Background Recurrent aphthous stomatitis (RAS) is one of the most common oral chronic ulcerative disease in which proinflammatory cytokines such as interleukin 1 (IL-1) and interleukin 6 (IL-6) are thought to play an important role. The aim of this study was to investigate the possible association between polymorphisms in the IL-1 cytokine family, IL-6 or its receptor and RAS in the Czech population. Methods A total of 248 subjects, 184 healthy controls and 64 patients with RAS were genotyped for IL-1A-889C>T, IL-1B-511C>T, IL-1B+3953C>T, IL-1RN86 bp variable number of tandem repeats (VNTR) in intron 2, IL-6-597G>A, IL-6-572G>C, IL-6-174G>C and IL-6R+48992A>C by polymerase chain reaction (PCR) methods. Results No significant differences between investigated polymorphisms in healthy subjects and patients with RAS were detected (P>0.05). In addition, complex analysis also revealed similar IL-1 or IL-6 haplotype frequencies between both groups (P>0.05). Conclusions In conclusion, IL-1 and IL-6 or its receptor gene variants cannot be used as markers for identification of Czech patients with increased risk of recurrent aphthous stomatitis.