The Branchio-oto-renal (BOR) syndrome is an autosomal dominant disorder characterized by branchial clefts, preauricular sinuses, hearing loss, and renal anomalies. Recent studies have shown that mutations in EYA1 are associated with BOR. However, the underlying molecular mechanisms by which mutations in the EYA1 gene cause BOR syndrome are unknown. We have investigated 12 unrelated Caucasian families for mutations by heteroduplex analysis and direct sequencing of products from the polymerase chain reaction. In this study, we identified two novel frameshift deletions and a single base substitution that introduces a stop codon mutation in the C-terminal region of the EYA1 gene. No obvious relationships were observed between the nature of the mutations and the variable clinical features associated with BOR syndrome.