Cardinal Joseph Ratzinger, as he was known before being elected Pope Benedict XVI, came to the office in 1981 and led it for nearly a quarter of a century.
Just weeks before his elevation to the papacy in 2005, he wrote of his outrage at corrupt clerics who had soiled the "garments and face" of the Church.
"How much filth there is in the Church, and even among those who, in the priesthood, ought to belong entirely to Him [Jesus Christ]," he said.
The year after becoming Pope, he barred the founder of the influential Legion of Christ order, Mexico's Fr Marcial Maciel, from his ministry amid allegations that he had fathered children and molested students.
It was a bold step to take against a cleric who was close to the late Pope John Paul II, and is offered by some as solid proof of Benedict's intolerance of abuse, at a time when he is accused of having failed to take adequate action against suspects while still Cardinal Ratzinger.
Tried and defrocked
When Joseph Ratzinger became Prefect of the CDF, he inherited an office dating back, under various titles, to the great inquisitions of the 16th Century.
In its first incarnation, it was known as the Sacred Congregation of the Universal Inquisition and its chief mission was to defend the Church against heresy. The 17th Century astronomer Galileo was one famous target.
Known under its present name since 1965, the office is entrusted with promoting and safeguarding both Catholic doctrine and "morals throughout the Catholic world".
The job of investigating sexual abuse by priests is just one of its duties and, up until the present century, only the most contentious cases were brought to the CDF's attention, such as when a priest challenged his bishop's decision to defrock him.
In the Wisconsin case, the priest accused of abusing up to 200 pupils at a school for deaf children wrote directly to Cardinal Ratzinger, saying he had repented and asking to be left alone. No response has been found but Church proceedings against Fr Lawrence Murphy were halted.
In a recent article in Canada's National Catholic Reporter , Church affairs analyst John Allen argues that the CDF underwent a revolution in 2001 when Cardinal Ratzinger subjected all sexual abuse allegations against priests to the authority of his office.
Critics regard this decision as an attempt by the CDF to control information, noting that his directive made no mention of calling police.
It is a charge which Monsignor Charles Scicluna who, as the CDF's Promoter of Justice, is effectively its chief prosecutor, flatly denied earlier this month.
The rule "was never understood as a ban on reporting [crimes] to the civil authorities", he told L'Avvenire, the official newspaper of the Italian bishops' conference.
What the Pope's directive did do, Monsignor Scicluna told reporters, was set off an "avalanche" of cases in Rome.
Some 3,000 sexual abuse cases spanning 50 years have been processed by the CDF this century, he said, most of them originating in the US.
Of these cases, 300 involved allegations of "genuine paedophilia", he said. Most of the others concerned homosexual attraction to adolescents.
About 20% of the 3,000 cases resulted in priests being defrocked, he was quoted as saying by L'Avvenire. In most of the other cases, priests were deemed too old to face a full trial but other penalties such as bans on celebrating Mass or hearing Confession were imposed.
In his article, John Allen likens Pope Benedict to Elliot Ness, a man on a mission to clean out Church "filth".
"To accuse the current Pope of hiding [cases] is false and defamatory," Monsignor Scicluna told reporters.
At the CDF, he insisted, Cardinal Ratzinger showed "wisdom and firmness" in handling cases.
Today, the office is still handling cases involving appalling allegations.
US Cardinal Joseph Levada, current head of the office, recently ordered a fresh investigation into alleged serious sexual and other abuse by some two dozen priests at a school for deaf children in Verona, Italy.
The CDF is made up of 23 members - cardinals, archbishops and bishops - and 33 "consulters", with a staff of 37 at the Vatican.
Dealing specifically with sex abuse cases are Monsignor Scicluna, seven other priests and one lay criminalist.
For a church with more than a billion followers and about 400,000 priests, and with a remit to handle all sexual abuse cases involving priests, it seems a small team.
John Allen suggests that more could be done at local level, without Rome having to intervene directly.
"New ways should be found to hold bishops accountable for cleaning up their own mess," he says.
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