Bossert in the coastal resort of Bertioga, he suffered another stroke while swimming and drowned.[100] Mengele was buried in Embu das Artes under the name "Wolfgang Gerhard", whose identification he had been using since 1971.[101]
Mengele sailed to Argentina in July 1949, assisted by a network of former SS members. He initially lived in and around Buenos Aires, then fled to Paraguay in 1959 and Brazil in 1960, while being sought by West Germany, Israel, and Nazi hunters such as Simon Wiesenthal who wanted to bring him to trial. He eluded capture in spite of extradition requests by the West German government and clandestine operations by the Israeli intelligence agency Mossad. He drowned in 1979 after suffering a stroke while swimming off the Brazilian coast, and was buried under a false name. His remains were disinterred and positively identified by forensic examination in 1985.