33-year-old Denny Pantoja pleaded not guilty to charges of criminal possession of a weapon, and endangering the welfare of a child.
He is being held on $100,000 bail.
Police now say the child shot himself, though the father reportedly initially told several different stories about how the boy was wounded.
The father of the young boy who accidentally shot himself is set to be arraigned Saturday night in Bronx Criminal Court.
In the meantime, there are still many questions surrounding what happened.
Police say Pantoja initially told police his son was shot during a robbery at a check cashing store, but detectives were skeptical. He later admitted his son shot himself. People in the neighborhood tell Eyewitness News that illegal guns are common in the area. They say most people have them for protection.
"This is a bad neighborhood, this is the way it is," said business owner John Scott, "People want to protect themselves, some people take different precautions to do it."
The 5-year-old boy who shot himself is in stable condition at Lincoln Hospital.
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