The jury of seven men and five women acquitted Lynn on two other counts and deadlocked on attempted-rape and child-endangerment charges against his codefendant, the Rev. James J. Brennan.
District Attorney Seth Williams said his office would review the evidence before deciding whether to retry Brennan, who was accused of trying to rape a 14-year-old boy in 1996.
Williams and activists hailed Lynn's conviction as an unprecedented victory for thousands of children who were abused by priests over decades.
"This monumental case in many ways will change the way business is done in many institutions - be they religious institutions, educational institutions, day camps - where people will not protect predators," Williams said.
Lynn, 61, sat stone-faced with his eyes cast downward when jurors read their verdict after nearly 13 days of deliberations. His family members sobbed in the courtroom's front rows as he took off his black clerical blazer, spoke briefly to his lawyers, and ambled through a side door to a cell.
The lawyers, Thomas Bergstrom and Jeffrey Lindy, said that they would petition the judge on Monday to release Lynn on house arrest, and that they expected to appeal the conviction.
"He's upset. He's crushed," Lindy told reporters. "He didn't want to do anything other than help kids."
The verdict followed years of investigation and a trial that put a spotlight on thousands of confidential church records and decades of complaints of child-sex abuse by priests in the Philadelphia region. Many were locked away in the archdiocese's secret archives, files that cataloged decades of misconduct allegations against priests.
At the center was Lynn, the former aide to Cardinal Anthony J. Bevilacqua who emerged as a primary target during two grand jury investigations over the last decade.
As clergy secretary from 1992 to 2004, Lynn was the administrator the cardinal tapped to investigate the complaints, and recommend treatment or assignments for accused priests.
Prosecutors asserted that his job became more about protecting the church than protecting children. Lynn, they said, lied to some victims, never sought out others, and, in a few cases, suggested to priests that they may have been seduced by their young accusers.
Jurors found Lynn guilty of endangerment for letting Edward Avery, then a parish priest, live and celebrate Mass at St. Jerome Church in Northeast Philadelphia in the mid-1990s.
The evidence showed that Lynn knew Avery had abused a teen boy he met at a Montgomery County parish in the 1970s. In 1994, Lynn included Avery on a list of 13 priests he deemed "guilty of sexual misconduct with minors."
But instead of being removed, Avery was treated at a church-owned hospital and reassigned to hospital chaplaincy. He was allowed to live in the rectory at St. Jerome, a sprawling parish with an elementary school.
In 1999, Avery twice sexually assaulted a 10-year-old altar boy at the church. Defrocked in 2006, Avery pleaded guilty to the assault in March.
The onetime altar boy, now 23, was one of nearly 20 alleged victims who testified at the trial. Most described, often in graphic and tearful testimony, how their parish priests had groped, molested, or raped them when they were young and how the abuse shaped and in some cases ruined their lives.
In a disputed ruling, the judge let prosecutors introduce evidence about nearly two dozen other priests who weren't charged or represented in the case. The prosecutors argued that it was necessary for jurors to understand how Lynn's decisions reflected a long-standing pattern or practice by church leaders. But the effect was weeks of testimony that seemed to put the church itself on trial.
Jurors weren't necessarily convinced of a larger plot. They acquitted Lynn of conspiring with Avery or others.
"This was not about the Catholic Church - this was about what people did," said Isa Logan, a 35-year-old bank worker from West Philadelphia who served as jury foreman.
Lynn's lawyers noted that he was acquitted on three of the original four charges against him. (The judge had ruled another conspiracy count unproven during the trial.)
And they held to their argument that he was being made a scapegoat for decisions and failings of his bosses, notably Bevilacqua, who ultimately approved or rejected Lynn's recommendations involving priests' assignments.
They pointed to a handwritten note found weeks before trial suggesting that the cardinal directed his top deputies to shred Lynn's list of abusive priests.
During three days of sometimes combative testimony, Lynn insisted he had done more than any other church official to remove predator priests. "I did my best with what I could do," Lynn testified.
Prosecutors never denied that others were equally culpable, and grilled Bevilacqua during a private deposition two months before his death in January. The other church officials implicated in the shredding, Bishops Joseph R. Cistone and Edward P. Cullen, were not called as witnesses.
Williams would not say whether they, or others, might still face prosecution.
"Many members of the Roman Catholic Archdiocese of Philadelphia had dirty hands," the district attorney said in his first public comments since the judge lifted a yearlong gag order. "My job is to find people we can prove guilty beyond a reasonable doubt."
Brennan, who has been on restricted ministry since his accuser filed a complaint in 2006, said he was relieved by the outcome. His attorney, William J. Brennan, no relation, maintained that the priest, who was the subject of a single accusation, should never have been tried with Lynn.
Lynn has been living with relatives in Reading since being suspended last year from his post as pastor of St. Joseph in Downingtown. His lawyers said the judge's decision to imprison the monsignor immediately - Avery was allowed to remain free on bail for 10 days after admitting to abusing the altar boy - was disproportionately unfair and legally flawed.
Lynn has attended every hearing for a year, and has no criminal history or even a passport, Lindy said.
"He has been living under the sword of Damocles for a decade or more," said the lawyer. "He is not going anywhere. He knew this day could come."
That argument enraged Assistant District Attorney Patrick Blessington, the prosecution leader who in the final weeks of the trial - and as deliberations continued for weeks - repeatedly exploded at Lynn and a defense team he liked to point out was being paid by the church.
Blessington argued the evidence showed that Lynn was arrogant and contemptuous of the criminal justice system, and that he lied to victims, investigators, grand jurors, and the jurors at trial.
"Treat him like the criminal he now is," Blessington told the judge. "This is a case that is going to call for a lengthy jail sentence. Let's start it today. Today, to jail. That's justice."
The trial drew worldwide attention, and scarred tens of thousands of Philadelphia-area Catholics and their clergy. The investigation that led to Lynn's conviction also prompted the archdiocese to remove five active priests for past sexual misconduct with minors, suspend 17 others while it reviewed claims against them, and revamp its policies for handling abuse complaints.
In a statement after the verdict, the archdiocese said it was on "a journey of renewal" and reform. "The lessons of the last year have made our church a more vigilant guardian of our people's safety," it read.
Advocate groups such as the Survivors Network of Those Abused By Priests and BishopAccountability.org praised the verdict and its potential impact.
"Because of the Lynn verdict, bishops and church officials are now accountable - they are no longer immune from judgment and punishment," said Terence McKiernan, president of BishopAccountability.org.
Two men arrested in February 2011 with Lynn, Avery, and Brennan face September trials. The Rev. Charles Engelhardt and former schoolteacher Bernard Shero are accused of molesting the same altar boy at St. Jerome, but were granted separate trials because neither was supervised by Lynn. Engelhardt belongs to the Oblates of St. Francis de Sales, an independent religious order.
The archdiocese, Lynn, and others have been named in at least nine lawsuits filed by alleged abuse victims since the case broke. Most of those suits incorporated the grand jury findings on Lynn and the church, and will now rely on the thousands of previously secret documents aired publicly at the trial.
The verdict "has set a pathway and a standard for prosecutors across the United States," said Marci Hamilton and Jeffrey Anderson, lawyers for seven plaintiffs.
Contact John P. Martin at 215-854-4774, firstname.lastname@example.org, or follow @JPMartinInky on Twitter.
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