Former House speaker Dennis Hastert — stooped, silent and trailed by cameras — pleaded not guilty in federal court here Tuesday, responding to felony charges related to alleged hush-money payments made to hide what law enforcement says is an embarrassing secret dating back decades.

Hastert’s arraignment, his first public appearance since his indictment, lasted less than 20 minutes. He barely spoke, and did so softly when he was questioned about the charges against him. He did not even say “not guilty” — those words were uttered by Hastert’s attorney.

“Yes” and “Yes, sir,” Hastert said to U.S. District Judge Thomas M. Durkin, who released him on a $4,500 bond. Hastert and his attorneys remained silent afterward as they rushed past reporters into a waiting Lincoln.

Tuesday’s much-anticipated hearing did little to answer the larger questions that have captivated Hastert’s neighbors in Illinois and his former House colleagues in Washington since the May 28 indictment.

Who was Hastert allegedly seeking to keep quiet, and why? What could he have done that was worth $3.5 million to conceal? And did Hastert, a former teacher, Scout leader and wrestling coach, abuse those positions of trust?

The Post's Chris Cillizza breaks down former House speaker Dennis Hastert's indictment on charges that he broke bank laws by withdrawing large sums of money and lying about it to federal authorities. (Editor's note: This video has been updated.) (Nicki DeMarco/The Washington Post)

Hastert’s not-guilty plea suggests that he is prepared to fight the charges in court, raising the specter of another high-profile trial of a top Illinois politician in the Everett M. Dirksen U.S. Courthouse.

Most recently, Chicago’s federal courthouse was the venue of two lengthy trials for former Illinois governor Rod Blagojevich (D). The first ended in a mistrial in 2010; the second a year later ended in convictions on 17 corruption counts, including efforts to sell a Senate seat that came open when Barack Obama won the presidency. Blagojevich is now serving a 14-year prison term.

Hastert is charged with trying to mask more than $950,000 in withdrawals from various accounts in violation of federal banking laws that require the disclosure of large cash transactions, and with lying to federal investigators. But it is the alleged purpose of his cash withdrawals that has generated the most shock. According to the indictment, Hastert agreed to pay an unnamed person $3.5 million “to compensate for and conceal his prior misconduct” against that person.

A federal law enforcement official familiar with the investigation has told The Washington Post that the misconduct involved the alleged sexual molestation of a male student. The indictment identifies the person only as a resident of Yorkville, Ill. — a town about 50 miles west of Chicago where Hastert worked as a high school teacher, Boy Scout leader and wrestling coach from 1965 until 1981 — and as someone who has known Hastert for “most of [his] life.”

During the hearing, Durkin did not question Hastert about the substance of the charges against him. Instead, the judge asked the former speaker whether he understood the indictment and went over the conditions of his release.

Most of the hearing pertained to a long disclosure that Durkin — the judge — made about his various connections to Hastert. He described a pair of campaign donations he made to Hastert more than a decade ago and a period in which he worked with Hastert’s son Ethan while a lawyer in private practice. “I have no doubt I can be impartial in this matter,” Durkin said, adding that he had never met Hastert.

But he acknowledged that the potential appearance of a conflict of interest created grounds for disqualification. Durkin gave Hastert and prosecutors until Thursday to review his disclosures and determine whether to waive his offer to step aside. If either party declines, the case will be randomly assigned to another federal judge in Chicago. “I don’t want this issue to linger,” Durkin said. “I will not be offended whatever the result, I assure you.”

Hastert relinquished his passport Tuesday and agreed to remove firearms from his property in Plano, the town next to Yorkville where Hastert has lived for decades.

Hastert entered the courtroom about 15 minutes before the hearing. He consulted with his attorneys briefly but mostly sat quietly, his face resting on his curled fingers. After the hearing, neither Hastert nor his attorneys made any comment as they left the building, getting into a chauffeured SUV on Dearborn Street.

Thomas C. Green, Hastert’s lead attorney, is a Washington litigator who has represented figures in political scandals dating to Watergate.

Terry Sullivan, a former Illinois state prosecutor now in criminal defense practice in Chicago, said a jury might question FBI tactics that led to the false-statements charge: “The FBI does so well because they surprise people at their house in the morning. You don’t have a lawyer there, you’re trying to shake off sleep, and they sit down at your kitchen table.”

But Hugh Mundy, a professor at John Marshall Law School in Chicago, said prosecutors may not have an especially hard time proving their case, because they do not have to establish that Hastert had the intent to deceive the authorities.

The case, he said, remains remarkable for the contrast between the charges filed and the alleged conduct underlying them. “It sort of strikes me as a situation where a guy robs a bank and the government charges him with speeding in the getaway car,” Mundy said. “This is certainly the most sensational structuring charge that I’ve ever seen. . . . It’s usually not sexual abuse from decades ago.”

Legal observers here say they have doubts about whether the case will go to trial. They say that while Hastert is not charged with any sex-related crimes, he may not want a trial that examines the “prior misconduct” alleged in the indictment. “I wouldn’t want to go to trial, because what is [now] dirty laundry under the bed will no longer be under the bed,” said Richard Kling, a professor at the Chicago-Kent College of Law. “If I were he, I would want to get away from this building as quickly as I possibly could.”

But Sullivan said that Hastert, in the course if defending himself against the banking charges, could deny engaging in any long-secret wrongdoing — claiming, perhaps, that the unnamed recipient wrongly accused him but he decided to pay anyway.

“If all you have is your reputation, and you’re 73, and you don’t really need that money . . . it’s still plausible to me,” he said.

Several institutions associated with Hastert have distanced themselves from the former speaker since the indictment. He resigned from his lobbying firm, Dickstein Shapiro, which has removed virtually all references to him from its Web site. Wheaton College changed the name of the J. Dennis Hastert Center for Economics, Government, and Public Policy, and the Yorkville Wrestling Club said last week that its yearly Denny Hastert Wrestling Invitational probably will be renamed.

Hastert was first elected to the House in 1986, gaining the speaker’s gavel in 1999 after ethical clouds and midterm election losses prompted House Republicans to revolt against Speaker Newt Gingrich (R-Ga.), and as his Gingrich’s heir apparent, Rep. Bob Livingston (R-La.), was accused of carrying on an extramarital affair while supporting efforts to impeach President Bill Clinton for lying about his own affair with a White House intern. Hastert, then a deputy whip, emerged as a reliable and well-liked Republican who was untainted by personal peccadillos.

He went on to lead the House through the response to the Sept. 11, 2001, terrorist attacks, the approval of an Iraq war resolution and the passage of key parts of President George W. Bush’s legislative agenda, including the No Child Left Behind education law and the expansion of Medicare prescription drug benefits.

Hastert stepped down as leader after Republicans in 2006 lost their 12-year majority following a series of scandals. He resigned his seat less than a year later.

Some of the scandals concerned money and influence, such as the cash-for-earmarks schemes of Rep. Randy “Duke” Cunningham (R-Calif.). But Hastert was more deeply criticized as not acting decisively after learning that Rep. Mark Foley (R-Fla.) had sent suggestive e-mails to teenage boys serving as House pages. Foley resigned after his conduct was made public.

According to the indictment, the hush-money scheme emerged in 2010 — after Hastert left office and embarked on a career as a lobbyist. Hastert allegedly agreed to pay $3.5 million and paid out about $1.7 million before federal agents confronted him in December about the withdrawals.

Agents asked whether he had perhaps lost faith in the American banking system and was thus compelled to liquidate his savings.

“Yeah . . . I kept the cash,” he responded, according to the indictment. “That’s what I’m doing.”

Susan Berger in Chicago and David A. Fahrenthold in Washington contributed to this report.