One of the accused pirates had a bandaged head, while another was carried into the court building. The 11 were scheduled for a court appearance Friday afternoon.
In addition to the piracy count, the charges include attacks to plunder a vessel, assault with a dangerous weapon, and use of a firearm during a crime of violence.
Five of the men were captured March 31, after the frigate USS Nicholas exchanged fire with a suspected pirate vessel west of the Seychelles, sinking a skiff and confiscating its mother ship.
The other six were captured after they allegedly began shooting at the amphibious dock landing ship USS Ashland on April 10 about 380 miles off Djibouti, a small nation facing Yemen across the mouth of the Red Sea.
The 11 had been held on U.S. ships for weeks off Somalia's pirate-infested coast and nearby regions as officials worked to determine whether and where they could be prosecuted and prepare legal charges against them.
The indictment did not indicate the pirates' nationality.
The Somali mission to the United Nations said it is attempting to sort out jurisdictional issues.
"We prefer those kids to be tried in Somalia," said Omar Jamal, first secretary for the mission.
The U.S. Attorney's office confirmed that all 11 suspects are from Somalia.
The suspects were taken from the USS Nassau amphibious assault ship Thursday and flown to Virginia on a government plane in the custody of the Justice Department.
The transfer of the case to a U.S. court comes amid discussions about setting up an international court to prosecute piracy suspects, which some nations have been reluctant to do because of difficulties transporting suspects, fears they may claim asylum and thorny jurisdiction issues.
U.S. warships are part of an international flotilla protecting shipping in the region. The navies of other countries have also have taken alleged pirates home for trial.
Kenya, south of Somalia, has taken some to its courts but now says pirates are putting too much strain on the country's court system.
Some pirates have been released after capture because no nation could be found to try them.