Archbishop of San Francisco William J. Levada wrote a letter to parishioners of the Archdiocese on January 30, 2004, announcing the release of the results of the John Jay study on child sexual abuse in the U.S. Catholic Church from 1950 to 2002. Archbishop Levada stated that between 1950 and the present, the total number of priests in ministry for the Archdiocese was estimated to be 3,606, including diocesan priests, religious order priests and priests on assignments from other dioceses or working as summer replacements. The Archdiocese did not include in this total religious order priests who worked in private universities, high schools or grammar schools operated by a religious order.
A total of 56 priests in ministry for the Archdiocese of San Francisco were accused of child sexual abuse by 148 victims. Of the 56 priests with allegations made against them, 51 were deemed credible.
As of January 2004, the Archdiocese of San Francisco had 66 pending child sexual abuse lawsuits against it, all of which were filed during the one-year legislative window allowing survivors of sexual abuse to bring claims which were otherwise time-barred by the statute of limitations.
The Archdiocese of San Francisco was established in 1853 and once encompassed virtually all of northern California. During the period of time of the John Jay study from 1950 to 2002, there were periods of time when the territory and personnel of neighboring dioceses were part of the Archdiocese of San Francisco.
On May 13, 2005, Cardinal William Levada, former Archbishop of San Francisco, was appointed the Prefect of the Congregation for the Doctrine of the Faith (CDF) by Pope Benedict XVI. The CDF is responsible for conducting investigations of clergy accused of sexually abusing minors. Twenty years prior, when Levada worked as auxiliary bishop in the Archdiocese of Los Angeles, Levada shelved the report presented by Rev. Thomas Doyle, Raymond Mouton, Jr. and Rev. Michael Peterson, calling for immediate action to deal with child sexual abuse in the Catholic Church. Cardinal William Levada held his position at the CDF until June 2012.