To identify novel genetic causes of branchio-oto-renal （BOR） syndrome in a Chinese family. Clinical characteristics and treatment of a family with a BOR syndrome were retrospectively analyzed. Genetic analysis was conducted by trio whole exome sequencing （WES） and the duplicated exons were verified by fluorescence quantitative PCR （real-time PCR）. In this family, the affected individual had deafness, structural malformation of inner ear and middle ear, pre-auricular fistula, cervical fistula and renal atrophy consistent with the clinical diagnosis of BOR syndrome. Neither the father nor the mother had similar phenotype. WES and quantitative fluorescent PCR revealed that the patient had a partial duplication involving exons 13 to 18 of gene. This mutation has not been reported in literature or any database. Bilateral pre-auricular fistulas and cervical fistulas were surgically removed and the surgery wound healed well, while hearing AIDS had been worn to assist hearing. This study is the first to detect a novel partial duplication （exons13-18） of gene leading to BOR syndrome, and expands the mutant spectrum of gene in Chinese population.