A White House official speaking on condition of anonymity because the investigation was still unfolding said the attack was being treated as an act of terrorism.
President Barack Obama vowed that those responsible will "feel the full weight of justice."
As many as two unexploded bombs were also found near the end of the 26.2-mile course as part of what appeared to be a well-coordinated attack, but they were safely disarmed, according to a senior U.S. intelligence official, who also spoke on condition of anonymity because of the continuing investigation.
The fiery twin blasts took place about 10 seconds and about 100 yards apart, knocking spectators and at least one runner off their feet, shattering windows and sending dense plumes of smoke rising over the street and through the fluttering national flags lining the route. Blood stained the pavement, and huge shards were missing from window panes as high as three stories.
"They just started bringing people in with no limbs," said runner Tim Davey of Richmond, Va. He said he and his wife, Lisa, tried to shield their children's eyes from the gruesome scene inside a medical tent that had been set up to care for fatigued runners, but "they saw a lot."
"They just kept filling up with more and more casualties," Lisa Davey said. "Most everybody was conscious. They were very dazed."
As the FBI took charge of the investigation, authorities shed no light on a motive or who may have carried out the bombings, and police said they had no suspects in custody. Officials in Washington said there was no immediate claim of responsibility.
WBZ-TV reported late Monday that law enforcement officers were searching an apartment in the Boston suburb of Revere. Massachusetts State Police confirmed that a search warrant related to the investigation into the explosions was served Monday night in Revere but provided no further details.
Some investigators were seen leaving the Revere house early Tuesday carrying brown paper bags, plastic trash bags and a duffel bag.
Police said three people were killed. An 8-year-old boy was among the dead, according to a person who talked to a friend of the family and spoke on condition of anonymity. The person said the boy's mother and sister were also injured as they waited for his father to finish the race.
Hospitals reported at least 144 people injured, at least 17 of them critically. The victims' injuries included broken bones, shrapnel wounds and ruptured eardrums.
At Massachusetts General Hospital, Alasdair Conn, chief of emergency services, said: "This is something I've never seen in my 25 years here ... this amount of carnage in the civilian population. This is what we expect from war."
Some 23,000 runners took part in the race, one of the world's oldest and most prestigious marathons.
One of Boston's biggest annual events, the race winds up near Copley Square, not far from the landmark Prudential Center and the Boston Public Library. It is held on Patriots Day, which commemorates the first battles of the American Revolution, at Concord and Lexington in 1775.
Boston Police Commissioner Edward Davis asked people to stay indoors or go back to their hotel rooms and avoid crowds as bomb squads methodically checked parcels and bags left along the race route. He said investigators didn't know whether the bombs were hidden in mailboxes or trash cans.
He said authorities had received "no specific intelligence that anything was going to happen" at the race.
The Federal Aviation Administration barred low-flying aircraft within 3.5 miles of the site.
"We still don't know who did this or why," Obama said at the White House,...