The 12-member jury acquitted Monsignor Lynn, of the Archdiocese of Philadelphia, on a conspiracy charge and a second count of endangerment after a three-month trial that prosecutors and victims rights groups called a milestone in the sexual abuse scandals that have shaken the Catholic church.

Despite the mixed outcome, the guilty verdict was widely seen as a victory for the district attorney’s office, which has been investigating the archdiocese aggressively since 2002, and it was hailed by victim advocates who have argued for years that senior church officials should be held accountable for concealing evidence and transferring predatory priests to unwary parishes.

Monsignor Lynn sat impassively as the jury read the verdicts, but some relatives behind him were in tears. Judge M. Teresa Sarmina of the Common Pleas Court revoked his bail and the monsignor stood up, removed his black clerical jacket and was led from the courtroom by sheriff’s deputies. His conviction could result in a prison sentence of three-and-a-half to seven years.

The trial sent a sobering message to church officials and others overseeing children around the country, a message punctuated by the conviction of Monsignor Lynn, who was an aide to the late Cardinal Anthony J. Bevilacqua.

“I think that bishops and chancery officials understand that they will no longer get a pass on these types of crimes,” said Nicholas P. Cafardi, a professor of law at Duquesne University, a canon lawyer and frequent church adviser.  
“Priests who sexually abuse youngsters and the chancery officials who enabled it,” he said, “can expect criminal prosecution.” 

The trial cast a harsh light on the top leadership of the archdiocese, especially Cardinal Bevilacqua, the archbishop of Philadelphia from 1988 to 2003, who died in January. Monsignor Lynn’s own lawyer told the jury that “in this trial, you have seen the dark side of the church.”

The revelations of sexual abuse and seeming official indifference have tormented an archdiocese that was long known for imperious leaders and an insular camaraderie among its priests – “the priestly equivalent of the blue wall of silence,” said Rocco Palmo, the Philadelphia-based writer of Whispers in the Loggia, a blog on Catholic affairs. It has also been costly: the financially ailing archdiocese said this week that legal fees and internal investigations spurred by the abuse cases had cost $11.6 million since early 2011.

Cardinal Bevilacqua and his aides, the prosecutors argued, sought to avoid scandal and costly lawsuits at almost any price, putting the reputation of the archdiocese ahead of protecting vulnerable children.

Before the verdict, Monsignor Lynn’s lawyers promised to appeal any conviction, arguing that the law on child endangerment at the time did not apply to supervisors and that the judge had allowed prejudicial evidence, among other issues.
Monsignor Lynn, 61, served as secretary for clergy for the 1.5 million-member Archdiocese of Philadelphia from 1992 to 2004, in charge of recommending priest assignments and investigating abuse complaints. Prosecutors said he played down credible accusations and reassigned known predators to unwary parishes.
The prosecutors presented a flood of evidence, legal experts said, that the archdiocese had concealed abuse accusations and that Monsignor Lynn had not acted strongly to keep suspected molesters away from children, let alone to report them to law enforcement.

But the tortuous jury deliberations and mixed verdict showed the difficulty of placing criminal blame on one church official when there was evidence that others, starting with the cardinal at the time, had worked to prevent bad publicity and lawsuits. The jurors also wrestled with the definition of conspiracy, at one point asking the judge to define “agree,” and with the question of criminal intent on the part of Monsignor Lynn, who presented himself as an affable man who tried his best.
This article has been revised to reflect the following correction:
Correction: June 22, 2012

A previous version of this article incorrectly stated that the jury had deadlocked on two counts against Msgr. William J. Lynn; the jury acquitted Monsignor Lynn of conspiracy and a second count of endangerment.