Police picked the man up sometime Wednesday evening and brought him to New York City for questioning, sources said.
The man was previously known to investigators and is not anyone new in the case, law enforcement sources said. He worked and lived in Patz's neighborhood when the boy disappeared.
Police Commissioner Ray Kelly said in a statement that the man "has made statements to NYPD detectives implicating himself in the disappearance and death of Etan Patz 33 years ago."
An intensive search for Patz was renewed several weeks ago when police dug up the basement of a handyman's workshop near Patz's SoHo home. A new layer of concrete had been laid over the foundation of the basement shortly after Patz disappeared.
That search yielded no new evidence of value, police said.
The man in custody Thursday so far has not provided details that would lead them to Patz's body, sources said.
Several sources have indicated some skepticism exists about the man's story, but police are being thorough in their investigation of any possible leads.
One other man has remained a longtime possible suspect: Jose Ramos, a drifter and onetime boyfriend of Patz's babysitter. In the early 1980s, he was arrested on theft charges, and had photos of other young, blond boys in his backpack. But there was no hard evidence linking Ramos to the crime. He is in prison in Pennsylvania on a separate case.