Adis Medunjanin and Zarein Ahmedzay are charged as co-conspirators
Two men have pleaded not guilty in a New York court to taking part in an alleged plot to set off home-made bombs on the city's subway system.
The men, Zarein Ahmedzay and Adis Medunjanin, were classmates of Afghan immigrant Najibullah Zazi, who pleaded guilty three days ago.
Mr Zazi had said that he and the others had been recruited by al-Qaeda during a trip to Pakistan in 2008.
US officials called the plot one of the most serious threats since 9/11.
Zarein Ahmedzay and Adis Medunjanin, both 25, are US citizens from Queens in New York who reportedly attended high school with Mr Zazi.
They are accused of conspiracy to use weapons of mass destruction, conspiracy to commit murder in a foreign country, and providing material support to the al-Qaeda terrorist network.
US prosecutors said the men were planning an attack on city subway lines last September under the direction of al-Qaeda that would have been similar to the 2005 attacks on public transit in London that killed more than 50 people.
Najibullah Zazi faces life in prison without parole
"The facts alleged in this indictment shed further light on the scope of this attempted attack," Attorney General Eric Holder said in a statement. "This attack would have been deadly."
In a separate development, two news organisations have asked a judge to make public a sealed plea agreement between prosecutors and Najibullah Zazi, arguing that the documents may show whether pressure was applied to Mr Zazi, the BBC's Laura Trevelyan reports from New York.
It has been reported that Mr Zazi co-operated with investigators to prevent charges being brought against his relatives, our correspondent adds.