Objective To explore the possible relationship between recurrent aphthous ulcer (RAU) and single nucleotide polymorphism (SNP) of transforming growth factor-β1 (TGF-β1)-509T/C and interleukin-10 (IL-10)-1082A/G sites.Methods A total of 138 RAU patients were recruited for this study. The control group consisted of 124 subjects. TGF-β1-509T/C and IL-10-1082A/G sites were detected by restriction fragment length polymorphism-polymerase chain reaction (RFLP-PCR) and sequence specific primer-polymerase chain reaction (SSP-PCR). Relative risk ratios were estimated by odds ratios (OR) and 95% confidence interval (95%CI).Results Significant differences were found in the genotype frequencies or allele frequencies of TGF-β1-509T/C and IL-10-1082A/G sites between the RAU patients and controls (PConclusion TGF-β1-509T/C and IL-10-1082A/G sites are associated with the risk of RAU. The TGF-β1 gene-509T allele and IL-10 gene-1082G allele may serve as genetic determinants for RAU.