In opening statements at the trial of priests accused of conspiring to cover up clergy sex abuse, Assistant District Attorney Jacqueline Coehlo said of Lynn: "You can't protect the church without keeping the allegations in the dark. He kept the parishioners in the dark and he kept the faithful in the dark," the Philadelphia Inquirer reported.
Lynn, who is accused of endangering the welfare of children, is the highest-ranking member of the U.S. Catholic hierarchy to have his case reach trial on charges related to coverup allegations.
Another priest overseen by Lynn, the Rev. James Brennan, is accused of anal rape of a 14-year-old boy in 1996 at the priest's apartment in a Philadelphia suburb.
He pleaded not guilty to charges that include rape and sexual assault and is being tried with Lynn.
The Rev. Edward Avery, who Pope Benedict XVI defrocked in 2006, was originally to go on trial with Lynn but was sentenced Thursday to 2 1/2 to 5 years in prison after pleading guilty.
He was accused of engaging in oral sex with a 10-year-old altar boy at a Philadelphia parish in the late 1990s.
An additional Philadelphia priest and a former lay teacher at a Catholic school charged with sexually abusing the same boy involved in Avery's case have also pleaded not guilty and are expected to go on trial later this year.
Prosecutors said they planned to present evidence Lynn learned in the 1990s of allegations two priests had engaged in inappropriate conduct with minors, but failed to stop them from being assigned to roles involving contact with children or to inform parishioners of the allegations.
The two priests later sexually abused two boys in separate incidents, prosecutors allege.
Lynn's defense attorneys argue the charges against him are baseless because he wasn't directly responsible for the welfare of the two boys.
They allege his superiors were responsible for the coverup and point to recently discovered diocesan files suggesting Cardinal Anthony Bevilacqua, a former archbishop of Philadelphia who died Jan. 31, ordered shredded documents Lynn prepared that named priests accused of sexual abuse.
Defense lawyers say the documents show Lynn wasn't part of a coverup conspiracy. Prosecutors say the documents prove he had prior knowledge of abuse allegations against Avery.
Bevilacqua, who led the Philadelphia diocese from 1988 to 2003, wasn't charged. He provided videotaped witness testimony in November that may be played at the trial, The Wall Street Journal reported.