Authorities charged the two Kazakhs, Azamat Tazhayakov and Dias Kadyrbayev, both 19, with conspiring to obstruct justice by disposing of a backpack containing fireworks they found in Tsarnaev's dorm room. The third man, Robel Phillipos, also 19, was charged with making false statements to investigators.
Tsarnaev, who attended the University of Massachusetts at Dartmouth, is being held at a prison hospital where he is recovering from wounds sustained in a gun battle with police. His older brother, Tamerlan, died in the gunfight.
Kadyrbayev and Tazhayakov face a maximum sentence of five years in prison and $250,000 fine. Phillipos faces a maximum sentence of eight years in prison and a $250,000 fine.
In their initial appearances at Boston federal court on Wednesday, Kadyrbayev, Tazhayakov and Phillipos were put in the custody of U.S. Marshals after prosecutor Stephanie Siegmann argued that all three presented a "serious risk of flight."
None of the suspects addressed the court, other than to respond to the judge's questions. U.S. Magistrate Judge Marianne Bowler reprimanded Phillipos for not seeming to pay attention to the proceedings.
"I suggest you pay attention to me rather than looking down," Bowler said.
Kadyrbayev's lawyer, Robert Stahl, said before the hearing that his client was "not a target" of the bombing investigation, but declined to comment on any other specifics. He said his client had "cooperated fully" with investigators and "wants to go home to Kazakhstan."
Phillipos' attorney, DeRege Demissie, declined to discuss the case in detail after the hearing.
A month prior to the bombings, Dzhokhar Tsarnaev told Kadyrbayev and Tazhayakov over a meal that he knew how make a bomb, Tazhayakov told the FBI, according to court papers.
Kadyrbayev and Tazhayakov had entered the United States on student visas and lived in New Bedford, Mass., according to court papers. Phillipos is a resident of Cambridge, Massachusetts.
On April 18, three days after the Marathon bombings, authorities released pictures of two men they identified as the suspects in the attack. Investigators at the time said they did not know the suspects' names and called on the public for help in identifying them.
Dzhokhar's three classmates quickly figured out their friend was one of the suspects, according to court papers. After seeing Tsarnaev's photo in TV news reports, Kadyrbayev texted him to say that he resembled the suspect, according to the complaint.
Tsarnaev's response included the phrase "lol" and "you better not text me," as well as "come to my room and take whatever you want," according to the court papers.
The three went to his dorm room that night and found a roommate who said that Dzhokhar had left.
The trio spent some time watching movies and then discovered an emptied-out fireworks tube, according to court papers. That discovery scared Tazhayakov, who then began to believe that Tsarnaev was involved in the bombing, according to court papers.
They decided to remove the backpack, fireworks and a laptop to help their friend "avoid trouble," according to court papers.
Tazhayakov is currently enrolled at UMass Dartmouth but has been suspended, the university said on Wednesday. Kadyrbayev and Phillipos are not currently enrolled in the school.
After waking up the next morning to learn that police were hunting for Dzhokhar Tsarnaev and that his brother, Tamerlan, was dead, Kadyrbayev decided to throw away the backpack with the fireworks tubes inside, according to court papers. He put the backpack and fireworks in a dumpster near his apartment.
A New Hampshire fireworks store last month confirmed that the elder bombing suspect, Tamerlan Tsarnaev, bought two large boxes of fireworks in February.
Investigators recovered the backpack on April 26 in a New Bedford landfill. In addition to the fireworks, it included a homework assignment sheet from a class that Dzhokhar Tsarnaev was enrolled in.
In his first three interviews with police, Phillipos denied having gone to Tsarnaev's room on April 18, but in a fourth interrogation, on April 26, he confessed to the visit, the court documents said.
The parents of the Tsarnaev brothers have said in interviews in the North Caucasus region of Russia that they do not believe their sons were responsible for placing the bombs.
Tamerlan Tsarnaev's body has still not been claimed, a spokesman for the state's chief medical examiner said. His widow, Katherine Russell, on Tuesday said she wanted the medical examiner to release her husband's body to his family.