The remains, believed to be around 700 years old, were taken from St Leonard’s Church, Hythe, Kent, sometime between 4pm on Sunday and 10.40am on Monday, police said.
Reverend Andrew Sweeney branded the crime “shocking and unsettling” in a statement issued by police, adding: “Each skull represents the mortal remains of a human being who deserves to rest in peace.”
A lock on a church door was damaged during the theft, a Kent Police spokesman said.
Officers are appealing for anyone with information about the burglary, or who has been offered a skull for sale, to come forward.
Inspector Maxine Harris said the skulls were “not free for the taking”, adding: “They are part of an important collection. We are keen to see them back in their rightful place in the crypt.”
St Leonard’s – known as the “church with the bones” – is famed for the collection, according to the Church of England.
The display in the crypt, known as the ossuary, is open to visitors and boasts the “largest and best-preserved collection of ancient human skulls and bones in Britain”, the Diocese of Canterbury said.
It features a total of 1,022 skulls as well as other bones. References to the collection date back to 1678, according to the church.
There are several theories about the origin of the skulls but research has suggested they most likely belong to Hythe residents who had been buried in the churchyard in or around the 13th century, the church website said.
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Thieves stole 21 ancient skulls from a church crypt display of what is thought to be the largest collection of its kind in Britain.