In his book, "The Anguish of the Jews: Twenty-Three Centuries of Antisemitism", he provided a thorough account of the history of the world's persecution of the Jews, without dwelling on the lurid details of the atrocities. He covers Pagan anti-Semitism in the ancient world, the struggles between Judaism and the early church, Christian Anti-Semitism in the Middle Ages in the various countries of Europe, the age of the Ghetto, the rise of scapegoat Anti-Semitism in the modern, post religious world (particularly in Russia), leading to Hitler's New Paganism and the Holocaust, as well as economic/racial/social Anti-Semitism in America. In the end, Flannery reviews how things stand today. In relation to the Holocaust, Flannery illustrated the sympathies for the Nazi regime and the "Final Solution" expressed by prominent Arab personages at the time, such as the close confidant of Adolf Hitler, Haj Amin al-Husseini. He traced antisemitism back to the 3rd century BC, and identified the following strains: Political and economic antisemitism, Theological or religious antisemitism, (also known as anti-Judaism), Nationalistic antisemitism, and Racial antisemitism, as practiced by the Nazis. In an interview in 1967, Flannery said: "The anti-Semite, not the Jew, is the real Christ-killer. He thinks he's religious, but that's a self-delusion. Actually he finds religion so heavy a burden, he develops 'Christophobia.' He's hostile to the faith and has an unconscious hatred of Christ, who is for him, Christ the Repressor. He uses anti-Semitism as a safety valve for this hostility and is really trying to strike out at Christ." Father Flannery was awarded honorary doctorates from several institutions, including Hebrew Union College Jewish Institute of Religion, Cincinnati and Seton Hall University. He received the prestigious Nicholas and Hedy Munk International Brotherhood Award of the Canadian Council of Christians and Jews and many other signs of esteem from Christian and Jewish Organizations. Flannery believes the vast majority of even well-educated Christians have been relatively ignorant of what has happened to the Jews throughout history and the culpable involvement of many facets of the Church. Apart from a few recent publications, there is little about anti-Semitism in Christian history books or social studies. The author states that, by comparison, the Jews themselves are largely and acutely aware of their painful history and physical and verbal attacks in the press. Flannery also was one of the 53 authors to respond to Simon Wiesenthal's book The Sunflower. Legacy After his death,