Facial nerve dehiscence (FND) and ossicular injury occurred more frequently in patients with cholesteatomatous than non-cholesteatomatous otitis media. FND and ossicular injury commonly occur intraoperatively in patients with otitis media, both with and without cholesteatoma. This study was designed to analyze differences in FND and ossicular injury between patients with cholesteatomatous and non-cholesteatomatous otitis media. Patients who underwent tympanomastoidectomy due to otitis media from January 2010 to July 2012 were analyzed retrospectively. Clinical features (age, sex, bacteria, and severity of preoperative hearing loss) and intraoperative findings (FND and state of ossicular injury) were compared in patients with cholesteatomatous and non-cholesteatomatous otitis media. Of 212 patients with otitis media, 148 (69.8%) had non-cholesteatomatous and 64 (30.2%) had cholesteatomatous otitis media. Of these groups, 88.6% and 88%, respectively, had positive bacterial cultures. Facial nerve dehiscence was detected in 41 patients (27.7%) with non-cholesteatomatous and 41 (64.0%) with cholesteatomatous otitis media. Dehiscence of the tympanic segment was most frequently observed in both groups. Ossicular injury was detected in 52 (35.1%) and 51 patients (78.1%), respectively. Erosion was most frequent in the incus, followed by the stapes and malleus.