Dzhokhar Tsarnaev, 19, has been charged with one count of using and conspiring to use a weapon of mass destruction against persons and property within the United States resulting in death, along with one count of malicious destruction of property by means of an explosive device resulting in death. The charges were read to him in his hospital room.
Under the weapon of mass destruction charge, Tsarnaev faces the death penalty. The White House said the suspect will not be tried as an enemy combatant.
"We will prosecute this terrorist through our civilian system of justice, under U.S. law," said White House press secretary Jay Carney. "United States citizens cannot be tried in military commissions."
The suspect made his first appearance before a magistrate judge at Beth Israel Hospital. Authorities said he is awake and responded sporadically in writing to questions.
Tsarnaev is still unable to talk because of wounds to his neck and throat, but authorities are asking him in writing whether there are any more unexploded bombs or any other accomplices. Investigators are trying to determine whether the brothers were part of a larger network.
Tsarnaev is still in serious but stable condition. Officials say he knows his 26-year-old brother, Tamerlan Tsarnaev, was killed during a furious getaway attempt.
As Tsarnaev begins to communicate, authorities said preliminary evidence suggests the brothers' religious views and Internet preachings of an Al-Qaeda leader motivated them to bomb the marathon.
ABC News has learned the college student told investigators the whole attack was devised from the Internet without any foreign help and they say it was likely his older brother devised the plot and did most of the work. Authorities say it appears the older brother's radical religious views and hatred for American and Christianity motivated the attack.
The FBI also wants to question the older brother's wife, who converted to Islam.
Authorities are looking into whether the gunshot wound to the surviving suspect's neck was self-inflicted.
Tsarnaev was taken into custody on Friday after a massive manhunt that effectively shut down the city of Boston. He was discovered hiding in a boat covered by a tarp, which was parked on the property of a home in Watertown, Mass.
"When we were moving up to the boat, he was actually laying down on the boat with one leg out and one hand out," said a law enforcement officer who was at the scene. "As we got closer, he sat up and that's when we were able to effect the arrest."
ABC News George Stephanopoulos spoke with former FBI special agent Brad Garrett about what authorities must consider after speaking to the suspect.
"The real trick with that, George, is figuring out where his mind is," Garrett said. "What are his motivations? Why does he want to talk to us?"
The older brother and deceased suspect, identified as 26-year-old Tamerlan Tsarnaev, reportedly called his mother Friday as FBI investigators closed in on them. According to ABC News, Tamerlan told her that they were being shot at. She also said that she was the one who encouraged Tamerlan to learn more about Islam, and that Dzhokhar did whatever his older brother said. That was how she raised them, in accordance to Islam.
Dzhokhar Tsarnaev is also likely to face state charges in connection with the fatal shooting of MIT police officer Sean Collier in Cambridge, said Stephanie Guyotte, a spokeswoman for the Middlesex District Attorney's Office.
The Bureau of Alcohol, Tobacco, Firearms and Explosives was tracing the suspects' weapons to try to determine how they were obtained. Neither of the brothers had permission to carry a gun. Cambridge Police Commissioner Robert Haas said it was unclear whether either of them ever applied for a gun permit, and the applications are not considered public records.
The younger brother would have been denied a permit based on his age alone. Only people 21 or older are allowed gun licenses in Massachusetts.
Questions are piling up about the older brother's activities. The FBI investigated him in 2011 at the request of Russian authorities. Tamerlan Tsarnaev went on a six-month visit to Russia in 2012. Investigators are also looking at him in connection to an unsolved triple murder in 2011. Tamerlan Tsarnaev was a friend of one of three men found dead in an apartment with their necks slit and their bodies reportedly covered with marijuana.
"Exactly when did Russia call to ask about this individual? What did he do when he went back for six months? Did he sit in his aunt and uncle's home for six months or was he doing something else?" said Sen. Dianne Feinstein, the head of the Senate Intelligence Committee.
Many of those injured in the deadly marathon bombings are still recovering in the hospital. Of at least 170 injured, 48 are still recovering in the hospital and two remain in critical condition.
A private funeral service was held Monday for 29-year-old Krystle Campbell, who was one of three killed in the twin bombings. She had moved to Boston to help care for her ailing grandmother. A memorial service will also honor 23-year-old Lu Lingzi, a Boston University graduate student from China. An 8-year-old boy was also killed.
Massachusetts will held a moment of silence to mark the deadly Boston Marathon bombings at 2:50 p.m. Monday, the time the first of two bombs exploded near the marathon finish line. Massachusetts Gov. Deval Patrick said bells would toll across the state after the minute-long tribute to the victims.
Bouquets of flowers and handwritten messages were piled on the sidewalk to remember the victims.
President Barack Obama also planned to participate in the moment privately at the White House, with no press coverage.
ABC News and The Associated Press contributed to this report.