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-co-ordinated 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, adding, "Make no mistake: We will get to the bottom of this."
With scant official information to guide them, members of Congress said there was little or no doubt it was an act of terrorism.
"We just don't know whether it's foreign or domestic," said Rep. Michael McCaul, R-Texas, chairman of the House Committee on Homeland Security.
A few miles away from the finish line and around the same time, a fire broke out at the John F. Kennedy Library. The police commissioner said that it may have been caused by an incendiary device but that it was not clear whether it was related to the bombings.
The first explosion occurred on the north side of Boylston Street, just before the finish line, and some people initially thought it was a celebratory cannon blast.
When the second bomb went off, spectators' cheers turned to screams. As sirens blared, emergency workers and National Guardsmen who had been assigned to the race for crowd control began climbing over and tearing down temporary fences to get to the blast site.
The bombings occurred about four hours into the race and two hours after the men's winner crossed the finish line. By that point, more than 17,000 of the athletes had finished the marathon, but thousands more were still running.
The attack may have been timed for maximum carnage: The four-hour mark is typically a crowded time near the finish line because of the slow-but-steady recreational runners completing the race and because of all the friends and relatives clustered around to cheer them on.
Runners in the medical tent for treatment of dehydration or other race-related ills were pushed out to make room for victims of the bombing.
A woman who was a few feet from the second bomb, Brighid Wall, 35, of Duxbury, said that when it exploded, runners and spectators froze, unsure of what to do. Her husband threw their children to the ground, lay on top of them and another man lay on top of them and said, "Don't get up, don't get up."
After a minute or so without another explosion, Wall said, she and her family headed to a Starbucks and out the back door through an alley. Around them, the windows of the bars and restaurants were blown out.
She said she saw six to eight people bleeding profusely, including one man who was kneeling, dazed, with blood trickling down his head. Another person was on the ground covered in blood and not moving.
"My ears are zinging. Their ears are zinging," Wall said. "It was so forceful. It knocked us to the ground."
Competitors and race volunteers were crying as they fled the chaos. Authorities went onto the course to carry away the injured, while race stragglers were rerouted away from the smoking site.
Roupen Bastajian, a state trooper from Smithfield, R.I., had just finished the race when he heard the blasts.
"I started running toward the blast. And there were people all over the floor," he said. "We started grabbing tourniquets and started tying legs. A lot of people amputated. ... At least 25 to 30 people have at least one leg missing, or an ankle missing, or two legs missing."
The race honoured the victims of the Newtown, Conn., shooting with a special mile marker in Monday's race.
Boston Athletic Association president Joanne Flaminio previously said there was "special significance" to the fact that the race is 26.2 miles long and 26 people died at Sandy Hook Elementary School.
Associated Press writers Jay Lindsay, Steve LeBlanc, Bridget Murphy, Rodrique Ngowi and Meghan Barr in Boston; Julie Pace, Lara Jakes and Eileen Sullivan in Washington; and Marilynn Marchione in Milwaukee contributed to this report.