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Congenital cholesteatoma is a rare lesion resulting from failed involution of epidermoid rest cells, which take part in the formation of the mucosa of the middle ear cleft during embryonic development. We report the first case report of a large congenital hypotympanic cholesteatoma with extension to the jugular foramen and carotid canal, in a 13-year-old girl, which was excised successfully by endoscopic-assisted hypotympanotomy infra-cochlear approach.