Boston Police Commissioner Ed Davis said Monday night that the death toll had risen to three. Scores were injured at the scene.
One of the dead was an 8-year-old boy, according to a state law enforcement source.
CNN said hospitals reported at least 144 people are being treated, with at least 17 of them in critical condition and 25 in serious condition. At least eight of the patients are children.
At least 10 people injured had limbs amputated, according to a terrorism expert briefed on the investigation.
One or more bombs were responsible for the explosions, two high-level law enforcement sources told Reuters.
Boston police said that an explosion occurred at the John F. Kennedy Presidential Library and Museum in Boston after the two other blasts.
Police spokeswoman Neva Coakley said "there has been another explosion at JFK." Rachel Day, a spokeswoman for the John F. Kennedy Library, located about three miles from the marathon's finish line, said that there was a fire at the library but no one was injured.
The US Federal Aviation Administration said it had placed temporary flight restrictions in the airspace over the site of two explosions. The restrictions will not affect commericial air operations at Boston's Logan Airport, the FAA said.
In Washington, President Barack Obama owed, "Any responsible individuals, any responsible groups, will feel the full weight of justice."
Boston "is a tough and resilient town," he said, adding that Americans will stand by Bostonians "every single step of the way."
Obama directed his administration to aid Boston authorities in investigating the cause of what local reports said were twin explosions that rocked the finish line of the Boston Marathon.
Separately, Vice President Joe Biden, in a telephone conference call about proposals to tighten gun laws, offered his prayers as he reacted to images he saw on television from Boston.
"As I'm speaking here, they just turned on the television here in my office. Apparently there has been a bombing. I don't know any of the details about what caused it, who did it. I don't think it exists yet," Biden said.
"But our prayers are with those people in Boston who have suffered injury. I don't know how many of them there are. I'm still looking at it on television now," he said.
About three hours after the winners crossed the finish line, there was a loud explosion on the north side of Boylston Street, just before the photo bridge that marks the finish line. Another explosion could be heard a few seconds later.
Smoke rose from the blasts, fluttering through the national flags lining the route of the world's oldest and most prestigious marathon. TV helicopter footage showed blood staining the pavement in the popular shopping and tourist area known as the Back Bay.
Emergency services at finish line (Photo: AP)
Runners who had not finished the race were diverted straight down Commonwealth Avenue and into a family meeting area, according to an emergency plan that had been in place.
Moment of blast (Photo: AP)
The nearby Prudential Tower, the city's second-tallest building with an upscale shopping mall on the ground, was evacuated, along with the luxury Mandarin Oriental hotel, according to media reports.
Race day got started with 26 seconds of silence in honor of the victims of the December school shooting in Connecticut. A little more than 2 hours later, the lead runners passed the Mile 26 marker, which was decorated with the Newtown, Connecticut, seal and dedicated to the memory of those killed there.
The annual 26.2-mile (42-kilometer) marathon takes place on Patriot's Day, a state holiday that celebrates the evacuation of Boston by the British in the American Revolution.
Yitzhak Benhorin, AP and Reuters contributed to this report
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