The decision comes after nine days of deliberations and an emotional, three-and-a-half month retrial. In May 2015, Hernandez's first trial ended in a hung jury after 18 days of deliberations.
Etan vanished on May 25, 1979, without a trace, after his parents let him walk less than two blocks alone from his SoHo home to his school bus stop for the first time.
Hernandez, 56, a husband and father of three from New Jersey with no prior criminal record, was arrested and charged in Patz's death in May 2012, after a relative contacted police, saying Hernandez had, many years before, confessed to hurting a young boy. Hernandez worked in the bodega that was near Etan's Prince Street school bus stop.
"We're obviously terribly disappointed," said Hernandez's lawyer Harvey Fishbein. "We will appeal."
Fishbein said that the emotion won over evidence in the case, and that no matter what, "unfortunately, in the end, we don't believe this will resolve the story of what happened to Etan in 1979."
Hernandez's lawyer Harvey Fishbein speaks to reporters after his client was found guilty. (DNAinfo/ Irene Plagianos)
For the Patz family, however, Hernandez's conviction is seen as long overdue justice. Etan's father, Stan, said they became convinced of Hernandez's guilt after his first trial.
"I’m really grateful this jury finally came back with what I’ve known for a long time, that this man, Pedro Hernandez, is guilty of doing something really terrible so many years ago," Patz said, speaking to reporters briefly after Tuesday's verdict.
Stan Patz sits surrounded by Manhattan prosecutors, before speaking to the press. (DNAinfo/Irene Plagianos)
At the center of the prosecution's case against Hernandez were the several hours of videotaped confessions he gave to police, in which he described how he choked the child, placed his limp body in a plastic bag, threw him in a box and dumped him in a garbage heap a couple of blocks away.
After decades of searching, neither Etan's body, nor any other physical evidence, was ever discovered in the case. He was officially declared dead in 2001.
Defense attorneys argued vehemently that Hernandez had a low IQ, suffered from hallucinations and delusions and was an "unreliable" source. They claimed his confession to police were coerced. His attorneys placed the blame for Etan's murder on Jose Ramos, a convicted child molester, now jailed in Pennsylvania, who dated Etan's babysitter.
Prosecutors, however, said there was never enough evidence to link Ramos to Etan's disappearance.
They, instead, tried to convince jurors that Hernandez was indeed telling the truth, though they acknowledged that the details of his confessions did not always match up. They painted a very different version of Hernandez, as someone who was calculating and manipulative.
Prosecutors said Hernandez had seen the little boy numerous times at the bodega where he worked, brought him down into the basement where he sexually abused him, then killed the boy to hide what he had done.
On Tuesday, jurors said it was a tough process, but they felt they were thorough with their deliberations.
"We looked at everything very carefully, and I think in the end we came to a very clear, logical result," juror Michael Castellon said.
Below, watch jurors discuss the verdict:
Jurors found Hernadez guilty on one count of second degree murder and one count of kidnapping. They found him not guilty on the first count of second degree murder, a charge that included intent. Jurors decided he did not intend to kill Etan before heading into the basement. Hernandez in his taped confessions said something inside him just "snapped" after he lured the boy there.
He faces 25 years to life for each count, and is slated for sentencing on Feb. 28.
Several of the jurors from Hernandez's first trial, who became convinced of his guilt, flanked Stan Patz when the verdict was read. A number of those jurors were an everyday presence at the trial, which Castellon said current jurors were informed of by a court officer.
"We felt obligated to stick with it," said Jennifer O'Connor, a juror from the first trial — who exchanged a hug with Castellon after the trial — adding that her message to the jurors this time around was "we love you."
Etan's mother testified early in the trial last month that her son was a "trusting" boy who she watched walk a block to his bus stop, and then never saw again.
Etan's disappearance 37 years ago, became a nationwide story, and led to far-reaching change in the way law enforcement handles missing children. May 25, the day he vanished, has been named National Missing Children’s Day. He was one of the first missing children to appear on milk cartons.
Hernandez has remained in jail since his 2012 arrest.