Ali al-Marri, 43, appeared Monday in U.S. District Court in Peoria, where he entered his not guilty plea. He was arrested in central Illinois in 2001. He didn't say much during his 30-minute hearing before a US district judge except a quiet "yes" or "no."
Federal authorities alleged the graduate student was an al-Qaida agent tied to organizers of the Sept. 11, 2001 attacks.
Al-Marri was a legal U.S. resident when he was arrested but became the only "enemy combatant" in custody on American soil.
The native of Qatar was held without charges for more than five years at a Navy brig in South Carolina.
President Barack Obama last month ordered al-Marri surrendered to civil authorities after he was indicted in Peoria on federal charges of providing material support to terror and conspiracy.
Al-Marri's case has been transferred to Illinois, where a federal grand jury indicted him.