The present study was aimed at identifying the association between interleukin family gene polymorphisms and recurrent aphthous stomatitis (RAS) risk using a meta-analysis. We searched the PubMed, web of science, Embase and ScienceDirect-Elsevier databases for research on the interleukin polymorphism and RAS risk. In total 12 studies were included to investigate the relationships between RAS risk and six polymorphisms by calculating pooled odds ratios (ORs) and 95% confidence intervals (CIs). A significant association was found between IL-1β+3954C/T polymorphism and RAS risk. A high risk of RAS was found in RAS patients with the G allele or GG genotype of IL-6-174 polymorphism. Low risk of RAS was found in the C allele of IL-10-592C/A polymorphism under an allele model, but a high risk of RAS was found in IL-10-1082G/A polymorphism. In the subgroup analysis, no correlation was found between the IL-10-1082 polymorphism and RAS risk in the caucasian population with the allele model. In conclusion, an IL-1β+3954C/T polymorphism was determined to be related to susceptibility to RAS, and individuals with the G allele and GG genotype of IL-6-174 or the A allele of IL-10-592 or the G allele of IL-10-1082 appeared to be more vulnerable to developing RAS.