Inner ear malformations constitute about 20% of congenital sensorineural hearing loss. In this review article an updated classification of cochlear malformations is provided. Incomplete partition and cochlear hypoplasia cases are each divided further into three groups. There are two main difficulties in the surgery of inner ear malformations; gusher and facial nerve abnormalities. Radiological features of malformations necessary to identify these problems preoperatively are discussed. Facial nerve abnormalities that may occur are described. Two different types of cerebrospinal fluid leakage are defined and necessary measures to prevent leakage are described. Standard and modified surgical approaches to overcome the described problems are described with literature findings. Finally meningitis which may occur with and without cochlear implantation in this special group of patients is emphasized. This is common in incomplete partition type I patients and is usually due to a fistula in one of the windows (usually oval window) which occurs as a result of cerebrospinal fluid pressure. This is a medical emergency leading to potential meningitis and measures that should be taken to stop the leak as soon as possible are described.