To compare the overall clinical outcomes of cochlear implantation in children with structural inner ear abnormalities, with results of implantation in children with radiologically 'normal' inner ears. To study the incidence and performance outcomes of cochlear implantation in children with inner ear malformations (IEMs). It is a retrospective case control study of 57 normal and 57 abnormal inner ear patients operated for cochlear implant between Jan 1, 2014 and Aug 1, 2017, by Veria technique. The age range was between 12 months and 15 years. The prevalence of IEMs was 13.8%. Of the 57 cases with IEMs, 33.3% were of enlarged vestibular acqueduct, 7% were of isolated Incomplete Partition type-2, 21.1% cases were of Mondini's dysplasia, 3.5% of Incomplete partition type-1 and 8.8% of cochlear nerve hypoplasia. Most commonly encountered malformation was EVA while IP-1 was the least common malformation. A CSF gusher was experienced in 11 cases. There was a statistically significant difference between the CAP and SIR scores of both IEM and control groups, both at 1 year and at 2 years (1 year CAP score p value < 0.001, 2 year CAP score p value 0.002 and 1 year SIR score, p value < 0.001, 2 year SIR score, p value 0.013). There was progressive improvement in the scores (of both groups) at the 2 year mark, compared to 1 year scores. Cochlear implantation is safe and surgically feasible in children with IEMs. However, the hearing outcome and speech perception outcomes are poor than those of patients with normal anatomy, with an exception seen in enlarged vestibular aqueduct.