To determine the prevalence of SLC26A4 (PDS) gene mutations in cochlear implant recipients with inner ear malformation, and the correlation between SLC26A4 (PDS) gene mutation and inner ear malformation and intra-operative testing of the electrically evoked auditory nerve compound action potentials (ECAP).Peripheral blood samples were collected from 48 cochlear implant recipients with temporal bone malformation and 50 healthy controls. Genomic DNA was extracted from the blood; PCR and direct sequencing were used to detect the mutations of SLC26A4 (PDS) gene. During the implantation of artificial cochlea the 48 recipients underwent intraoperative neural response telemetry (NRT) to measure the electrically evoked auditory nerve compound action potentials (ECAP).SLC26A4 (PDS) mutations were detected in 70.3% (26/37) of the patients with enlarged vestibular aqueduct (EVA), and 18.2% (2/11) of the patients with other malformations of inner ear. Fifteen different mutations were identified, 8 of which had never been previously reported. The IVS7-2A>G mutation was the most prevalent mutation of SLC26A4 (PDS) gene, accounting for 45.9% (17/37) in the EVA patients. No association was detected between SLC26A4 mutation and ECAP.Mutations in the SLC26A4 (PDS) gene is a major cause of EVA, with IVS7-2A>G as the most common mutation form.