Six months after a former bodega clerk admitted to the infamous cold case murder of 6-year-old Etan Patz, he has been indicted — the closest prosecutors have come to a possible conviction in this 33-year-old mystery.

A grand jury today indicted Pedro Hernandez, 51, on two counts of murder in the second degree and one count of kidnapping in the first degree. He was first arrested by the NYPD in May, after a member of his family told police he was responsible for Patz’s murder.

In custody, Hernandez told police he lured the boy into SoHo basement on May 25, 1979, by offering him a soda. He confessed to strangling Patz and then wrapping his body in plastic wrap and putting it in the trash. Shortly after, Hernandez moved from his West Broadway apartment, eventually to Maple Shade, N.J., where he was living at the time of his arrest.

Police said Hernandez told family members over the years he had “done a bad thing and killed a child in New York,” prompting one relative to turn him in.

His own attorneys have raised the question as to whether mental health issues led him to make a false confession, but the Manhattan district attorney’s office said Hernandez’s confession will stand.

“This indictment is the outcome of a lengthy and deliberative process, involving months of factual investigation and legal analysis. 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,” Erin Duggan, a spokesperson for the Manhattan DA, said in a statement. “The grand jury has found sufficient evidence to charge the defendant, and this is a case that we believe should be presented to a jury at trial.”

Hernandez’s attorney, Harvey Fishbein, insists his client has an I.Q. in the “borderline-to-mild mental retardation range.”

“Nothing that occurs in the course of this trial will answer what actually happened to Etan Patz,” Fishbein said. “The indictment is based solely on statements allegedly made by my client, who has, in the past, been repeatedly diagnosed as suffering from schizophrenia, and who has, over the last six months, been found to suffer from schizotypal personality disorder, which is characterized by, among other things, unusual perceptual experiences, commonly referred to as hallucinations.”

Patz’s disappearance on his first walk alone to the school bus stop grabbed national headlines in 1979. His face become one of the first to appear on a milk carton in an effort to garner information leading to his whereabouts.

Potential prosecution problems

Paul Callan, former deputy chief of homicide in the Brooklyn district attorney’s office, said it’s unusual for a suspect to be indicted six months after an arrest, and it could suggest some holes in the case.

“It’s a real uphill battle to get a conviction in such an old case,” Callan said. “Witnesses’ memories fade, physical evidence doesn’t exist anymore.”

In New York, a defendant cannot be convicted solely on a confession. Prosecutors must present corroborating evidence, which could prove challenging, Callan suggested, especially because Patz’s body was never found.

“The defense will come in and say they don’t even know that Etan Patz was murdered, maybe he was kidnapped,” Callan said.

One point the prosecution might argue, he predicted, is that Hernandez confessed the crime to multiple people over the years with consistent detail, suggesting truthfulness. Jurors may also be more eager to reach a resolution in such an iconic cold case.

“This is the case that put child predators on the radar screen of mothers in America. A jury will like to convict and punish the person responsible,” Callan added.