This study has been conducted to evaluate the allele, genotype and haplotype frequencies of the polymorphic gene coding TGF-β in recurrent aphthous stomatitis (RAS). TGF-β gene typing was done by polymerase chain reaction with sequence-specific primers (PCR-SSP) assay. Allele frequencies were estimated by direct gene counting. C allele at codon 25 was significantly increased, while G allele at this position was significantly decreased in patients compared to the controls. A significantly higher frequency of CG genotype at codon 25 was found in control group. CC genotype and TT genotype at codon 10 of the gene was significantly decreased, while CT genotype at the same position was significantly increased in patients, indicating that CT heterozygosity at codon 10 TGF-β is associated with greater risk of RAS. CG and TG haplotypes were significantly decreased while CC and TC haplotypes were significantly increased in patients compared with controls. This study indicates the TGF-β single nucleotide polymorphisms could play a role in RAS pathogenesis. Thereby certain SNPs of TGF-β gene have an association with RAS pathogenesis.