The suspect, Pedro Hernandez, is in custody in New York. His wife had to leave the house in Maple Shade and the house remained under police control Wednesday night, KYW-TV, Philadelphia, reported.
Paul Browne, a New York police spokesman, would say only the search was part of an "ongoing investigation," the New York Daily News reported.
"It's not clear what they are looking for," Robert Gottlieb, who represents Hernandez's wife, said.
Legal experts have suggested prosecutors might have difficulty convicting Hernandez of a crime that has become one of New York's most enduring mysteries. Etan vanished during the short walk to the school bus stop.
Hernandez, then 18, was working as a clerk at a bodega. He told police he lured the boy to a basement, strangled him and dumped the body in the trash.
But he has a history of mental disorders, raising the possibility of a false confession.