Pedro Hernandez, 51, wore a gray sweat suit and answered "not guilty" at the hearing in the notorious case of Etan Patz, whose disappearance helped spawn the movement to publicize cases of missing children.
While Hernandez's defense will revolve around his mental state, he isn't pursuing an insanity defense, his lawyer, Harvey Fishbein, has said.
An insanity defense would mean acknowledging he committed the crime but arguing that he was too psychologically ill to know it was wrong. Hernandez will maintain he didn't kill Etan Patz and argue he made a false confession because of his mental problems, among other factors, Fishbein said.
"The only part that mental disease plays in this case is its role in the confession," he said before the court date.
Psychiatric exams of the jailed Hernandez have found that he has an IQ in the borderline-to-mild mental retardation range, his lawyer has said. Hernandez also has been found to suffer from schizotypal personality disorder, which is characterized by hallucinations, according to his lawyer.
Etan's led to an intensive search and garnered huge publicity. His photo was among the first put on milk cartons, and his case turned May 25 into National Missing Children's Day.
Hernandez was a teenage stock clerk at a convenience store when Etan disappeared on his way to school on May 25, 1979. Hernandez was a married father with no criminal record and living in Maple Shade, N.J., when police approached him based on a tip this year. The tip came after federal authorities dug up a basement in the neighborhood hoping for clues, putting the cold case back into the limelight once again.
Investigators say Hernandez told them he lured the boy into the convenience store with the promise of a soda. According to police, he said he led the child to the basement, choked him and left his body in a bag of trash about a block away.
Following the arrest, court hearings for Hernandez were postponed for weeks, with both sides saying they were continuing to investigate.
Authorities seized a computer and a piece of old-looking children's clothing from Hernandez's home, scoured the basement of the building where he had worked in what was then a grocery store and interviewed his relatives and friends - but nothing incriminating came of it, according to a person familiar with the investigation. The person wasn't authorized to discuss findings not yet made public and spoke to The Associated Press on condition of anonymity.
Under New York state law, a confession can be enough to convict someone as long as authorities can establish that a crime occurred.
The boy's body has never been found. Etan's parents, Stan and Julie Patz, have been reluctant to move or even change their phone number in case their son tried to reach out.
Etan was declared legally dead by his father more than a decade ago so he could sue convicted child molester Jose Ramos in the boy's death. Ramos was found responsible - a ruling made because he didn't entirely cooperate with questioning during the lawsuit - and Fishbein could seek to make that a factor in Hernandez's defense.
Ramos, now 69, had been dating the boy's baby sitter in 1979 and was the prime suspect for years, but he was never charged. He was later convicted of molesting two different children. He completed a 27-year sentence last month but was immediately arrested upon his release from a Pennsylvania prison, because authorities said he had given them a false address for where he'd be living.
When New York City police checked out the Bronx address he provided on his Megan's Law registration form, they found no one living there who knew Ramos. And when police tracked down the cousin whose name Ramos had listed, she told them she hadn't had any contact with him in 35 years and did not plan to allow him to live with her, police said. Ramos was ordered to stand trial on a charge of failing to register properly as a sex offender.
Associated Press writer Jennifer Peltz contributed to this report.