Mr Reid was trained by al-Qaeda, indictment says
The 28-year-old entered "not guilty" pleas on all nine charges.
If convicted, he could spend the rest of his life in prison.
The US Justice Department says it believes Mr Reid to be a highly trained terrorist linked to the al-Qaeda network led by Osama Bin Laden.
Impassive
Mr Reid was brought to the court in a motorcade amid tight security. He was wearing an orange prison uniform and heavy shackles at his ankles and wrists.
He stood impassively in the dock, keeping his head lowered for much of the 10 minute hearing.
The magistrate, Judith Dean, read out the charges against him and asked whether he pleaded guilty or not guilty, to which he replied in a soft voice "not guilty".
Moments later he was taken away.
The indictment said Mr Reid did "attempt to use a weapon of mass destruction ... consisting of an explosive bomb placed in each of his shoes."
It also said he "received training from al-Qaeda in Afghanistan." But it provided no other details about Mr Reid's alleged ties to the network.
Al-Qaeda connection
In a statement, Tamar Birckhead, one of Mr Reid's court-appointed attorneys, said the indictment does not accuse Mr Reid of acting for a terrorist group.
"We note that the indictment does not allege that any of the crimes charged were committed on behalf of or to further the cause of al-Qaeda or any other terrorist organisation. We are aware of no basis for such an allegation," Ms Birckhead said.
"The charges contained in the indictment are exceptionally serious and reflective of our intention to prosecute Richard Reid to the fullest extent of the law," said Michael J Sullivan, US attorney for Massachusetts.
The US authorities say that Mr Reid was on a suicide mission on 22 December and would have blown up an American Airlines flight between Miami and Paris had he not been overpowered by passengers.
Scouting missions
Prosecutors believe he carried out scouting missions for the al-Qaeda network, identifying targets in the Middle East.
They also believe he may have been an associate of Zacarias Moussaoui, the only man so far indicted in connection with the 11 September attacks that killed some 3,000 people in the US.
The two men worshipped at the same south London mosque.
Mr Reid was tackled and subdued by other passengers when he apparently tried to light a fuse, and was then taken into custody in Boston.
No date for the trial has been set and Mr Reid will remain in custody.