PURPOSE: Hypodontia is the congenital absence of one or more (up to six) permanent and/or deciduous teeth, being one of the most common alterations of the human dentition. Genetic polymorphisms are variations of DNA sequences occurring in a population. This study investigated whether G-915C single nucleotide polymorphism (SNPs) in the PAX9 gene promoter is associated with hypodontia in humans. MATERIAL AND METHODS: The polymorphism in region G/C-915 of PAX9 gene (NCBI ref SNP ID: rs 2073247) of 240 patients was analyzed, being 110 controls and 130 individuals with third molar agenesis. After DNA extraction, the region of interest was amplified by PCR technique using two different primers. The significance of the differences in observed frequencies of polymorphisms in both groups was assessed by odds-ratio and chi-squared test with 95% confidence interval. RESULTS: Genotype CC was more frequent in patients with agenesis (11.5%) compared to the control (1.8%), while GG was more prevalent in the control group (39.1%) compared to the individuals with agenesis (26.2%). CONCLUSION: These data showed that the allele C could be associated with the third molar agenesis.