MSX1 has a critical role in craniofacial development, as indicated by expression assays and transgenic mouse phenotypes. Previously, MSX1 mutations have been identified in three families with autosomal-dominant tooth agenesis. To test the hypothesis that MSX1 mutations are a common cause of congenital tooth agenesis, we screened 92 affected individuals, representing 82 nuclear families, for mutations, using single-strand conformation analysis. A Met61Lys substitution was found in two siblings from a large family with autosomal-dominant tooth agenesis. Complete concordance of the mutation with tooth agenesis was observed in the extended family. The siblings have a pattern of severe tooth agenesis similar that in to previous reports, suggesting that mutations in MSX1 are responsible for a specific pattern of inherited tooth agenesis. Supporting this theory, no mutations were found in more common cases of incisor or premolar agenesis, indicating that these have a different etiology.