Branchio-oto-renal (BOR) syndrome is an autosomal dominant inherited disorder characterized by malformations of the ear associated with hearing impairment, branchial fistulae or cysts, and renal malformations. Mutations in the gene EYA1 have been found to be responsible for BOR syndrome in approximately 40% of the subjects. Here we report a Japanese family with BOR syndrome associated with a frameshift mutation in EYA1. This mutation, 1667-1668insT, has not been previously reported and is also the first frameshift mutation in exon 16 of this gene. We describe the detailed clinical features and medical highlights of the family members, and based on their clinical histories we propose that genetic testing for EYA1 mutations would contribute to the diagnosis of BOR syndrome, facilitate genetic counseling for recurrence, give precautions regarding possible renal disorders later in life, and impact the consideration of surgical intervention for middle ear anomalies.