"Yes, I do, thank you," he answered when asked by a judge if he grasped the accusations against him.
Then U.S. Magistrate Judge W. Curtis Sewell asked whether he understood the possible penalties, including life in prison.
"Yes I do, sir," Lindh said in a quiet voice.
Wearing a green prison jumpsuit, his previous long hair and beard shorn, Lindh stood straight with his arms at his side throughout the hearing, glancing several times to prosecutors at his right as they outlined the charges against him. His attorney and several federal marshals stood behind him.
Five attorneys, all deeply experienced, have signed on to defend Lindh, and they were quick to fire their opening round, reports CBS News Correspondent Jim Stewart.
"For 54 days, the United States government has kept John Lindh away from a lawyer," said attorney James Brosnahan.
The government responded that the defendant was offered a lawyer, but turned one down.
"Mr. Walker had signed a statement waiving his right to a counsel when he spoke to the FBI," said U.S. Attorney Paul McNulty.
Lindh will be kept in custody for now but has another hearing Feb. 6. At that time, the judge will determine whether he will remain in custody without bail.
Heavy security surrounded Lindh's arrival at the courthouse in Alexandria, Va., just a few miles from the Pentagon, which was extensively damaged in the Sept. 11 attacks.
Snipers stood on the roof and armed officers patrolled outside the building, where the government also is prosecuting Zacarias Moussaoui, the only person charged with helping the Sept. 11 attackers.
Lindh's parets, who had met privately with their son and his attorney before the hearing, sat in the second row of the courtroom to watch the proceedings.
"John loves America. We love America," his father, Frank Lindh, said after the hearing. He said his son was innocent of the charges.
"It's been two years since I last saw my son. It was wonderful to see him this morning. My love for him is unconditional and absolute," said his mother, Marilyn Walker. "I am grateful that he has been brought home to his family, me, his home and his country."
Lindh faces four charges, according to the government's criminal complaint. Those are engaging in a conspiracy to kill Americans in Afghanistan, providing material support and resources to foreign terrorist organizations, engaging in prohibited transactions with the Taliban and providing goods and services to and for the benefit of the Taliban.
Lindh was captured in November near the northern Afghan city of Mazar-e-Sharif after an uprising by Taliban and al-Qaida prisoners there. An American CIA officer, Johnny "Mike" Spann, was killed during the uprising.
Lindh left this country two years ago to study Arabic and Islam in Yemen, and then apparently went to Pakistan and from there to Afghanistan.
A Californian who converted to Islam at age 16, Lindh said he trained for seven weeks in an al-Qaida camp where Osama bin Laden visited three to five times, giving lectures "on the local situation, political issues, old Afghan/Soviet battles, etc.," an FBI affidavit says.
When he learned of the Sept. 11 attacks on the radio, according to the affidavit, Lindh said it was his understanding "that bin Laden had ordered the attacks and that additional attacks would follow."
© MMII, CBS Worldwide Inc. All Rights Reserved. This material may not be published, broadcast, rewritten, or redistributed. The Associated Press contributed to this report