Lead prosecutor Patrick Blessington angrily declared he would seek the maximum seven year prison term for the monsignor, and, describing him as a flight risk, immediately moved to revoke the Lynn's bail.
"He deserves to go to prison like the criminal he is," Blessington said.
The verdict seemed to be a blow to both the defendants and the prosecution.
Judge M. Teresa Sarmina revoked the monsignor's bail and immediately remanded him into custody. He was led out of the courtroom by two sheriff's deputies to a holding area. Sarmina said she would consider a motion for house arrest.
The only count on which Lynn was convicted involved a victim that he acknowledged in testimony he had dropped the ball on. He had apologized for his failings on the witness stand.
Jury foreman Isa Logan, 35, said the 13 days of deliberations had been hard going, but the jury had followed the law as the judge told them about it.
None of the other jurors wanted to comment.
District Attorney Seth Williams said at a news conference that other church officials shared responsibility for the abuse.
"No doubt there were many others who were culpable," said Williams. "But Lynn was charged because the church's own documentation demonstrated his direct participation.
"Many bad men have done evil things and then hidden behind higher-ups. With this verdict, there should be no doubt about the nature of Monsignor Lynn's actions," Williams said. "As a Catholic, I am hopeful that his successors in the church, and in other institutions, will not tolerate such behavior in the future."
The Archdiocese of Philadelphia, in a statement, said it had embarked on a "journey of reform and renewal that requires honesty and hope" and offered an apology to victims of clergy sexual abuse.
"Now and in the future, the Church will continue to take vigorous steps to ensure safe church environments for all the faithful in Philadelphia," the statement said.
In Northeast Philadelphia, Ed Burgoon, 76, a member of St. Jerome's parish, was shocked at the outcome of the trial.
Burgoon said Brennan had been scheduled to celebrate his daughter's wedding but was transferred the week before the ceremony.
Burgoon was surprised the jury had come to a stalemate over the charges against Brennan.
"He's the one I thought would be convicted, not Lynn," Burgoon said. "Lynn was just doing what the archbishop was telling him to do."
Brennan should be tried again, Burgoon said. He compared the case against the Philadelphia clergy to the concurrent case playing out in Bellefonte against former assistant Penn State football coach, Jerry Sandusky.
Burgoon was sanguine about the Sandusky's chances with the jury: "I believe he'll get away with it. Penn State can buy anything."
What does Burgoon think is next for Brennan?
"He may go back to being a priest," Burgoon said. "God help us."
Outside the Basilica of SS. Peter and Paul in Center City, John Barone of Rochester said the guilty verdict was "a long time coming."
Barone, a nonpracticing Roman Catholic, said the jury's message was loud and clear.
"Watch out," Barone said.
"It puts people on notice that no matter how high you are, you can't shield yourself with a collar."
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Jennifer Lin, John Martin, Melissa Dribben and Julie Zauzmer contributed to this article.