Jose Padilla, a US citizen held without charge for more than three years as an enemy combatant, has been charged with planning to undertake "violent jihad".
Jose Padilla was arrested in Chicago in May 2002
Mr Padilla, 35, was arrested in Chicago in May 2002 on suspicion of planning to explode a radioactive "dirty bomb".
The indictment does not mention that allegation, accusing him and four other people of conspiracy to kidnap, murder and maim US citizens overseas.
The charge came as another American was convicted of belonging to al-Qaeda.
A jury in Virginia found Ahmed Omar Abu Ali, 24, guilty of nine counts including plotting to kill President Bush and to hijack a plane.
His lawyer says he will appeal.
The government had been resisting calls to try Mr Padilla in civilian courts.
The indictment avoids a Supreme Court battle over how long the government could hold a US citizen without charges.
A lower court in September upheld the government's right to hold Mr Padilla indefinitely - but his lawyers had been planning to fight that ruling.
In connection with Tuesday's indictment, Mr Padilla is being transferred from military to civilian jurisdiction.
The BBC's Jonathan Beale in Washington says that amounts to a U-turn by the government.
Mr Padilla has been under military arrest and was one of only two US citizens designated an enemy combatant.
'Terrorist support cell'
US Attorney General Alberto Gonzales said the charges related to allegations that Mr Padilla travelled overseas to train as a terrorist.
If convicted, he could face life in prison.
The other men named in the indictment are Adham Hassoun, Mohomed Youssef, Kifah Jayyousi and Kassem Daher.
"All of these defendants are alleged members of a violent terrorist support cell that operated in the United States and Canada," Mr Gonzales said in announcing the indictment.
Three of the men had been charged before. The new indictment adds Mr Padilla and Mr Daher.
Mr Padilla's lawyers had challenged Mr Bush's right to hold Mr Padilla indefinitely as an "enemy combatant".
They argued that the president was exceeding his authority by denying such prisoners access to lawyers and courts.
Mr Padilla is a former Chicago gang member who converted to Islam.