Ward has made a number of comments concerning religion which have sparked controversy. Those most heatedly debated concern Judaism and his own purported Catholic faith.

On Dec. 9, 1996, Ward said that Christianity is "morally superior" to Judaism because it is based on unconditional forgiveness. Judaism, Ward said, "was left in the backwater of history because Judaism could not go beyond the rules and rituals and the need for revenge." When one apology from Ward was rejected, Ward replied: "Jews need to get a thicker skin."

Writer Aleza Goldsmith (Jewish News Weekly) wrote on September 21, 2001, "During his program on Wednesday, Sept. 12 -- the day after the terror attacks -- Ward compared the tactics of religious fundamentalists to those used by Nazis. Fundamentalists, he said, included 'the ultra-Orthodox' in Israel." He also alleges that the beliefs of Muslim, Jewish and Christian Fundamentalists are similarly dangerous in character.

Ward has also has made controversial comments regarding the Catholic Church. On March 16, 1996, Ward charged that the "right wing fascist" who ran the Catholic Church during the Vietnam war did not allow opposition to the war.

On March 24, 2006, Ward criticized the confrontational antics of the gay group ACT-UP. Ward was upset with the recent invasion of a mosque, but justified the 1989 invasion of a Catholic church (St. Patrick's Cathedral). According to The Catalyst, Ward said that "homosexuals had a good case to make (against the Catholic Church). He explained his answer by arguing that the Church 'has encouraged homophobia and homophobic actions.' He even went so far as to say that the Roman Catholic Church 'is encouraging people to be violent against gays, that is justifying the violence against gays, and that is taking a position that will spread a fatal disease, then you can understand why people would be upset by that and would consider the need to do some kind of form of public protest'."