Msgr. Lynn is the highest-ranking diocesan official ever charged with alleged crimes in connection with the scandal of sexual abuse of children by clergy that has roiled the Catholic Church in the United States for the past decade.
He faces two charges of endangering the welfare of a child.
Father Brennan, 48, is accused of attempting to rape a 14-year-old boy in 1996.
Both priests remain free on bail and on administrative leave from the archdiocese, so they may not function publicly as priests.
A third defendant in the trial, former priest Edward Avery, 69, pleaded guilty March 23 to involuntary deviate sexual intercourse with a boy in 1999, as well as to a charge of conspiracy.
Assistant District Attorney Jacqueline Coelho in her opening argument emphasized the alleged conspiracy of archdiocesan officials, especially Msgr. Lynn. Coelho repeatedly referred to the "secrets" and the archdiocese's "secret archive files" of priests accused of sexual assault or misconduct dating to the 1940s, and to Msgr. Lynn as the keeper of those secrets.
As archdiocesan secretary for clergy from 1992 to 2004, his role, Coelho said, was as a "human resources manager" charged with "investigating crimes committed against children by priests" and to "protect the church, protect children and protect priests' privacy."
"You can't protect children without bringing allegations (of misconduct) to light," she said. "(Msgr.) Lynn kept secrets in the dark, in the secret archives; he kept parishioners in the dark."
Coelho cited the cases of 12 archdiocesan priests and their alleged sexual abuse of minors. The cases were all part of the 2005 grand jury report that widely exposed the crisis of sexual abuse by priests in the Philadelphia Archdiocese over more than 60 years.
The cases have become notorious and underscored what Coelho termed a conspiracy to endanger children in a "concerted effort to protect the church from scandal."
Msgr. Lynn's defense attorney, Thomas Bergstrom, echoed Sarmina's opening injunction to the jurors that the defendants are presumed innocent during the trial, and that the jury must find his client guilty beyond a reasonable doubt.
Bergstrom acknowledged that sex abuse occurred in the archdiocese, but said he does not represent the church or the archdiocese, but only Msgr. Lynn.
His client, Bergstrom said, "knows (sexual abuse of a child) is awful, but he and perhaps he alone is the one who tried to correct it."
Bergstrom said Msgr. Lynn met with victims and priests accused of abuse, and documented everything in memorandums and letters. Msgr. Lynn forwarded that information and recommendations on priestly assignments "to the chain of command," but had no authority to assign priests as secretary for clergy.
"The only man in the archdiocese that can assign priests is Cardinal (Anthony J.) Bevilacqua," Bergstrom said.
The late cardinal led the archdiocese from 1988 to 2003. Archbishop Charles J. Chaput is the current head of the Philadelphia Archdiocese.
Bergstrom said evidence in the trial would show that Cardinal Bevilacqua rejected Msgr. Lynn's recommendation for assignment of then-Father Avery. The cardinal instead assigned him to hospital ministry and residence in a parish where Avery would later be accused of sexual assault of a boy, in the incident to which he pleaded guilty.
"Some have the theory that there is a massive conspiracy to harm children in the archdiocese," Bergstrom said. "But that's not this case, not his (Msgr. Lynn's) case."
Bergstrom then described how his client tried to address the issue of priest misconduct.
More than a year after Msgr. Lynn took the helm of the clergy office, reports started to surface about allegations of priest sex abuse from past decades. The priest and an aide began an investigation of priest personnel files and in locked document archives at the archdiocesan headquarters in Philadelphia. They wanted to assess, Bergstrom said, "how bad is this problem?"
Their result, he said, were 323 files from which they compiled 35 names of priests with accusations or credible evidence of sexual abuse.
Their memo of Feb. 18, 1994, attached a list with the names, which was sent up through the archdiocesan administration of the time to Msgr. Lynn's superiors, including Cardinal Bevilacqua.
Although the cardinal ordered the memo shredded, a copy was placed in a locked box not discovered until 2006 and not produced for the court in the trial until recently.
William Brennan, the defense lawyer for Father James Brennan -- the two are not related -- emphasized for jurors the ease with which names could be confused in the trial. Another priest with the same last name -- Father Robert Brennan -- was named in the grand jury report and cited by Coelho as an allegedly abusive priest.
Brennan the lawyer said evidence will cast doubt on the veracity of the attempted rape claim and perhaps on the character of the person making it.
Coelho's vivid descriptions of alleged sexual abuse by priests going back to 1948 through the 1990s gave a preview of the kind of details that are likely to emerge in the trial.
All attorneys suggested the trial might last from several weeks to several months.