By Joseph Ax and Karen Freifeld

NEW YORK, Nov 15 (Reuters) - The man who confessed to the 1979 killing of 6-year-old Etan Patz made a brief courtroom appearance on Thursday, standing silently as a prosecutor told the judge that murder charges had been formally filed more than three decades after the child's disappearance.

Pedro Hernandez, 51, did not enter a plea during the hearing in Manhattan, which lasted just minutes. His lawyer later told reporters that Hernandez was innocent and would eventually plead not guilty, despite the previous confession.

Patz disappeared from a Manhattan street on May 25, 1979, on his first walk alone to the school bus stop. He was one of the first missing children whose face appeared on a milk carton as part of an appeal for information from the public. The boy's body has not been found, although he was legally declared dead years ago.

Hernandez confessed in May to luring the boy and strangling him. He had worked at a deli near the Patz home in the downtown Soho neighborhood in the late 1970s before moving to New Jersey.

"Statements made by my client are not reliable. They are what we term false confessions," said attorney Harvey Fishbein, who has previously described Hernandez as suffering from schizophrenia.

The hearing came a day after prosecutors announced a grand jury indictment against Hernandez that charged him with kidnapping and murder. The next scheduled court date is Dec. 12.

It was Hernandez's second court appearance - the first came shortly after his arrest in May - in a case that has haunted the city for more than three decades and altered the way the United States responds to missing children.

The Patz family was not present in court on Thursday.

"This trial will take time and take money and it will not tell the city - and unfortunately will not tell the Patz family - what happened to Etan Patz," said Fishbein, who has said his client did not commit the crime.

He said Hernandez remained under psychiatric treatment and that to his knowledge police had not uncovered any evidence beyond the confession that would point to his client as the killer.

A spokeswoman for the Manhattan district attorney's office, Erin Duggan, said prosecutors believe Hernandez's confession will withstand scrutiny.

"We believe the evidence that Mr. Hernandez killed Etan Patz to be credible and persuasive, and that his statements are not the product of any mental illness," she said in a statement issued on Wednesday.

A report prepared by a state mental health expert deemed Hernandez fit to stand trial.

For years, another man, Jose Ramos, a friend of Patz's babysitter, was the prime suspect in the case, although he was never criminally charged. Ramos was found liable for Patz's death in a 2004 civil case.

Ramos, 69, was recently released from a Pennsylvania prison after serving 20 years for molesting children but was immediately rearrested on other charges.

Fishbein said he would request any evidence against Ramos from law enforcement as part of Hernandez's defense.

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