The Justice Department charged "enemy combatant" Ali Saleh Kahlah al-Marri for his alleged role in terrorist activities, according to a source familiar with the case.
A federal grand jury unsealed the indictment Friday, after handing it up a day earlier in a federal court in Illinois.
The two-page indictment alleges that al-Marri provided material support for terrorism, but it doesn't address how he is believed to have broken the law and aided terrorists.
Al-Marri was charged with two counts of providing material support and resources to a foreign terrorist organization, Al Qaeda.
The case against him alleges that he "knowingly conspired with others" to help Al Qaeda as early as July 2001 and continuing through Dec. 12, 2001.
Al-Marri, who is currently being held on U.S. soil, was first arrested in Illinois a few months after the Sept. 11 terrorist attacks on New York and Washington.
At the time, al-Marri was charged with credit card fraud and other crimes. But in June 2003, President Bush declared him an "enemy combatant," accusing him of being a sleeper agent.
Authorities transferred him to a Navy Brig in South Carolina, where he has been ever since.
Charging al-Marri indicates a major shift from the Bush Administration, which insisted that he should face a military tribunal and stay out of the civilian court system.
Al-Marri and his legal team have challenged his detention, insisting that he has been subjected to torture and other cruel, inhuman and degrading treatment.
They say he is currently in solitary confinement "under severe restrictions" and has not seen his family in nearly six years, speaking to them only a couple of times.
The Supreme Court is currently expected to hear his challenge sometime in April.
New York University's Brennan Center, which is representing al-Marri, says on its Web site that they have "long argued that America's criminal justice system can and should handle cases in which individuals are accused of terrorism."
White House Press Secretary Robert Gibbs declined to comment on the al-Marri charges at a Thursday briefing.
FOX News' Mike Levine and Catherine Herridge contributed to this report.