Louis Lanzano / AP

In this Nov. 15, 2012 file photo, Pedro Hernandez appears in Manhattan criminal court in New York. Hernandez, who is charged with killing 6-year-old Etan Patz in 1979, pleaded not guilty Wednesday to murder, despite police saying he confessed to the crime.

The man charged with killing a 6-year-old New York City boy who was infamously abducted in 1979 pleaded not guilty Wednesday, even as his lawyer insisted his confession to police was false.

Pedro Hernandez, 51, wore a gray sweatsuit and answered "not guilty" at the hearing in the case of Etan Patz, whose disappearance helped spawn the movement to publicize cases of missing children. A grand jury had indicted him on two counts of second-degree murder and one count of first-degree kidnapping.

"My client had no motive and no history," defense attorney Harvey Fishbein said outside court after seeking dismissal of the case.

"There is a serious question as to what happened in May 1979," Fishbein said. "There is no crime scene. There are no witnesses to a crime."

Fishbein also noted a body was never recovered. He said Hernandez confessed falsely after seven hours of questioning by police, and that he is still under medical and psychiatric care.

"My client is not happy that he is in jail," Fishbein said.

Hernandez was previously found fit to stand trial. Fishbein said previously that while Hernandez's defense will revolve around his mental state, he isn't pursuing an insanity defense.

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 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.

Stanley K. Patz

Etan Patz, who vanished in New York on May 25, 1979.

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.

The defendant's wife and daughter attended the hearing but did not speak to reporters.

Etan's disappearance 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.

Watch US News crime videos on NBCNews.com

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 repeatedly denies having anything to do with Etan's disappearance.

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.

Ramos is currently jailed in Pennsylvania on charges of failing to properly register as a sex offender under Megan's Law after he was released earlier this year from prison. 

Associated Press writer Jennifer Peltz contributed to this report.

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NYPD via AP file

Etan Patz vanished in New York on May 25, 1979. Despite an extensive search, his body was never found.

A grand jury has indicted a former SoHo bodega clerk on charges he lured 6-year-old Etan Patz into a basement and killed him 33 years ago, sources familiar with the case told NBC 4 New York.

Pedro Hernandez is charged with murder and kidnapping, the sources said.

Hernandez, who has a history of mental illness, was arrested last spring, decades after Patz disappeared off a SoHo street in a tragic case that has mystified New York City.

Previous story: Grand jury considers charges in Etan Patz disappearance

Police said Hernandez had admitted to luring Patz into a bodega where he worked, near the boy's house, and choking him to death in the basement.    

Hernandez's attorney, Harvey Fishbein, said the trial would not solve the mystery of what happened to Patz.

Hernandez, he said, suffers from schizophrenia and has hallucinations. Fishbein said the entire case is based on statements made by his mentally ill client.

"The statements alleged by the people are not supported by any evidence whatsoever despite extraordinary investigative efforts by the police, back then and now," Fishbein said.

Read the indictment here (PDF)

Police Commissioner Ray Kelly said at the time that police focused on Hernandez, who now lives in Maple Shade, N.J., after the Missing Persons Squad received a tip from someone who remembered Hernandez speaking of having killed a child.

A spokeswoman for the Manhattan District Attorney said the grand jury found sufficient evidence to charge Hernandez and that the office believes the case should go to trial.

"This indictment is the outcome of a lengthy and deliberative process, involving months of factual investigation and legal analysis," said spokeswoman Erin Duggan.

Jonathan Dienst is WNBC’s chief investigative correspondent. Shimon Prokupecz is a WNBC investigative producer.

NYPD via AP file

Etan Patz vanished in New York on May 25, 1979. Despite an extensive search, his body was never found.

NEW YORK -- A Manhattan grand jury is hearing evidence against Pedro Hernandez in the 1979 disappearance of Etan Patz, NBC 4 New York has learned.

A decision is expected by Thursday whether Hernandez will be indicted on kidnapping and murder charges.

Police have said Hernandez confessed in May to attacking Etan. They said he admitted to grabbing the 6-year-old off the street and killing him in the basement of a SoHo bodega where he had been working. The body was then allegedly left in a trash bag out on the street and was never found.

It was 33 years ago when Patz disappeared as he walked alone for the first time to get his school bus.

Developments in the case have made headlines across the globe for decades as police tried to rule in or rule out possible suspects.

Defense lawyers have said Hernandez has a history of mental illness and his confession is unreliable. Hernandez's attorney, Harvey Fishbein, declined to comment to NBC 4 New York on Tuesday about news a grand jury had started meeting.

A spokeswoman for Manhattan District Attorney Cy Vance also declined comment.

Also on NBCNewYork.com: LIPA executive quits after Sandy furor

After his arrest in Camden County, N.J., Hernandez was held at the Bellevue Psychiatric Center but was later moved to Rikers Island after receiving medication.

A court hearing is scheduled for Thursday at 100 Centre St. at which prosecutors are expected to announce any possible charges handed up by the grand jury.

Last week, one-time lead suspect Jose Ramos was released from a Pennsylvania prison on unrelated child sex crime offenses. He was immediately arrested on a Megan’s law violation for allegedly not correctly listing an address where he would be living after his release.

Patz’s family continues to live in Soho. They have not commented on the arrest of Hernandez.

Jonathan Dienst is WNBC’s chief investigative correspondent. Shimon Prokupecz is a WNBC investigative producer.

Stanley K. Patz via AP

Etan Patz

Authorities have concluded their search of a Manhattan basement for the remains of Etan Patz, who vanished 33 years ago on his walk to the school bus stop.

No remains were found, and NBC New York has learned from a law enforcement official that field tests on a concrete slab that contained a "stain of interest" over the weekend were negative for blood.

Meanwhile, dozens of items, including strands of hair, a piece of paper and other possible bits of forensic evidence, were gathered and will be analyzed further at an FBI laboratory.

The Patz family was briefed Sunday on the investigation and what has been found at the site.

The search for remains of 6-year-old Patz began Thursday in the basement of a building on Prince Street in the SoHo area. The concrete floor was torn up and investigators sifted through the dirt and soil below for evidence.  

NBC New York was first to report the activity in the SoHo building Thursday.  

Everything that investigators have collected, including numerous swabs that will be tested for DNA evidence, is being sent to the FBI laboratory in Virginia.  

Some bones were found, but they were determined to be non-human, and were discovered among Chinese food takeout containers, sources said.  

Sources told NBC New York that the paper found in the debris is yellow, with handwriting on it, and a piece of tape that contains two or more hairs. Its significance was not clear, but one source said it was important enough to be collected and analyzed.  

At the time of Patz's disappearance, the 13-by-62 basement at 127B Prince St. was being used as a workshop by Othniel Miller, a handyman who was friendly with the Patz family.  

Investigators collect hair, paper in search for Etan Patz, missing since 1979

Miller, now 75, has been interviewed by investigators several times over the years, but he recently made statements that raised their suspicions, according to law enforcement sources.  

In a recent interview with investigators, he blurted out “What if the body was moved?” according to an official.  

Sources also say they have evidence to suggest Patz had been in the basement before.  

Miller hasn't been named a suspect, and his lawyer says he has nothing to do with the case.

Investigators have also recently questioned a second person, Jesse Snell, in connection with the re-examination of evidence. NBC New York has learned that on the morning Patz disappeared in 1979, Snell was observed at the building where police are searching now, and also worked with Miller. Investigators would not elaborate on why they met with Snell.  

For more, visit NBCNewYork.com

One other man has remained a longtime possible suspect: Jose Ramos, a drifter and onetime boyfriend of Patz's baby sitter. In the early 1980s, he was arrested on theft charges, and had photos of other young, blond boys in his backpack. But there was no hard evidence linking Ramos to the crime.  

He is in prison in Pennsylvania on a separate case.

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Updated at 11:04 p.m. ET: Dozens of items, including strands of hair, a piece of paper and other possible bits of forensic evidence have been found in a SoHo basement in the four days that investigators have been searching for clues in the 1979 disappearance of Etan Patz, NBC New York has learned.

Law enforcement sources tell NBC New York that investigators from the FBI, NYPD and Manhattan district attorney's office have told the Patz family that no human remains have been found. The family was briefed Sunday on the investigation and what has been found at the site.

Investigators discovered a "stain of interest" on a drywall Saturday while taking apart the basement in their search for the remains of Etan, according to law enforcement sources. But by Sunday, a law enforcement source told Reuters that "nothing conclusive had been found."

The stain was discovered Saturday in the ongoing search for clues in the case of the 6-year-old boy who went missing 33 years ago on his short walk to the school bus stop.

NBC New York was first to report the break in the cold case on Thursday.

By Saturday, investigators had finished ripping up the basement's concrete floor with jackhammers and saws, and were digging through the dirt in hopes of finding the boy's remains, or any other evidence.

See the original story at NBCNewYork.com

It was while investigators were taking apart the basement floor and walls that they found a "stain of interest" on a drywall, according to law enforcement sources. Officers from the NYPD Emergency Services Unit used a chainsaw to cut out a piece of the wall, which is being preserved for analysis at the FBI Laboratory in Virginia. It's not clear how significant it is.

Other debris was also being tested, a process that could last into next week, chief police spokesman Paul Browne said.

At the time of Patz's disappearance, the 13-by-62 basement at 127B Prince Street was being used as a workshop by Othniel Miller, a handyman who was friendly with the Patz family.

Miller, now 75, has been interviewed by investigators several times over the years, but he recently made statements that raised their suspicions, according to law enforcement sources.

Stanley K. Patz / AP

Etan Patz, who vanished on May 25, 1979, and has never been found, after leaving his family's SoHo home for a short walk to his school bus stop in New York.

In a recent interview with investigators, he blurted out “What if the body was moved?” according to an official.

Sources also say they have evidence to suggest Patz had been in the basement before.

Miller hasn't been named a suspect, and his lawyer says he has nothing to do with the case.

Investigators Saturday were mostly concentrating their search towards the rear of the basement, where a cadaver-sniffing dog recently picked up a scent.

It's unclear what the renewed probe may turn up, if anything.

"We're hopeful that we can bring some level of comfort to the parents, perhaps find some — obviously, the body of this poor child — but evidence that may lead to a successful investigation in this case," Police Commissioner Ray Kelly said. He was a lieutenant working on organized crime cases when Etan Patz vanished.

As for whether authorities were optimistic, he said, "I really can't say."

Earlier: Etan Patz case: Police dig in basement, question second man in search for boy who disappeared in 1979

Through a lawyer, Miller denied having anything to do with Etan's vanishing, which helped turn missing children into a nationwide cause. Miller's grandson, Tony Miller, said Friday outside his home that his grandfather is a "good guy" who "wouldn't do this."

Investigators have also questioned a second person, Jesse Snell, in connection with the re-examination of evidence. NBC New York has learned that on the morning Patz disappeared in 1979, Snell was observed at the building where police are searching now, and also worked with  Miller. Investigators would not elaborate on why they met with Snell.

The investigation into the disappearance of Patz has stretched through decades and countries, from basements to rooftops and seemingly everywhere in between.

No one has ever been charged criminally — and Etan Patz, the little boy with sandy brown hair and a toothy grin, was declared dead in 2001.

This week, after more than a decade of relative quiet, the case suddenly ran hot again, after the cadaver-sniffing dog picked up the scent.

The investigation has reached similar highs before — only for the trail to go cold for years at a time.

Vanished in 1979
Patz vanished on May 25, 1979, while walking alone to his school bus stop for the first time, two blocks from his home in New York's SoHo neighborhood.

There was an exhaustive search by the police and a crush of media attention. The boy's photo was one of the first of a missing child on a milk carton. Thousands of fliers were plastered around the city, buildings canvassed, hundreds of people interviewed. SoHo was not a neighborhood of swank boutiques and galleries as now, but of working-class New Yorkers rattled by the news.

Etan's parents, Stan and Julie, offered a $25,000 reward for information leading to the boy's whereabouts, and sightings were frequently reported, to no avail. In 1986, a child resembling Etan was spotted in Israel, which prompted detectives to circulate his photo there. Nothing came of it.

A name gradually emerged as a possible suspect: Jose Ramos, a drifter and onetime boyfriend of Etan's baby sitter. In the early 1980s, he was arrested on theft charges, and had photos of other young, blond boys in his backpack. But there was no hard evidence linking Ramos to the crime.

Missing persons cases, like homicides, are generally considered cold after six months, but they're never closed. And with seemingly no new leads, the case would go quiet for years. In three decades, 10 detectives have been assigned to head up the case. The FBI and police are working jointly.

"Those cases are still maintained by someone, but the attention they get diminishes over time," said Joseph Pollini, a retired NYPD lieutenant in the cold case squad, now a professor at John Jay College of Criminal Justice. "There's often nothing you can do, when you have no new leads."

Reviving the case
A fresh lead came in 2000, after Ramos, now in prison in Pennsylvania for sexually molesting two boys in unrelated cases, admitted he was with Etan the day he disappeared. He was said to have told a cellmate: "Etan is dead. There is no body, and there will never be a body."

That prompted police to scour for clues in the building where Ramos lived at the time. They dismantled the furnace and searched it for DNA. But they found only animal traces.

By the next year, father Stan Patz, who never moved or even changed their phone number in the hope their son would reach out, had Etan declared dead in order to sue Ramos in civil court. He was tired of waiting for justice, he said at the time.

A civil judge in 2004 found him to be responsible for the disappearance and presumed death of the boy, after he disobeyed her orders to answer deposition questions under oath for a lawyer representing Etan's parents. Ramos says he didn't do it.

The ruling provided a tiny measure of comfort to the family, though Stan Patz never collected the $2 million the judge ordered Ramos to pay. But the criminal case continues, and prosecutors lacked enough evidence to charge Ramos criminally.

The case was quiet until 2010 when new district attorney Cyrus R. Vance said he was going to revisit it.

Ramos is scheduled to be released from prison in Pennsylvania in November. His pending freedom is one of the factors that has given new urgency to the case.

The basement space being searched sits beneath several clothing boutiques. Investigators began by removing drywall partitions so they could get to brick walls that were exposed in 1979. The work will continue through the weekend.

About 50 law enforcement agents including forensics experts and an anthropologist are on scene. While cadaver-sniffing dogs are capable of detecting scents much older than 33 years, it's also possible the dog picked up an animal scent or was plain wrong.

The swank cobblestone street remained closed off and was a veritable media circus, with trucks and crews parked along the curb and gawking tourists stopping to snap photos.

The Patz family hasn't commented or turned up near the site, though it's visible from their home — they've seen the circus before.

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Updated at 5 p.m. EDT: NEW YORK -- Police and the FBI were back Thursday at a lower Manhattan building where Etan Patz went missing in 1979, NBCNewYork.com reported.

Patz was six years old when he disappeared May 25, 1979 on his way to the school bus stop, touching off one of the most high-profile missing child cases in New York history. He was among the first missing children ever shown on the side of a milk carton, and President Ronald Reagan declared May 25 National Missing Child Day in his honor.

Officials are searching the basement of a building on Prince Street in SoHo, based on a re-examination of evidence, police said. Authorities plan to dig up the basement, which is connected to a handyman who had contact with Patz just before he disappeared, according to a law enforcement official.

The 15-by-30 basement is at 127B Prince Street, about 200 feet from the building where Patz lived.

Authorities in the afternoon got an alert from a cadaver dog they brought in.

For more, visit NBCNewYork.com

NYPD spokesman Paul Browne said there is dry wall in the basement that wasn't there in 1979, and authorities plan to remove it and dig through the basement and brick walls.

Sources also say they have evidence to suggest Patz had been in the basement before.

Investigators recently went to the DA seeking a search warrant  based on the new information. They plan to be at the building through the week and possibly into the weekend, officials told NBCNewYork.com.

Authorities from the city medical examiner's office were also on scene to help determine whether any findings are human remains.

FBI spokesman Tim Flannelly said the Patz family was notified before the search began.

"We're hoping that there will be real results," Flannelly said. "This little boy disappeared in 1979, and here we are in 2012 still hopeful that we can bring closure to the investigation."

Two years ago, Manhattan District Attorney Cyrus Vance Jr. said he was reopening the case, taking a fresh look at the evidence.

Vance declined to specify at the time why the case was reopened.

Patz was legally declared dead in 2001.

Stanley K. Patz via AP

This undated image provided Friday, May 28, 2010 by Stanley K. Patz shows Patz's son Etan, who vanished in New York on May 25, 1979.

The prime suspect has long been Jose Ramos, who had connections to Patz's former babysitter. Ramos is serving 20 years in prison in Pennsylvania for an unrelated child molestation case.

In the 1980s, U.S. Attorney Stuart GraBois resumed the investigation of Ramos. When GraBois asked Ramos how many times he had sex with Patz, Ramos "broke down," GraBois told CBS' "60 Minutes" in 2000.

During that questioning, Ramos admitted to having taken a young boy to his apartment on May 25, 1979, and that he later recognized the boy as Patz, declared missing on the news.

But Ramos said the boy had refused his advances, and that he let him go. Without any evidence, GraBois was not able to charge Ramos with the crime.

The Patz family filed a civil case against Ramos, and in 2004 State Supreme Court Justice Barbara R. Kapnick declared Ramos responsible for Patz's death. The family was awarded $2 million, which they have not collected.

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