Objective: To evaluate the auditory perception outcomes of cochlear implant (CI) in children with different types of inner ear malformations (IEMs) and to compare them with CI users with the normal cochlea. Design: Retrospective and prospective data collection. Settings: Tertiary referral hospital. Participants: There were 274 CI users with and without IEMs as two groups. Both groups’ chronological age at implantation and duration of cochlear implant usage was matched (±8 months). Main outcome measures: All subjects were evaluated preoperatively and postoperatively with Ling’s sound test and auditory perception test battery, which includes the Meaningful Auditory Integration Scale (MAIS), close-set Pattern Perception Test (PPT), and open-set Sentence Recognition Test (SRT). Also, children with IEMs were assessed for language development. Results: The incidence of IEMs were incomplete partition-II, 40 (29.19%), incomplete partition-I, 36 (26.2%), cochlear hypoplasia, 26 (18.9%), enlarged vestibular aqueduct, 14 (%10.2), incomplete partition-III, 10 (%7.2), common cavity, 8 (5.8%) and dilatation of vestibule, 3 (2.1%) patients. The significant difference was seen in Ling’s sound test and auditory perception test battery scores of children with incomplete partition-I, cochlear hypoplasia, and common cavity (p-value < .005). Conclusion: IEMs group showed different progress according to the type of ear anomaly. Although CI users with enlarged vestibular aqueduct (EVA) had the highest scores, users with common cavity had the lowest scores. Taking these results, caused by anatomical differences, in to account is very critical in follow-ups and rehabilitation programs. Each cochlear implant user should be evaluated according to his/her individual needs.