Recurrent aphthous stomatitis (RAS) is a common disorder with an unclear etiopathogenesis. Involvement of the immune system in the development of this condition is strongly suggested. As the variations in the inflammasome-related NLRP3 gene have been suggested to affect immune system activity, this case-control study was performed to determine whether these genetic variants are associated with RAS. We studied a group of 69 Iranian patients with RAS in comparison with 56 healthy controls. We determined four single nucleotide polymorphisms (SNPs) of NLRP3 and performed association analyses of NLRP3. Genotyping was conducted using the TaqMan method. The NLRP3 rs3806265 T allele was significantly more frequent in the patients with RAS than in the healthy controls (P=0.003). While a significant negative association was found between the C allele at the same position with RAS (P=0.003), the TT genotype was significantly more frequent at position rs3806265 in NLRP3 in patient group than in the controls (P=0.002). However, the frequency of CT genotype at the same position was significantly higher in healthy controls than in the case category (P=0.002). Considering the high frequency of the presence of NLRP3 rs3806265 TT genotype in patients with RAS, it seems that this gene polymorphism could affect individual susceptibility to RAS.