The FBI agents involved in Thursday's search were acting on a recently received tip that led them to the building in lower Manhattan near where the boy disappeared May 25, 1979, the New York Daily News reported.
Law enforcement sources told The New York Times a cadaver dog had sniffed around the basement in recent weeks and indicated the possible presence of human remains.
"There are a large number of people who will be working 24 hours a day, over at least the next five days, sifting through the debris coming out of that basement," NYPD spokesman Paul Browne said.
The basement on Prince Street in the SoHo neighborhood is less than a block from the Patz home and, the Times said, had a reputation of being a rendezvous for sexual liaisons at the time. The search plan calls for the removal of drywall to look for signs of blood, and breaking up the concrete floor to look for old clothing or remains.
No one was ever charged in Etan's disappearance but a family acquaintance, Jose Ramos, was later convicted of child molestation and admitted he had seen Etan the morning he disappeared.
Patz, the first missing child whose face appeared on the side of a milk carton, was kidnapped as he walked alone to school. A nationwide manhunt that ensued after the disappearance produced no results.
Investigators in the case are re-examining Ramos, who is in prison on unrelated charges, ABC News reported.