The Manhattan district attorney's office said the panel charged Pedro Hernandez, 51, with two counts of second-degree murder and one count of kidnapping, the cable television station NY1 reported.
Before the indictment was handed up, sources told the New York Post the panel was being asked to bring a murder indictment against Hernandez based on little more than his own confession. Prosecutors contend, however, they have credible and persuasive evidence, and that Hernandez was mentally competent, NY1 said.
Hernandez said in May he killed Etan. But his attorney said in a statement Hernandez is mentally ill and has a history of hallucinations.
The boy disappeared more than 30 years ago while walking to a school bus stop a block from his family's SoHo apartment. His body hasn't been found.
At the time, Hernandez was working at a nearby store.
Hernandez is to appear in Manhattan Criminal Court Thursday.