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Starting in 1979, he served as the bishop of Rochester, New York, for 32 years. During that time, he had a reputation as a theological leftist and supported sodomite clerics in the diocese.
In a 2020 court deposition, Clark admitted to covering up for sexual predator priests during his tenure as bishop.
Mitchell Garabedian, an attorney representing 94 sexual abuse victims suing the diocese of Rochester, revealed, "The testimony by Bp. Matthew Clark under oath in his deposition of March 3, 2020, indicates that Bp. Clark hid pedophilia from the public for decades just as clergy sexual abuse victims had suspected." Garabedian further noted, "Bp. Clark had an utter disregard for the safety and well-being of children."
The diocese of Rochester quickly pushed back against the claims, writing, "While any individual would have difficulty providing accurate memory of events that occurred over a period of more than 33 years, Bp. Clark was further hindered by his struggle with early Alzheimer's disease."
Garabedian responded, "He was very forthright. He didn't seem like he was confused at all. Anyone would agree that he was very clear and understanding and he answered the questions."
Speaking of Clark after his death, Jamie Fazio, who is a chaplain at Rochester's Nazareth University, eulogized, "I think he was a Francis bishop before Pope Francis." He added, "The church needs to be on the margins and be in solidarity with those who have been excluded and silenced."
Clark was one of the youngest prelates in the United States when he was consecrated in 1979. He quickly made a name for himself, celebrating so-called LGBT Masses. The dissident pro-homosexual New Ways Ministry praised Clark for his work, calling him "a longtime supporter of LGBT people in the Catholic Church."
Clark also advocated for female "ministers" in the Church. In 1998, then-Cdl. Joseph Ratzinger asked Clark to remove Fr. James Callan as pastor of Corpus Christi parish. Callan was confusing parishioners by allowing a woman to dress in what appeared to be priestly vestments and lead Communion services.
The Rochester prelate also had a close relationship with fellow notorious homosexualist Bp. Howard Hubbard of Albany. Abuse attorney Jeff Anderson described Hubbard as "a serial predator that enjoyed a position of power and trust over priests and parishioners for decades."
Clark was also the spiritual director for New York's Cdl. Timothy Dolan. In 2012, Pope Benedict XVI accepted Clark's resignation. Clark was diagnosed with Alzheimer's in 2019.
Albany priest Fr. John Minker released an explosive report on overt homosexual activity and cover-up in New York's dioceses, and the report named both Hubbard and Clark. In 2004, only a few days after meeting with Bp. Hubbard, Fr. Minker was found dead in his apartment. Father Minker's death was ruled a suicide, despite suspicious circumstances.