Branchio-oto-renal (BOR) syndrome is an autosomal dominant disorder that is characterized by branchial cysts or fistulae, external ear malformations and/or preauricular pits, hearing loss and renal anomalies. Recent advances in molecular genetics have shown a human homologue of the Drosophila 'eyes absent' gene (EYA1) on chromosome band 8q13.3 to be the most common cause of BOR syndrome. Several mutations have been identified in the EYA1 gene in patients with BOR syndrome worldwide. Here, we report a second Korean family with BOR syndrome with a novel nonsense EYA1 mutation.