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Cochlear implants (CIs) are a key option of hearing rehabilitation in certain children. Scientific, surgical and technological advances in CI technology have enabled implantation in a significant number of children with sensorineural hearing loss (SNHL). There are established criteria to characterize appropriate patients, improving successful performance post operatively by standard metrics of speech perception. Clinical outcomes are, however, modified by several patient-related. An increasing body of evidence in such domains has resulted in expansion of candidacy criteria. Approximately 20% of all congenital hearing loss is associated with inner ear malformations (IEMs). Implantation of such children was associated with uncertain surgical and clinical success, and hence was limited in the early years of CI surgery. To date, the literature regarding outcomes in this special population has varied. Studies have been mixed when comparing children with IEMs to those with normal anatomy regarding success with CI. Results may be related to the type and severity of IEM. There may also be differences in children with congenital deafness versus progressive hearing loss. The current data are limited as there is not a standardized testing paradigm for evaluation in children. The variability in the data suggests further research is required to fully understand the nuances in management of these complex children. The goal of this review is to discuss surgical management and outcomes of children who meet criteria for CI in the setting of an IEM.