Background: Development of dentition is controlled by numerous genes, proven by experimental animal studies and mutations that have been identified by genetic studies in man. Purpose: In the present study a nonsense mutation has been identified in the PAX9 gene that was associated with molar tooth agenesis (hypodontia or oligodontia). Methodology: The proband of family 1 originally came for treatment to the Department of Pedodontic and Preventive Dentistry. The proband of family 2 was an orthodontic patient of the Department of Orthodontics and Maxillofacial Orthopedics. All family members were clinically examined by one of the authors and agenesis of teeth was also verified with panoramic radiographs. DNA was extracted from venous blood samples using standard methods. The coding region of the PAX9 gene were amplified using four sets of primers Amplification was performed in 100 ml with DNA concentration of 1.5 ng/ml, 1.5 mM MgCl2 and 1 mU polymerase. Results: The A340T transversion creates a stop codon at lysine 114, and truncates the coded PAX9 protein at the end of the DNA- binding paired-box. All the affected members of the family were heterozygous for the mutation. The tooth agenesis phenotype involves all permanent second and third molars and most of the first molars and resembles the earlier reported phenotype that was also associated with a PAX9 mutation [1]. Conclusion: The phenotype is presumably a consequence of haplo insufficiency of PAX9. In other family with molar tooth agenesis, similar sequence changes in PAX9 could not be found.