Cochlear implantation in children with cochlear malformation is on the rise. However, only one case has been reported in Japan. The objective of this paper is to report the authors' experiences with cochlear implants in children with cochlear malformations and, to investigate the morphological classification of cochlear malformation, surgical procedure, complications, and speech perceptions after implantation. Five children (6 ears, including 1 Usher's syndrome and 1 CHARGE association) with congenital inner ear malformations were implanted with multichannel cochlear implants (Nucleus Mini 22 device) between 1994 and 1998. Malformations included common cavity deformity 2, and incomplete partition 4. On the other hand, 4 cases with incomplete partition deformity underwent cochlear implantation by the transmastoid facial recess approach, 2 patients with common cavity deformity received implantation by the transmastoid labyrinthotomy approach. Complications such as facial twitching, cerebrospinal fluid (CSF) gusger, and flap-related problems were encountered. Facial twitching occurred in 1 of 2 patients with common cavity where the electrode array extended into the internal auditory canal. CSF gusher was encountered in 1 of 4 patients with incomplete partition, and revision surgery was performed one week later. One patient had delayed cochlear implant infection and a split pericranial flap was used to cover the defect in the skin flap. Within 6 months, however, the revised pedestal site broke down because of recurrent flap infection. Finally, the cochlear implant was explanted, and the patient underwent a new cochlear implantation in the contralateral ear. All the patients had satisfactory speech reception and word acquisition, but still poor phonetic expression.