Many relics were handed down by Jesuit families and often given to the school for safe keeping.
"We were founded out of persecution and based abroad; these objects were shipped over to keep them safe," Graffius says.
Items from Stonyhurst College's collection are increasingly loaned for exhibitions, with one of the grisly jewels in the crown currently on display at the British Museum's "Shakespeare: Staging the World" exhibition.
The show, which opened this month, brings together a series of objects from Tudor England to help conjure up the turbulent times for a 21st-century audience.
Jan Graffius, the curator of the school's collections, says: "Some things have a powerful ability to speak.
We all know how sensitive the eye is and how precious our eyesight is.
The bones bear the clear mark of knife slashes where the victim was quartered and some skin still remains attached.Undoubtedly one of the star attractions will be the eyeball held by Stonyhurst from a Catholic martyr who was executed in 1606.The eye's owner, Edward Oldcorne, was unlucky to have been caught.A pair was given to Mary Queen of Scots, who wore it in a locket.The collection has a series of objects from the Stuarts, as the school was sympathetic to their cause.