Hernandez is charged with killing the 6-year old who disappeared in 1979 in one of the biggest missing person cases the city hsa ever seen.
Monday's hearing was a rare public appearance for Etan Patz's parents.
His father stoically watched the 2012 videotaped confession of his son's killer played in court, but mother Julie Patz left before the chilling words of former grocery clerk Pedro Hernandez.
In the confession, Hernandez demonstrated on his own neck how he choked the then 6 year old after luring him into a basement of a bodega in SoHo 33 years before.
Hernandez claimed he couldn't stop, that something took over him. "He wasn't dead. He was still gasping."
The 53 year old then dispassionately described how he put the boy in a garbage bag. "He was still alive. He was moving his legs. Even though he was still alive I put him in the plastic bag."
Hernandez said he put the boy in a cardboard box, and dumped it in an alley. He said when he went back the next day, the box was gone.
Etan's disappearance sparked the missing child movement. Authorities chased false leads for years, even digging up the SoHo basement a month before a tip led to Hernandez who immediately confessed.
"There is no corroborating evidence as far as we're concerned, there is no evidence other than the confession," said defense attorney Harvey Fishbein.
Which is why the admissibility of the confession and others Hernandez made will be critical. His attorney argues Hernandez was improperly interrogated and his rights violated for hours before that camera rolled.
('It doesn't sound like the ramblings of a crazy person when you hear that confession," we asked.)
"No, and we're not saying it is the ramblings of a crazy person. First of all, the confession you heard today was not the first one. This is the product of being repeated a number of times," said Fishbein.
It was the first time the public could hear Hernandez, who has pleaded not guilty, talk in his own words about the notorious case that plagued police for decades.
Judge Maxwell Wiley must decide whether Hernandez was properly advised of his rights and is mentally capable of understanding them.
In 2012, police got a lead that brought them to Hernandez, a high school dropout who had worked at a corner store near where Etan disappeared.
Hernandez, most recently a resident of Maple Shade, New Jersey, also told police that he confessed before: to his ex-wife, to a friend, and in front of about 15 people during a prayer circle at a church group. No one ever went to authorities.
"We were all holding hands and praying," he said of the church meeting. "And everybody was confessing, so I confessed. I told them I killed a child."
The hearing is expected to last several weeks.
(The Associated Press contributed to this report.)