Genetic factors predispose individuals to Behçet's disease (BD) and periodontal disease. IL-1 has been implicated in the pathogenesis of both BD and periodontal disease. The relationship between periodontitis and pathogenesis of BD has not yet been determined. Since IL-1 has been implicated in the pathogenesis of both BD and periodontal disease, we aimed to investigate the possible relation of the periodontal scores and SNPs of IL-1alpha-889C/T, IL-1beta-511C/T, and IL-1beta+3962T/C with BD compared to healthy controls (HC) and recurrent aphtous stomatitis (RAS). A total of 155 Turkish individuals were enrolled in this study. The periodontal status of all subjects was evaluated according to the WHO community periodontal index of treatment needs. For genotyping, CTS-PCR-SSP was employed. IL-1alpha-889C allele was significantly higher in BD patients (p = 0.03) and RAS (p = 0.02) compared to HC. The frequency of IL-1beta+3962T allele was significantly higher in RAS patients compared to HC (p = 0.015). Male gender (p = 0.04), age (p = 0.02) and carrying IL-1beta-511T allele (p = 0.01) were found to be a significant risk factors for higher periodontal scores in Turkish population. We can speculate that susceptibility to the development of periodontal disease could be influenced by IL-1 SNPs. Periodontitis-induced autoinflammatory response also may play a role in the development/severity of BD and RAS via IL-1 gene alteration.