Tooth agenesis is one of the most common developmental disorders in humans. The PAX9 gene, which plays an important role in odontogenesis, is associated with familial and sporadic tooth agenesis. A case-control study was performed in 102 subjects with tooth agenesis (cases) and 116 healthy controls. We genotyped four PAX9 gene polymorphisms using a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay. The allele and genotype frequencies of the four polymorphisms were not significantly different between the controls and the subjects with tooth agenesis. Similar results were observed in a subgroup analysis of test subjects only with mandibular incisor agenesis. Further analysis showed no significant difference in the haplotype distribution between the controls and the subjects with tooth agenesis or mandibular incisor agenesis. However, we found that the AGGC haplotype was associated with a decreased risk of tooth agenesis, compared with the most common haplotype, AGCC (odds ratio, 0.14; 95% confidence interval: 0.00-0.95). These results suggest that the four PAX9 polymorphisms alone have a non-significant main effect on the risk of tooth agenesis but that the AGGC haplotype may have a protective effect associated with a decreased risk of tooth agenesis.