Filip Müller was born to a Jewish family in Sered, Czechoslovakia (present-day Slovakia). In April 1942, at age 20, he was deported by the Nazis to Auschwitz. There he was assigned to work in the construction of the crematoria and installation of the gas chambers. As member of the Sonderkommando, he was ordered to undress the bodies of the dead and burn them in the ovens. He was one of very few people who lived to tell about these events. He wrote a memoir, first published in 1979, called Eyewitness to Auschwitz: Three Years in the Gas Chambers, also known as Auschwitz Inferno: The Testimony of a Sonderkommando. As the Red Army advanced westward at the end of World War II, he was sent to the Mauthausen concentration camp, where he survived to be liberated.
After the war, his testimony from his hospital bed was published in an obscure Czech publication, later reprinted in the The Death Factory (1966) by Ota Kraus and Erich Kulka. Müller then testified at the Second Frankfurt Auschwitz Trials held in 1964, and was interviewed in Claude Lanzmann's 1985 documentary Shoah.