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Phayer received his Ph.D. from the University of Munich in 1968 and joined Marquette's Department of History in 1970. He attained the rank of Professor in 1990 and retired in 2002. He is the Ida E. King Distinguished Visiting Scholar of Holocaust Studies at Stockton University.
Phayer has published numerous research articles and books relating to Nazi Germany, the Holocaust and the Catholic Church, including his most recent, Pius XII, the Holocaust, and the Cold War (2007). His previous work was The Catholic Church and the Holocaust 1930-1965 (published in 2000).
- Michael Phayer, Sexual Liberation and Religion in Nineteenth Century Europe, Totowa, NJ, Rowman and Littlefield, 1977.
- Michael Phayer, Protestant and Catholic Women in Nazi Germany, Detroit, Wayne State University Press, 1990.
- Michael Phayer and Eva Fleischner, Cries in the Night: Women Who Challenged the Holocaust, Kansas City, Sheed & Ward, 1997.
- Phayer, Michael (2000). The Catholic Church and the Holocaust, 1930–1965. Bloomington and Indianapolis: Indiana University Press.
- Phayer, Michael (2008). Pius XII, the Holocaust, and the Cold War. Bloomington and Indianapolis: Indiana University Press.
- Michael Phayer, "Canonizing Pius XII. Why did the pope help Nazis escape?", Commonweal, May 9, 2003 / Vol. CXXX (9).
- Michael Phayer, "'Et Papa tacet': the genocide of Polish Catholics", Commonweal, April 8, 2005 / Vol. CXXXII (7).
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