We studied temporal bone histopathology to obtain clues as to the role of eustachian tube (ET) disease in the pathogenesis of otitis media (OM) in patients with congenital anomalies. Thirteen temporal bones obtained from 13 individuals with various congenital anomalies were used. We looked in particular at severity of inflammation in the middle ear (ME) and ET, and at deformity of the ET cartilage. Evidence of OM was found in all the temporal bones. The ETs consistently showed a moderate degree of inflammation but without any particular correlation with the severity of ME inflammation. Deformity of the ET cartilage was present in six cases (46.2%), representing three cases of cleft palate and three of other congenital anomalies. Because the deformity of ET cartilage tended to be associated with more severe OM, we consider this cartilage deformity to be an important cause of tubal dysfunction, and thus of the high incidence of OM among individuals with congenital ear anomalies.