Babar Ahmad and Syed Talha Ahsan who were extradited from the UK have pleaded not guilty to US federal charges of providing suspected terrorist groups in Afghanistan and Chechnya with financial aid, arms and personnel.
The two suspects appeared in a New Haven, Connecticut federal district court, hours after being extradited along with three other suspects on Saturday.
If convicted, the two men face life sentences.
Abu Hamza al-Masri, Khalid al-Fawaz and Adel Abdul Bary, the three others extradited, appeared in front of a lower Manhattan court.
Al-Masri was formally arraigned for the 11 charges levied against him, but is not expected to enter a response until Tuesday.
The preacher is charged with conspiring with Seattle men to set up a terrorist training camp in Oregon and of helping
abduct 16 hostages, two of them US tourists, in Yemen in 1998.
Lawyers have asked that al-Masri, one of the last major terror suspects related to al-Qaeda to come to trial in the US, be given medical treatment. Upon entering the country, al-Masri's prosthetic arm was confiscated.
Khaled al-Fawwaz and Adel Abdul Bary who appeared alongside al-Masri in court, plead not guilty.
The court appearances came just hours after a last-ditch effort to stop the extraditions was rejected by a ruling of the London High Court.
The five defendants have been battling extradition for between eight and 14 years.
A motorcade carrying Egyptian-born al-Masri, the best known of the defendants, left the airport in New York on Saturday, taking him to a federal lockup next to the federal courthouse in lower Manhattan to face charges.
Al-Fawaz and Bary will be housed in the same lockup as al-Masri.
Ahmad, a computer expert from South London, had been held in a UK prison without trial for eight years after being accused of raising funds for terrorism with his co-accused, Ahsan, through a US-hosted website.
Ahmad made efforts to secure GPS devices, Kevlar helmets, night vision goggles, ballistic vests and camouflage uniforms, prosecutors said.
The two are expected to face hearings in Connecticut where the courts have jurisdiction over their case because their website was hosted in the US state.
On Friday, all five suspects left from the Mildenhall air force base, in eastern England, which is used by the US military.
The two jets provided by the US authorities took off shortly before midnight (23:00 GMT), Scotland Yard police headquarters said.
Long legal battle
Britain's High Court ruled on Friday that they had no more grounds for appeal in their years-long battles to avoid facing charges in the US.
The defendants will face 11 charges including planning to establish a "terrorist" training camp for Islamic jihadists in the US state of Oregon and conspiracy to take hostages in Yemen in 1998.
"In the past year, two parliamentary committees, numerous senior politicians from all parties, the mayor of London, and 150,000 ordinary members of the British public have called for Babar Ahmad to be tried in the UK"
- Fahad Ansari, Free Babar Ahmad Campaign
Bary and al-Fawaz were indicted with others, including Osama bin Laden, for their alleged roles in the bombings of two US embassies in east Africa in 1998. Al-Fawaz faces more than 269 counts of murder.
The High Court in London's decision to dismiss the appeal of the five defendants marks the end of a long legal battle over their fate.
Their appeal came after the European Court of Human Rights backed successive UK courts in ruling for extradition.
The Home Office said it wanted to deport them "as quickly as possible".
Judges Thomas and Ousley said in their ruling there was an "overwhelming public interest in the functioning of the extradition system" and that there was "no appeal from our decision".
Al Jazeera's Kristen Saloomey, reporting from New York, said though the legal battle in London may be over, a fresh one is about to begin in the United States.
This will be "a long, slow process ... with many appeals", that could take anywhere between one and three years, said our correspondent.
Al Jazeera's Saloomey went on to say that the controversial case has "tested the boundaries of national security and civil liberties in the United States".
Concerns about the case
Fahad Ansari, a human-rights lawyer with Free Babar Ahmad Campaign, told Al Jazeera on Friday he was disappointed with the High Court ruling.
"In the past year, two parliamentary committees, numerous senior politicians from all parties, the mayor of London, and 150,000 ordinary members of the British public have called for Babar Ahmad to be tried in the UK," he said.
|Babar Ahmad has been held in a UK prison without trial for eight years on suspicion of raising funds for terrorism
"This decision flies in the face of that and questions need to be asked as to how and why members of the judiciary have ignored both the public interest in Babar Ahmad being prosecuted in the UK."
The suspects applied to the High Court for a last-minute halt, with al-Masri's lawyers saying his deteriorating health means it would be "oppressive" to send him to a US prison.
Lawyers for al-Masri, said he suffered from depression, chronic sleep deprivation, diabetes and other ailments and was in need of medical tests.
Some lawyers and politicians also expressed concerns about the case, because Britain agreed to extradite Ahmad even though his alleged crimes were committed in Britain and British courts declined to prosecute him for lack of evidence.
Morris Davis, a Washington-based law professor, said the defendants will receive a fair trial in the United States.
"Justice will be done", said the Howard University professor. Citing the 14 years since the initial hostage situation, Davis told Al Jazeera "it's going to be several more years before [the defendants] actually show up in court".
However, our correspondent said some in the US want the defendants to be tried in a military tribunal, not a civilian court.
The cases, said Al Jazeera's Saloomey, raise the question of where "the proper place is to try al-Qaeda-related terror cases? Some people in the US believe these suspects don't deserve the same rights as US citizens".
In prison since 2004, Ahmad has been held without charge for the longest period of any British citizen detained since the September 11 attacks.
In a statement read on his behalf outside court, Ahmad said his case had exposed flaws in US-UK extradition arrangements. "I leave with my head held high, having won the moral victory," he said.
His father, Ashfaq Ahmad, said he would continue to fight for his son.
"It's not just one Babar Ahmad. Tomorrow there will be another Babar Ahmad and another one," he said.