In addition to scrutinizing images of surveillance cameras in the area, the FBI likely was issuing subpoenas for records from cell towers in the area to isolate and trace calls from around Copley Square at the time of the blasts, according to a former federal law enforcement official who now works in the intelligence community.
The unexploded devices that were recovered could provide a treasure trove of information such as fingerprints and indications of the bomb maker's design, and from the bombs that did explode, investigators would be looking for fragments and anything indicating the "signature" of the bomb makers, the official told CNN.
As authorities searched the scene, numerous suspicious packages were found, possibly because people fled the area, leaving items behind. Investigators were checking them.
All off-duty Boston police were called in.
The Marriott hotel at Copley Place was evacuated as a precaution.
The Lenox Hotel was also evacuated as a precaution, the Boston Globe reported.
Crowds were in the area watching the runners take part in the world's oldest annual marathon.
It was also Patriot's Day, commemorating the opening battle of the Revolutionary War.
Within seconds, the festive occasion turned into devastation.
"This is a horrific day in Boston," Massachusetts Gov. Deval Patrick said in a statement.
"My thoughts and prayers are with those who have been injured. I have been in touch with the president, Mayor (Thomas) Menino and our public safety leaders. Our focus is on making sure that the area around Copley Square is safe and secured. I am asking everyone to stay away from Copley Square and let the first responders do their jobs."
U.S. Attorney General Eric Holder spoke with FBI Director Robert Mueller and U.S. Attorney Carmen Ortiz, a Justice Department official said.
Holder has directed the full resources of the Justice Department to be deployed to ensure the matter is fully investigated, the official said.
The Federal Aviation Administration placed a flight restriction over the site of the blasts.
Other cities, including New York and Washington, tightened security as a result. Following standard protocol, the White House cleared out an area in front of the West Wing.
Mike Baingon, who works at the Atlantic Fish Company in Boston, said an explosion took place in front of the restaurant and that he was right by the front door at the time.
The explosions occurred at about 2:45 p.m., more than two hours after the first of the race's nearly 27,000 runners had crossed the finish line, CNN Producer Matt Frucci reported.
The race was halted as was subway service into the area.
Troops from the Massachusetts National Guard, already at the site as part of the marathon's security and crowd-management plan, were assisting police as well.