A radiation-induced mouse mutant, Brachyrrhine (Br), exhibits frontonasal dysplasia and renal hypoplasia, two malformations associated with deficiencies in mesenchymal condensation. The purpose of this study was to resolve the Br locus, evaluate possible candidate genes, and identify developmental defects in the mutant chondrocranium. Linkage analysis mapped the Br mutation to a critical region distal to D17Mit76, which contains only one gene, the transcription factor Six2. Sequence analysis of the Six2 gene, including 1.5 kb of the promoter, failed to reveal the Br mutation. However, homozygous Br/Br embryos showed almost complete absence of Six2 mRNA and protein in craniofacial and renal tissues while heterozygous Br/+ embryos displayed intermediate Six2 levels. Mutant embryos displayed malformations of neural crest-derived structures of the anterior cranium where Six2 is normally expressed. These data suggest a mutation in a novel cis-acting regulatory region inhibits Six2 expression and is associated with frontonasal dysplasia and renal hypoplasia.