Akayed Ullah faces numerous charges including providing material support to a terrorist organization, using a weapon of mass destruction and bombing a place of public use and a public transportation system.
Ullah was the only person seriously hurt in the December 11 attack, and he was arrested soon after the pipe bomb failed to fully explode. He made his first court appearance from his hospital room via a video link and later was transferred to the federal jail in Manhattan.
In this court room drawing, U.S. Marshals escort defendant Akayed Ullah, center, into court for his arraignment on charges that include providing material support to a terrorist organization and using a weapon of mass destruction, Thursday, Jan. 11, 2018 in NY.
The judge asked Ullah if he had seen the six-count indictment and had the opportunity to speak with his lawyers about it.
"In selecting this time and place, Ullah's alleged objective in the Port Authority bombing was painfully clear: to inflict as much damage as possible, and to strike fear into the hearts of New Yorkers in the name of ISIS", U.S. Attorney Geoffrey Berman said when announcing the indictment.
When asked by a judge if he had a plea, he responded saying not guilty.
She said Ullah recently had some stitches removed but had others that were still causing him a "great deal of discomfort".
FILE - In this December 12, 2017, file photo, a Bangladeshi man reads a national newspaper whose front pages shows the news of 27-year-old Bangladeshi man Akayed Ullah, in Dhaka, Bangladesh.
Ullah suffered burns and other wounds; no one else was seriously injured. The pipe bomb never fully exploded.
Ullah began to self-radicalize three years ago, authorities said, but law enforcement said he wasn't on their radar before the subway attack.
They also said in court papers that he admitted he wanted to cause carnage to avenge US aggression toward the Islamic State group.
Before the blast, Ullah posted messages to his Facebook page referring to ISIS and taunting President Donald Trump.