Lawyers for the two priests on trial Monday had requested a postponement to deal with the fallout from the guilty plea entered last week by a co-defendant.
They worried it might taint the jury. But, after two hours of closed door discussions, the judge proceeded to trial.
Monsignior William Lynn is the highest ranking church official yet to face criminal charges in the ongoing sex abuse scandal.
Lynn is accused of conspiracy and endangering children during the 12 years he headed up the office that investigated sex abuse allegations.
The state alleges that he and others buried allegations in a "secret archives file" and helped reassign known predators to other parishes where they continued to have access to children.
The prosecution contends Lynn was more concerned about the church's reputation and protecting it from lawsuits than protecting the victims.
Lynn's lawyer, Tom Bergstrom, says Lynn is a sacrificial lamb who did his best to root out sexual predators.
He told the jury that Lynn repeatedly passed information and recommendations up the chain of command to the late Cardinal Anthony Bevilacqua.
Bergstrom says Lynn is the one who unearthed the names of 35 abusive priests from the "secret archives file" only to have Bevilacqua order the list destroyed.
Bevilacqua died the day after the judge ruled he was competent to testify in the trial.
Father James Brennan is on trial accused of attempted rape and conspiring with Lynn.
Former priest Edward Avery was also to go on trial today, but he pled guilty late last week to sexually assaulting a 10-year-old boy and conspiracy.
Before the trial started this morning, the judge instructed the jury to keep an open mind and not read anything into Avery's absence and not to ask questions about it.