As victims of the bombing looked on, Tsarnaev, 19, gave a lopsided smile to his sisters upon arriving in the courtroom. He appeared to have a jaw injury and there was swelling around his left eye and cheek.
Then, after he leaned over toward a microphone and said, "Not guilty" over and over in a Russian accent, he was led out of the courtroom, making a kissing motion with his lips toward his family as he left. His sister sobbed loudly, resting her head on a woman seated next to her.
He faces 30 federal charges, including using a weapon of mass destruction to kill, and could get the death penalty if prosecutors choose to pursue it.
The proceedings took place in a heavily guarded courtroom packed not only with victims but with their families, police officers, members of the public and the media.
Tsarnaev looked much as he did in a photo widely circulated after his arrest, his hair curly and unkempt. He appeared nonchalant, almost bored during the hearing. The cast covered his left forearm, his hand and his fingers.
The April 15 attack killed three people and wounded more than 260. Authorities say Tsarnaev orchestrated the attack along with his older brother, Tamerlan Tsarnaev, who died following a shootout with police three days after the bombing.
Dzhokhar Tsarnaev was arrested on April 19 when he was found hiding in a boat in a suburban backyard. He was initially charged in the hospital, where he was recovering from wounds suffered in a police shootout.
Tsarnaev's two sisters, both in Muslim garb, were in court Wednesday. One was carrying a baby, the other wiped away tears with a tissue. His parents remained back in Russia.
Reporters and spectators began lining up for seats in the courtroom at 7:30 a.m. as a dozen Federal Protective Service officers and bomb-sniffing dogs surrounded the courthouse.
Four hours before the hearing, the defendant arrived at the courthouse in a four-vehicle motorcade that included a van, a Humvee and a state police car.
A group of about a dozen Tsarnaev supporters cheered as the motorcade arrived. The demonstrators yelled, "Justice for Jahar!" as Tsarnaev is known. One woman held a sign that said, "Free Jahar."
Lacey Buckley, 23, said she traveled from her home in Wenatchee, Wash., to attend the arraignment. Buckley said she has never met Tsarnaev but came because she believes he's innocent. "I just think so many of his rights were violated. They almost murdered an unarmed kid in a boat," she said.
A group of friends who were on the high school wrestling team with Tsarnaev at Cambridge Rindge and Latin waited in line outside the courtroom for hours, hoping to get a seat.
One of them, Hank Alvarez, said Tsarnaev was calm, peaceful and apolitical in high school.
"Just knowing him, it's hard for me to face the fact that he did it," said Alvarez, 19, of Cambridge.
Another ex-teammate, Shun Tsou, 20, of Cambridge, called Tsarnaev "a silent warrior type."
"There was nothing sketchy about him," said Tsou, adding that he had not formed an opinion on Tsarnaev's guilt or innocence.
Prosecutors say Tsarnaev, a Muslim, wrote about his motivations for the bombing on the inside walls and beams of the boat where he was captured. He wrote the U.S. government was "killing our innocent civilians."
"I don't like killing innocent people," he said, but also wrote: "I can't stand to see such evil go unpunished. ... We Muslims are one body, you hurt one you hurt us all."
Three people - Martin Richard, 8; Krystle Marie Campbell, 29; and Lingzi Lu, 23 - were killed by the bombs, which were improvised from pressure cookers. Authorities say the Tsarnaevs also killed Massachusetts Institute of Technology officer Sean Collier days later while they were on the run.
Numerous bombing victims had legs amputated after the two explosions, which detonated along the final stretch of the race a couple hours after the elite runners had finished.
Associated Press writer Arsen Mollayev in Makhachkala, Russia, contributed to this report.