Robert Lewis Dear, 57, Is accused of shooting a university police officer who tried to stop the attack, and an Iraq war veteran and a mother of two who were accompanying separate friends to the clinic.
The rampage touched off an hours-long standoff and shootout Friday that also sent nine other people to a hospital.
Colorado Springs police have declined to disclose any information on the motive for the attack, and a judge has ordered the sealing of investigatory court documents at the request of prosecutors.
Dear was expected to make his first court appearance Monday via a video feed.
He has been described by acquaintances as a reclusive loner who didn't seem to have strong political or social opinions.
Some of Dear's former neighbors in North Carolina said Dear would rarely speak with them and could be erratic.
He once called a small yellow wooden hut with no indoor plumbing or electric, about 15 miles east of Asheville, home.
Neighbors who live near Dear's former South Carolina home say he hid food in the woods and lived by selling prints of his uncle's paintings of Southern plantations and the Masters golf tournament.
After he moved to Colorado, he once gave a neighbor pamphlets opposing President Barack Obama.
"He didn't talk about them or anything. He just said, 'Look them over when you get a chance,'" Zigmond Post said.
A law enforcement official said Dear told authorities "no more baby parts" after being arrested, part of a rambling statement that investigators were parsing to understand the reasoning.
The official said the "no more baby parts" comment was among a number of statements Dear made to authorities after his arrest, making it difficult to know his specific motivation.
The law enforcement official spoke on condition of anonymity because the official was not allowed to publicly discuss the ongoing investigation.
U.S. Attorney John Walsh said investigators have been in touch with lawyers from the Justice Department's Civil Rights and National Security divisions, a move that suggests officials could pursue federal charges in addition to state homicide ones. Walsh did not elaborate.
One possible avenue could be the 1994 Freedom of Access to Clinic Entrances Act, which makes it a crime to injure or intimidate clinic patients and employees.
"The case may fit the criteria for a federal domestic terrorism case, but based on my experience, I would be very surprised if this is not simply a local prosecution," said Colorado Springs Mayor John Suthers, a former U.S. attorney and state attorney general. "Murder charges will be more than adequate on the local level."
Planned Parenthood said witnesses believe the gunman was motivated by his opposition to abortion.
Suthers, however, said it's unclear whether the shooting was intended to send an ideological message.
"That may or may not be the case here. We just have to see how things unravel," he said.
Whatever authorities decide is sure to be controversial, given the political murkiness of Dear's statements and the debate over Planned Parenthood, which was reignited in July when anti-abortion activists released undercover video they said showed the group's personnel negotiating the sale of fetal organs.
The organization has denied seeking any payments beyond legally permitted reimbursement of the costs for donating the organs to researchers.
Planned Parenthood has said that Colorado's 19 other clinics would be open for business Monday. The Colorado Springs clinic, though, has been heavily damaged and will be closed for an uncertain amount of time, said Vicki Cowart, the regional head of Planned Parenthood.
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