It has been reported that two genes MSX1 and PAX9, which encode transcription factors, are associated with selective tooth agenesis. Expression of these genes specifically marks the regions of the mesenchyme where the tooth buds are formed. A mutation in the MSX1 gene, detected in a single family, resulting in an Arg-->Pro substitution in the homeodomain of the protein product of this gene has previously been associated with the deficiency of second premolars and third molars. However, mutations of the MSX1 gene were excluded in the patients with agenesis of the other type of teeth. In a single family with the lack of first and second molars, a mutation in the PAX9 gene was found. In our group of patients with the deficiency of various teeth, in 20% of the patients and their relatives sequence analysis revealed a C-->T transition in the coding sequence of the PAX9 gene. However, this polymorphism does not alter amino acid sequence of the protein product of this gene.