The radiologic evaluation of the temporal bone in cochlear implant candidates can detect malformations of the inner ear in up to 20% of cases. The aim of our study was to analyze and classify malformations of the inner ear in patients with cochlear implants carried out from 2001 to 2009. Malformations of the inner ear, including malformations of the internal auditory canal were detected in 12.7% of children and 3.4% of adults. Mondini dysplasia was most common and occurred in 45% of cases. The surgical procedure had to be adapted according to the individual malformation. Modification of surgical access, management of intraoperative CSF gusher, choice of electrode array, intraoperative imaging and the use of navigation were the most important factors. Rehabilitation results were generally very positive and corresponded to the expectation depending on the duration of deafness, if no additional handicaps were present.