According to the Associated Press, his arm was in a cast and his left eye was swollen, as was his cheek.
Tsarnaev was charged with 30 counts, including the use of a weapon of mass destruction to kill.
The accused approached the stand several times repeating "Not guilty," in what the AP described as a Russian accent. The arraignment lasted seven minutes.
The courtroom was packed with onlookers trying to get a glimpse of the alleged bomber, including three dozen of the victims' family members. He reportedly smiled at his sisters when he entered the courtroom.
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It is unclear whether prosecutors will seek the death penalty against the bombing suspect, who is a naturalized American citizen of Chechen descent.
Although the death penalty was banned in Massachusetts in 1984, Tsarnaev was charged under federal law. Seventeen of the charges he faces are punishable by death.
Dzhokhar Tsarnaev is alleged to have planted two bombs at the finish line of the Boston Marathon last April, killing three people and injuring 260.
Tamerlan Tsnarnaev, Dzhokhar's older brother, was killed in a shootout with police shortly after the incident.
The younger brother was captured by police in a massive manhunt that ended in a suburban Boston backyard.
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