The radical preacher entered no plea to 11 charges including hostage-taking, conspiracy to establish a militant training camp and calling for holy war in Afghanistan.
Hamza, 54, who was extradited from the UK on Friday after a lengthy legal battle, went into the dock in New York without the hooks that replaced his hands that were blown off by a bomb. Officials ordered them to be removed for security reasons.
The courtroom in which the cases are to be heard is a few blocks from the scene of the 9/11 atrocity, which Hamza hailed as “a towering day in history”,
The overnight trip to the US came after an extradition fight that ended when the High Court ruled the men had no more grounds for appeal. They had been battling extradition for between eight and 14 years.
Two other suspects, Adel Abdul Bary, 52, an Egyptian, and Khaled al-Fawwaz, 50, a Saudi, are charged with conspiring with members of al-Qaeda to kill US nationals, with Bary linked to the 1998 bombings of the US embassies in Kenya and Tanzania, which resulted in the deaths of 224 people.
Babar Ahmed, 38, and Talha Ahsan, 33, both British, are accused of providing terrorists in Afghanistan and Chechnya with cash, recruits and equipment and appeared in court in New Haven, Connecticut. US Attorney Preet Bharara called the extraditions “a watershed moment in our nation’s efforts to eradicate terrorism”.