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Branchio-oto-renal (BOR) syndrome is an autosomal dominant disorder characterized by branchial cleft fistulae or cysts, preauricular pits, ear malformations, hearing loss, and renal anomalies. Mutations in the human homologue of the Drosophilia eyes absent gene (EYA1) are the most common cause of BOR syndrome. In this study, we found a Korean family showing clinical features of the disease. Mutation analysis of the EYA1 gene revealed a novel one-base-pair deletion resulting in truncated protein (c.321delT; p.Ala107fs). This is the first report of BOR syndrome caused by deletion mutation of the EYA1 gene in Korea.