Cholesteatomas that occur under an intact tympanic membrane in the absence of prior surgical procedures or perforation are defined as congenital cholesteatomas. These entities are rarely seen, because they do not cause any major symptoms unless they touch the ossicular chain. Likewise, isolated congenital ossicular anomalies that occur independently of external ear anomalies and craniofacial dysplasia are also rarely seen. Here, we report a patient who presented with congenital cholesteatoma associated with anomalies of the ossicular chain and discuss its pathogenesis.