The Supreme Court on Monday reversed a lower court decision that had reopened the case of the man convicted in the killing of Etan Patz, a 6-year-old boy whose 1979 abduction in Manhattan reshaped American childhoods.
The court’s unsigned opinion restores the conviction of the man, Pedro Hernandez, who the U.S. Court of Appeals for the Second Circuit had said last year was entitled to a new trial.
The three liberal justices — Sonia Sotomayor, Elena Kagan and Ketanji Brown Jackson — noted their objection to the majority’s ruling, which centered on the limits of federal courts to intervene in state-court matters.
Mr. Hernandez was found guilty in 2017 of kidnapping and murdering Etan, but an appeals court overturned that judgment last July. Months later, the Manhattan district attorney’s office, which prosecuted Mr. Hernandez, asked the nation’s highest court to review the decision.
On Monday, a defense lawyer for Mr. Hernandez, Harvey Fishbein, said the Supreme Court’s order meant his client would not get a new trial and that his team was “terribly disappointed.”
“We firmly believe that an innocent man is in jail for a crime that he did not commit,” Mr. Fishbein said.
In a statement, the Manhattan district attorney, Alvin L. Bragg, said the case had “changed a generation of New Yorkers.”
“This office has remained steadfast in its pursuit of justice for Etan and the Patz family and will continue to stand by this important conviction,” he said.
The Supreme Court’s action sends the matter back to the lower courts and is the latest development in a case that stumped investigators for decades. Mr. Hernandez, a handyman who lived in New Jersey, was arrested in 2012 and first put on trial in 2015. But after 18 days of deliberations, the trial ended in a hung jury. The case went back to trial and, in 2017, a Manhattan jury convicted Mr. Hernandez after nine days of deliberations.
Mr. Hernandez is being held in state prison at Elmira Correctional Facility.
The reversal of Mr. Hernandez’s conviction last year reopened a case that had appeared finally settled. From the first days Etan went missing, when he was walking the two blocks from his home in the SoHo neighborhood to a school bus stop, the case generated intense public interest. Etan’s abrupt disappearance — and the killing of 6-year-old Adam Walsh two years later — ushered in an era of heightened caution among American parents.
In its 10-page opinion on Monday, the Supreme Court said the Second Circuit, a federal court, exceeded its authority by undoing Mr. Hernandez’s conviction in state court. Federal law imposes strict limits on the power of federal judges to grant relief to prisoners convicted in state courts.
The lower court opinion “appears to reflect serious doubt about the reliability of Hernandez’s confessions,” the majority said, but the relevant statute does not permit federal courts to “disturb a state-court conviction based on such an evaluation of the evidence.”
The liberal justices did not explain their disagreement. The ruling was issued as part of the court’s routine orders and without the justices holding oral arguments.
For decades, investigators in Manhattan struggled to figure out what happened to Etan. His body was never found, and in 2001, he was declared legally dead.
The critical break in the case came in 2012, when one of Mr. Hernandez’s relatives contacted investigators. New York police officers traveled to Mr. Hernandez’s home in Camden, N.J. After about seven hours of questioning, the police said, Mr. Hernandez confessed — first before being read his rights, and twice more after.
Mr. Hernandez was 18 at the time of Etan’s disappearance and worked at a bodega where investigators believed Etan had been killed.
There was no scientific evidence linking Mr. Hernandez to the crime, and his confessions to investigators were quickly called into question.
Mr. Hernandez’s lawyers argued that the statements were invented to placate the police. They asked the court to suppress them, saying they were a result of Mr. Hernandez’s low I.Q. and the product of psychotic delusions. The judge nonetheless said that they could be used as evidence.
During jury deliberations at the second trial in 2017, the jury asked the judge whether they should disregard one of Mr. Hernandez’s later confessions if they found that his first one was not voluntary. The judge gave a one-word answer: No.
A federal appeals court found that the judge should have explained a Supreme Court precedent about such serial confessions and ordered that Mr. Hernandez be released from his 25-years-to-life sentence or get a new trial.
Prosecutors in Manhattan, led by Mr. Bragg, argued to the Supreme Court that Mr. Hernandez’s conviction should not have been overturned because it was not based on an “error in the decades-long investigation, in the admission of Hernandez’s confessions or in the evidence presented at trial.” The appeals court had said that the judge overseeing the trial, Maxwell Wiley, had violated federal law and therefore invalidated a jury’s verdict.
In their response, Mr. Hernandez’s lawyers said that the judge’s instruction to the jury had touched on the central issue in the case.
“Far from exhibiting the kind of clear error for which summary reversal is typically reserved,” his lawyers wrote, “the Second Circuit’s decision is correct.”
The Supreme Court’s ruling on Monday ends the litigation over the jury instructions, but does not foreclose Mr. Hernandez from raising other objections to his conviction.
Mr. Hernandez’s case is scheduled to return to State Supreme Court in Manhattan on June 30.
