Purpose <p>Cochlear implantation (CI) is the state-of-the-art treatment option for sensorineural hearing loss condition including patients with congenital inner ear malformations. Recently our centre started treating children with CI who were diagnosed with inner ear malformations. Objectives of this retrospective study are to create three-dimensional (3D) model of malformed inner ears, identification of cochlear nerve bundle from pre-operative images, visualize electrode placement inside the cochlear portion from post-operative images, and evaluate hearing benefits post-operatively received from CI.</p> Methods <p>Slicer software was used to 3D segment the inner ear and the electrode from the pre-, and post of CT scans. Using the same software, cross-section of internal auditory canal (IAC) was navigated to visualize the presence or absence of cochlear nerve. Speech intelligibility rating (SIR) and pure tone average (PTA) thresholds were evaluated for the benefits received from CI.</p> Results <p>Our database showed a total of 12 children radiologically diagnosed with inner ear malformation and out of which 19 ears were treated with MED-EL CI devices. Enlarged vestibular aqueduct (EVA, incomplete partition (IP) types I, and II, cochlear hypoplasia (CH), cochlear aperture stenosis, common cavity (CA) were the different malformation types found in this cohort. Intra-operative gusher was observed in EVA and IP type II malformation types. Higher SIR scores and lower PTA thresholds were seen for less severe malformation types and vice-versa.</p> Conclusions <p>Severity of malformation have a negative effect on the hearing outcomes with CI. MRI is an important tool in the identification of cochlear nerve bundle in subjects diagnosed with malformed inner ear anatomies.</p>