A federal grand jury returned a 30-count indictment against Dzhokhar and many of the charges carry the possibility of life in prison or the death penalty.
The charges include: use of a weapon of mass destruction resulting in death; bombing of a place of public use resulting in death, malicious destruction of property resulting in death, conspiracy, and use of a firearm during and in relation to a violent crime, federal prosecutors said in a statement.
A fourth victim, a university police officer, died in a gunfight with the pair four days later as authorities raced to capture them.
Seventeen of the charges carry the possibility of the death penalty. The others carry the possibility of as much as life in prison.
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The indictment alleged that Tsarnaev, who had been inspired by Al Qaeda publications, left a confession in the boat where he was captured in a Watertown back yard, saying, "I don't like killing innocent people" but it was justified because of US government actions abroad.
Tamerlan was killed after a shootout with police on April 19 in Watertown. Dzhokhar was arrested after he was found hiding in the boat later that day.
The indictment alleges that sometime before the bombings, Dzhokhar downloaded several different pieces of extremist Islamic propaganda from the Internet, Boston.Com reported.
The bombings had raised questions about what motivated the brothers and whether US officials could have stopped them before they struck.