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At a brief hearing at the Seminole County jail in Sanford, Zimmerman, 28, spoke only to acknowledge the charge against him and confirm that he had legal representation. He was not required to enter a plea.
Zimmerman's lawyer, Mark O'Mara, made no application for bail and Seminole County judge Mark Herr sent the case for a formal arraignment on May 29 before circuit court judge Jessica Recksiedler.
But Herr agreed to a request from O'Mara, supported by prosecutor Angela Corey, to seal all documents in the case relating to the incident on February 26 when Zimmerman shot dead Martin, 17, during a confrontation in a gated community in Sanford.
Zimmerman was not arrested at the time because police believed his claims of self-defence, enraging Martin's family and sparking six weeks of mass protests in central Florida and elsewhere.
Zimmerman, wearing a grey one-piece Seminole County jail inmate suit and with his hands shackled in front of him, stared ahead intently during the four-minute hearing, listening as Judge Herr spoke on a closed-circuit TV monitor.
He answered said: "Yes, sir" twice as Herr asked him if he understood the charge and whether O'Mara was representing him.
After the hearing, O'Mara, who described his client as "stressed and tired", told reporters that he would be seeking to file a motion for bail in the coming days.
"He's tired, he's gone through some tribulations of his own with the intensity of this event. He's facing second-degree murder charges now that would frighten any one of us," he said.
"But I'm not concerned about his focus. My concern was that this matter was being handled in a piecemeal fashion, whether it was police, law enforcement or defence. It's supposed to happen in the courtroom. The job is better done the way we know how to do it."
O'Mara, who added that his client will plead not guilty, said he asked for the documents to be sealed because they would reveal sensitive information about the case, such as witness addresses.
"The concern is, with the focus this case has had to date, that there have already been requests to get that information," he said.
Special prosecutor Corey ended 44 days of uncertainty on Wednesday when she announced that Zimmerman would be charged with second-degree murder, an offence that carries a sentence from 25 years to life in prison.
He has been held in protective custody since his arrest on Thursday, with his brother Robert declaring that the family was disappointed by the severity of the charge.
"They [prosecutors] have thrown the book at him," Robert Zimmerman told CNN. "I would have hoped the more courageous decision would be to say we're not prosecuting, and here's why. Our brother could have been dead, our brother had to save his life by taking a life.
"The incident has been weighing on my brother in a way I couldn't possibly describe. As a family we're devastated. We are a strong family and we have been living a somewhat altered reality for some time."
"I trust that the system, the judge, the prosecutor and I will be able to, should the need arise, to get ourselves a fair and impartial jury to hear the case," he said.
Some legal analysts believe it might be difficult for state attorney Corey to make a murder charge stick against a defence under Florida's controversial "stand your ground" law, which allows for the use of deadly force if a citizen perceives his life to be in danger.
Zimmerman has claimed he was under attack from Martin, who was unarmed, and fired in self-defence.
"The only hurdle I see is a stand-your-ground motion to dismiss that will have to be made," Kenneth Nunn, a senior professor at the University of Florida's Levin College of Law, told the Guardian.
"The burden is on the defendant to show stand your ground applies, but the standard is only a preponderance of the evidence. If Zimmerman shows that then it is dismissed and Ms Corey's case goes away at that point. The prosecutor should be able to overcome that – but it's going to be a very difficult case."
Another law professor, Dan Markel, of Florida State University, agreed. "If everything we've seen reported so far about Zimmerman's side of the story is true, and there aren't other missing pieces of evidence, I have trouble fathoming how a jury would return a guilty verdict for murder, based on proof beyond a reasonable doubt," he said.
Also today, Martin's mother, Sybrina Fulton, issued a statement to "clarify" an earlier comment that she believed the shooting was "an accident".
"I made a comment that was later mischaracterised," she said. "In no way did I mean the shooting was an accident. We believe that George Zimmerman stalked my son and murdered him in cold blood," adding that she felt that it was the encounter that was accidental.
Frederica Wilson, the Miami congresswoman whose constituency includes Martin's home, said that Thursday's court hearing for Zimmerman was an important first step for the family following their protracted battle to have him arrested.
"I am thankful that the wheels of justice will continue to turn. This is just the beginning and we have a long process ahead of us," she said.
"The evidence influenced [Corey] to charge him but the outcry helped bring the case to justice. This case would never have been brought without that outcry. It was a case that almost slipped through the system without the public ever knowing about it."