The diaries, written after the end of the Second World War when Mengele had fled to Latin America, contain his philosophical reflections, autobiographical stories and poems written between 1960 and 1975.
Thursday's auction will include some 3,500 pages from "hidden journals" written by the doctor who carried out terrible medical experiments on prisoners at Auschwitz-Birkenau concentration camp.
The items, mostly small, spiral-bound notebooks, are expected to fetch between £185,000 and £247,000 when they go under the hammer at Connecticut-based auctioneers Alexander Autographs.
The company, which specialises in historical manuscripts, said the auction would include an "historically important" lot of 31 manuscripts in various forms, including bound journals.
"All writings are penned in ink in a legible hand, in generally excellent condition," an auction house spokesman said.
"They were seized in 2004 by the police at the home of a German couple with whom he was living in Sao Paulo."
He added they were then given to Mengele's son, Rolf, who only saw his father twice in his life.
About 40% of the writings are autobiographical, tracing Mengele's flight across Europe in the aftermath of the war.
He talks of himself in the third person, referring to himself as "Andreas".
In one commentary, Mengele complains that sexual promiscuity has led "to a dreadful mixing of the races with the northern Europeans... when you start mixing the races, there is a decline in civilisation".
Mengele was a member of the Nazis' elite SS, which ran death camps across occupied Europe.
Based at Auschwitz from 1943, he helped supervise the selection of prisoners on arrival to death camps, sending those considered unfit for slave labour to be gassed with deadly Zyklon B.
He gained his notorious reputation due to his pseudo-medical experiments in the camp.
He fled Europe at the end of the war after Germany's defeat, reaching Argentina at the start of the 1950s.
He then moved to Paraguay in 1961 and then went on to Brazil, where he lived in Sao Paulo and remained uncaptured despite Interpol's best efforts, dying in 1979 at the age of 67.
His death was only confirmed in 1985, after his body was exhumed.
The diaries appeared some time after that.