Authorities said they followed cell phone and computer records to Markoff, linking an e-mail account used to set up appointments on Craigslist with the two women who were attacked to his address in Quincy.
Markoff, dressed in khakis and a button-down shirt, did not say anything during the brief hearing. His attorney, John Salsberg, said his client was not guilty.
"Philip Markoff is not guilty. He has his family's support," he said. "All I have is words and that's not proof of anything."
Markoff's fiancee, Megan McAllister, who lived with him, told ABC News that police have got the wrong guy.
Police said they tracked Markoff down using surveillance videos at three hotels. In photos taken from hotel cameras, the man police have been seeking in connection with the crimes appears to be fixated on a BlackBerry. Investigators said that Blackberry is what led them to Markoff.
A police source close to the investigation said cops found Markoff by tracing Craigslist e-mails.
"They followed high-tech leads and old-fashioned shoe leather," Suffolk County District Attorney Dan Conley said in a news conference. "They've connected IP addresses and physical locations."
Markoff's friends and neighbors are shocked. After all, Markoff, a second-year medical student at Boston University, had no criminal history and was engaged to be married to a woman he met more than three years ago when they were volunteers in an emergency room. The university suspended Markoff after learning of the charges against him, a school spokeswoman said.
"I can't even put it into words, the disbelief I'm putting into works right now," Markoff's friend Jonathan Uva told "Good Morning America" today. "It's just a total disconnect from what we're hearing in the news."
Uva, who lives next door to Markoff in Quincy, Mass., said he went to sleep last night listening to police searching his friend's apartment.
"I'm a little unsettled, definitely," he said.
Another friend, Mike Dye, told "Good Morning America" that he'd had Markoff over to his apartment for parties and for the Super Bowl.
"I like to think I'm a good judge of character, hang out with people who are similar to myself," he said. "Didn't suspect anything like that."
"I would never believe this would be something he would do," friend Kym Direnzo said on "GMA."
Markoff's Facebook profile lists hundreds of friends who attend schools in Boston and upstate New York.
But for all the nice things they had to say about Markoff, his friends said there was a bit of mystery about him, though nothing overtly nefarious.
Friends said they didn't even know he and McAllister were engaged. Though they agreed they seemed like a nice normal couple, his friends said they thought the two were simply dating.
"He very rarely talked about himself," Uva said.
The couple's Web site, once flooded with well wishes from friends and family, is now filled with cruel postings from strangers, many directed at McAllister.
The site had detailed how they met when McAllister was a senior at the University of Albany and Markoff a sophomore. Their wedding date was set for Aug. 14.
Markoff's arrest came just hours after Warwick, R.I., police released new pictures of the man they believe is responsible for the attempted robbery of a woman at a Holiday Inn there last week.