Despite acknowledging that a "reasonable person might believe" he might be biased, the Chicago federal judge who heard former House speaker J. Dennis Hastert's not-guilty plea Tuesday will continue handling his case.

Prosecutors and Hastert's defense attorneys both agreed to waive U.S. District Judge Thomas M. Durkin's offer of disqualification in letters filed with the court Thursday. That means Durkin can continue to rule on potential pre-trial motions, preside over further proceedings, and perhaps sentence Hastert, if he ultimately pleads or is found guilty.

A grand jury charged Hastert on May 28 with acting to evade bank reporting requirements and then lying to FBI agents about it. According to the indictment, Hastert made large cash withdrawals to pay an unnamed individual to "compensate for and conceal his prior misconduct" -- misconduct, law enforcement officials have told The Washington Post, involving alleged sexual molestation of a male student during Hastert's days as a teacher and coach in rural Yorkville, Ill.

Each of the two charges carries a maximum prison term of five years, although Hastert could serve considerably less, perhaps a sentence of probation only, under federal sentencing guidelines.

At Tuesday's arraignment, Durkin made a lengthy disclosure, starting with a pair of campaign donations in 2002 and 2004 worth a combined $1,500 made to Hastert's political campaigns. Durkin at the time was a lawyer in private practice, and he said he made the contributions through a law partner and never met Hastert then or at any time since "as far as I recall."

But the disclosures did not end there: Durkin described sending an e-mail to Hastert's staff in the 1990s, inquiring about a judicial nomination -- an inquiry that was not returned. He described later working alongside Hastert's son Ethan at the same firm, Mayer Brown, working closely with him on one particular case. The two were "friendly business colleagues," Durkin said, but not personal friends. And he also disclosed that his brother, Jim Durkin, is a prominent Republican politician in Illinois who has been a political ally of Hastert's. But, again, Judge Durkin said, Hastert was "not a personal friend" of his brother, who is the minority leader of the Illinois House.

"I have no doubt I can be impartial in this matter," Durkin told the parties Tuesday. But he found, given the appearance of potential conflict, there existed formal grounds for disqualification under the Code of Conduct for United States Judges. However, that disqualification can be waived by the parties, and with Thursday's letters, it is.

A third party, lawyer Andy Martin, has sent letters to Durkin calling on him to step down regardless of whether the parties in the case want him to or not.

Martin is well known as a proponent of the notion that President Obama is secretly a Muslim and was not in fact born in the United States, as his Hawaii birth certificate indicates. Durkin has not yet responded to Martin's letters, which are posted on the public court docket.