In February 1869, McQuaid tried to remove the Reverend Thomas O'Flaherty from his position as pastor of Holy Family Church in Auburn.

[11] McQuaid lifted the suspension 23 years later, at the behest of the apostolic delegate, Francesco Satolli, on the condition that O'Flaherty not return to the diocese.

[12] When McQuaid first arrived in Rochester, the only true parochial schools were operated by the five German language parishes, educating a total of 2,000 students.

[14] In 1871, McQuaid announced his plan to create a system of tuition-free parochial schools in the diocese, staffed by the Sisters of St.

In 1929, Monsignor John Francis O'Hern was appointed the third bishop of the Diocese of Rochester by Pope Pius XI.

[27] He supported the Community Chest and Red Cross, and provided chaplains for Catholics students attending secular colleges in the diocese.

Pope Pius XI named Archbishop Edward Mooney, formerly the Apostolic Delegate to Japan, as the next bishop of Rochester in 1933.

During his tenure in Rochester, Mooney promoted the Catholic Action movement and the Knights of Peter Claver as a means of outreach to the African-American community.

To replace Mooney in Rochester, Pius IX in 1937 selected Bishop James E. Kearney of the Diocese of Salt Lake.

[31] Sheen resigned as bishop in 1969 to devote more time to his writings; Pope Paul VI elevated him to a titular archbishop.

[32] Pope John Paul II then named Reverend Matthew H. Clark of the Diocese of Albany as the next bishop of Rochester.

[33] In 1986, Cardinal Josef Ratzinger ordered Clark to withdraw his imprimatur, or church approval, from a sex education manual written by a diocesan priest.

[34] That same year, Clark defended one of his priests, the theologian Charles Curran, from criticism by Vatican officials for his stands on birth control, abortion rights for women, homosexuality, and divorce.

[37] Clark received some credit for clamping down on abusive priests;[38] in 2004, the diocese was deemed to be in "full compliance" with the US Conference of Catholic Bishops (USCCB) Charter for the Protection of Children and Young People.

[39] Clark presided over the unpopular closing of many of Rochester's parochial schools and parishes, pledging to complete the "re-sizing" of the diocese prior to his retirement in 2012.

The event marked a year-long celebration of the 150-year anniversary and the year of the Eucharist, which Matano proclaimed on the Feast of Corpus Christi.

The diocese filed for bankruptcy protection in September 2019 due to the numerous lawsuits it faced for sexual abuse of children by its clergy.

[44] In August 1985, Brother John Walsh, vice principal of Cardinal Mooney High School in Greece, New York, was arrested on kidnapping charges.

[46] A former student at Cardinal Mooney sued the diocese in January 2020, stating that he had been sexually assaulted numerous times by Walsh between 1966 and 1969.

[47] Reverend Gerard Guli of Holy Rosary Parish in Rochester was arrested in April 1989 on first-degree sexual abuse charges.

[50] Reverend Eugene Emo was arrested in February 1996 on charges of sexually abusing a man with developmental disabilities in Cohocton, New York.

[51] Emo pleaded guilty to one felony count of first-degree sexual assault and was sentenced to six months in jail and five years probation.

[53] In May 2002, two men sued the diocese, stating that they had been sexually abused by Reverend Robert O'Neil, pastor of St. Christopher Parish in Chili, New York.

[54] Reverend Dennis Sewar of Annunciation Parish in Rochester was arrested in July 2005 on charges of sexual abuse and endangering the welfare of a child.

[56] After a judge removed the more serious charges, Sewar pleaded guilty in August 2006 to attempted endangering the welfare of a child and was sentenced to one year of probation.

[66] The diocese announced in April 2021 that 300 more sex abuse lawsuits had been filed against it between August 2019 and December 2020 under the Child Victims Act.

The defendant had accused Reverend Foster P. Rogers, assistant pastor at St. Alphonsus Parish in Auburn, of sexually abusing him in 1979 when he was 15 years old.

[67] The bankruptcy case is unresolved as of August 2024, meaning that people abused as children by the Diocese of Rochester have not received monetary compensation.

The RCPA publishes the monthly Catholic Courier newspaper, the Spanish-language El Mensajero Católico, the Official Directory of the Diocese of Rochester and related digital media.