The manifestations of branchio-oto-renal syndrome (BOR), Treacher Collins syndrome, tricho-rhino-phalangeal syndrome, van der Woude syndrome, and Langer-Giedion syndrome are well-defined; these conditions represent clinically and genetically separate syndromes. Autosomal-dominant branchio-oto-renal syndrome comprises preauricular pits, branchial fistulas, hearing loss, and renal anomalies. However, several families have been described without one or more of these clinical findings. In some families, the phenotypic expression is limited to branchial anomalies, preauricular pits, and hearing loss, with no renal dysplasia (branchio-otic or BO syndrome). In other families, branchial and renal anomalies occur without hearing impairment. It is not known whether the variable clinical manifestations are due to the effect of a single gene or whether these represent different syndromes. We investigated BO syndrome in a large family to determine whether BOR and BO syndromes are allelic to each other. The genetic linkage analysis provides evidence that BO syndrome is not allelic to the BOR gene at 8q13.