Bauer specialized in the Holocaust,
antisemitism — a word which he insisted should be written
unhyphenated — and the
Jewish resistance movement during the Holocaust, and he argued for a wider definition of the term. In Bauer's view, resistance to the Nazis comprised not only physical opposition but any activity that gave the Jewish people dignity and humanity in the most humiliating and inhumane conditions. Furthermore, Bauer disputed the popular view that most Jews went to their deaths passively — "
like sheep to the slaughter". He argued that, given the conditions in which the
Jews of Eastern Europe had to endure, what is surprising is not how little resistance there was, but rather how much. Bauer defended
Rudolf Kasztner and the
Aid and Rescue Committee, who have been criticized for allegedly not publicizing the
Vrba-Wetzler report which documented the deportation of the Hungarian Jews to
Auschwitz. According to Bauer, conditions prevented Kasztner and other Jewish leaders from publicizing what they knew, and prevented Jews from escaping. Not only did Kasztner hide what is awaiting the Jews of Hungary, after
George Mantello obtained the report over two months delay in Switzerland via Romanian diplomat
Florian Manilou who got it is Budapest from
Moshe Krausz, Kasztner implored him not to publicize it, which Mantello declined to comply with. At Yad Vashem while its chief historian, Bauer exclaimed that "
Hillel Kook saved no one!", although the
Emergency Committee for the Rescue of European Jewry (aka
Bergson Group), Kook's rescue activist group in America, kept pressuring President
Roosevelt to help the Jews of Europe. It forced Roosevelt to establish the
War Refugee Board in January 1944, also due to pressure by Jewish Treasury Secretary
Henry Morgenthau Jr and his team. The WRB saved large number of Jews, in part by the
Raoul Wallenberg mission in Budapest. According to American historian Professor
David Wyman the WRB saved an estimated 200,000 in Europe. Bauer believed that Hitler was the key figure who caused
the Holocaust, and that at some point in the later half of 1941, he gave a series of orders which called for the genocide of the entire Jewish population. Bauer pointed to the discovery of an entry in Himmler's notebook dated 18 December 1941 where Himmler wrote down the question "What to do with the
Jews of Russia?" According to the same notebook, Hitler's response to the question was "Exterminate them as
partisans." In Bauer's view, this is as close as historians will ever get to a definitive order from Hitler ordering the Holocaust. Bauer disagreed with those who argue that the Holocaust was just another genocide. Though he agreed that there were other
genocides in history, he argued that the Holocaust was the worst single case of genocide in history, in which every member of a nation was selected for annihilation. American historian
Henry Friedlander argued that the
Romani and the disabled were just as much victims of the Holocaust as the Jews were. However, Bauer said that the Romani were subject to genocide (just not "the Holocaust") and he supported the demands of the Romani for reparations from Germany. Another trend that Bauer denounced was the representation of the Holocaust as a mystical experience outside the normal range of human understanding. He argued against the work of some
Orthodox rabbis and
theologians who have said that the Holocaust was the work of
God and part of a mysterious master plan for the Jewish people. In Bauer's view, those who seek to promote this line of thinking argue that God is just and good, while simultaneously bringing down the Holocaust on the Jewish people. Bauer argued that a God who inflicts the
Shoah on his
Chosen People is neither good nor just. In January 2012, Bauer's article in the
Israel Journal of Foreign Affairs entitled "The Holocaust, America and American Jewry" precipitated a bitter debate between him,
Rafael Medoff (
Wyman Institute) and Alexander J. Groth (
University of California, Davis), on what the US Government and the Jews of America could and could not have done to rescue the Jews of Europe. Bauer has criticized the American political scientist
Daniel Goldhagen, who writes that the Holocaust was the result of the allegedly unique "eliminationist" antisemitic culture of the Germans. He has accused Goldhagen of
Germanophobic racism, and of only selecting evidence which is favorable to his thesis. Bauer was known for his criticism of other historians but directed his sharpest rebukes at politicians whom he believed manipulated the Holocaust to serve their agendas, particularly singling out Prime Minister
Benjamin Netanyahu. In an interview with
The Times of Israel in August 2023, he stated, "They use the Holocaust as a political tool. This is particularly true of the
prime minister. He has no understanding at all—he simply does not grasp what happened. He deals with Iran; he knows something about Iran, but he knows nothing about the Holocaust." Bauer was one of the architects of the
Working Definition of Antisemitism, which classifies mainstream Palestinian positions as antisemitic. He has argued that calling for
Palestinian right of return is antisemitic because he believes it is a prelude to the genocide of Jews. Concerning
Pope Benedict XVI's pilgrimage to Israel and
Jordan, Bauer argued that the Pope meant well and tried to walk the tightrope between Arab-Palestinian-Muslim and Palestinian-Christian enmity toward Israel and the Jews on the one hand, and the
collective trauma of Jews in Israel and elsewhere regarding the Holocaust on the other. ==Awards and recognition==