Branchio-oto-renal syndrome (BOR, OMIM 113650) is an autosomal dominant disorder characterised by the association of hearing loss (HL), structural ear anomalies, branchial arch defects, and renal anomalies.1 The prevalence approximates 1:40 000 in the general population, and has been reported in about 2% of deaf children.2 Age of onset for deafness varies from childhood to early adulthood.3 The clinical expression of BOR exhibits wide intra- and interfamilial variability. In addition, reduced penetrance for BOR has been assumed.4 The major feature of BOR, which occurs in 93% of patients, is HL, which can be conductive, sensorineural, or mixed. Besides the classical ear, kidney, and branchial arch anomalies, different developmental manifestations of BOR in other organ systems have been described. Among these, dysfunction of the lacrimal duct system is a common association.5-10 Thus, BOR represents a clinically and genetically heterogeneous disease complex that manifests predominantly during organogenesis. A gene locus for autosomal dominant BOR had been localised on chromosome 8q13.11,12 Subsequently, mutations in the human homologue of the Drosophila eyes absent gene (EYA1) have been shown to be causative for BOR (OMIM 601653).13 Branchio-otic syndrome (BOS) (OMIM 602588) was initially described as a disorder distinct from BOR, featuring the same clinical symptoms as BOR with the exception of renal anomalies.1 The large variety of clinical phenotypes and the description of mutations in the EYA1 gene for BOR and BOS patients13-15 show that BOR and BOS can represent allelic defects of the EYA1 gene. The identification of a second gene locus in a large BOS pedigree on chromosome 1q31 established the presence of genetic locus heterogeneity for BOS.4 No linkage to this locus has been published for BOR families and the gene defect is still to be identified. The issue of genotype/phenotype relationships regarding clinical features of BOR or BOS remains unsolved. We describe here a genome wide search for linkage in a large pedigree with BOS, in which linkage to the EYA1 locus on chromosome 8q13 had been excluded, resulting in a new locus (BOS3) on chromosome 14q.