A child in care was secretly circumcised against his parents' wishes, the Civil Appeal Court in London was told.
The father and mother, who are from Leeds but cannot be named for legal reasons, made the allegation before family judge Lord Justice Thorpe.
They claimed their son's racial and ethnic background had been ignored by subjecting him to the operation which they said violated their culture.
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The father said: "The boy was secretly seen by a medical doctor to circumcise him without informing his parents.
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"We say prayers before a circumcision happens because it is a very risky thing. Here they tried to do it secretly.
"Our children's racial, linguistic and ethnic backgrounds should have been taken into account," he said.
Leeds City Council took the three children of the family into care from late 2006 and contact with the parents was ended.
But at the court, the parents asked for contact to be resumed and claimed their children had suffered from a "catalogue of abuses" since they left the family home.
The alleged circumcision was the worst.
But Lord Justice Thorpe refused the applications and said the eldest child's wish to dispense with his guardian was merely "post-pubertal rebellion."
He told the parents that they might get access to their children in future if their mother behaved herself and co-operated with the local authority.