Robert Stahl, an attorney for Kadyrbayev, said his client was "shocked and horrified" by the bombings and had "no intent" to obstruct justice.
"I'm saying he didn't dispose of evidence, didn't understand it was evidence, and the rest will come out at trial," Stahl told reporters after the arraignment.
More than two dozen family members and friends attended the hearing to support Phillipos. During an argument for bail in May, his lawyer portrayed him as a frightened and confused young man who was subjected to intense interrogation during the investigation.
Tazhayakov's parents and sister were in court during the brief arraignment. A translator said the family traveled from their native Kazakhstan in April and plans to remain in the United States until the case is resolved.
Tazhayakov's attorney, Nicholas Wooldridge, said the government "rushed into things" by charging his client.
"This is a witch hunt," Wooldridge told reporters after his arraignment.
All three men are due back in court Oct. 29 for a status conference.
Assistant U.S. Attorney John Capin said he expects to call about 20 witnesses during a two-week trial. No date has been set yet for it.