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'."
The Catholic League responded to some of Ward's most provocative comments: "Bernie Ward's hatred of the Catholic Church has allowed him to misrepresent history and promote instead a bigoted portrayal of Catholicism. ... The Catholic Church has never encouraged violence against gays or any other group. Moreover, its teachings on sexual ethics have promoted restraint, the very virtue that is a necessary toxin against sexually transmitted diseases. Ward's apparent fixation on discrediting Catholicism will not win but it is a sad commentary on his twisted sense of reality."
The Catholic League, an organization for religious and civil rights, took exception when Ward compared a local bishop to Frank Nitti, "the man who carries out the executions, the man who closed the churches...." Furthermore, he said, "...when you become a pastor; you get your hands on the money...I would be very very very careful about donations or anything else that would go his (the bishop’s) way." Ward later issued a retraction stating that his comments were not appropriate, and that the named priest was innocent of any inappropriate conduct.
In June of 2007, Ward has referred to the United States Supreme Court as the "Catholic Mafia", and has stated that "the Justices should take their direction from the Constitution, not the Vatican."