BERLIN — When the time came to have their son circumcised at age 4, Muhsin Sapci and his wife, Gonca, both first generation immigrants from Turkey, assumed they would simply take the boy to the nearby Jewish Hospital, used by many Muslim families who also prefer to have the procedure done by a surgeon.

But since a German court’s ruling that equated circumcision with bodily harm — and a criminal act — many hospitals across the nation have stopped performing the procedure. The Sapcis are determined to have their son, Asil, who turns 4 this month, circumcised, but they do not know where to go.

“Right now everything is controlled, most people go to a doctor and the child is covered by insurance,” Mr. Sapci said. “If they try to outlaw it, it will still be done, but differently, and that could have consequences.”

Their quandary is indicative of the confusion that has been sown by the ruling on June 26 by a court in Cologne that, while not enforceable outside that region, has sent ripples of anger and anxiety throughout the country and beyond. It has raised vexing questions about the boundaries of religious practice and freedom in an increasingly secular Germany.