Aim The aim of the present study was to evaluate the distribution of single‐nucleotide polymorphisms (SNP) (variants FOKI [rs2228570], CDX2 [rs47908762], and GATA [rs4516035]) in the vitamin D receptor in individuals with type 2 diabetes mellitus and chronic periodontitis (DM2 + CP), CP alone, and healthy individuals, and to investigate the relationship with susceptibility to CP. Methods In total, 280 individuals (116 with DM2 + CP, 95 with CP alone, and 69 healthy individuals) were genotyped using real‐time polymerase chain reaction with allele‐specific probes. Significant differences (P < .05) were found among the groups with regard to socio‐epidemiological variables (sex, marital status, income, smoking habit, and schooling) and clinical‐epidemiological variables (age, number of teeth, probing depth, clinical attachment loss, gingival bleeding index, and visible plaque index). Results The C allele was significantly more frequent among the healthy individuals (34.8%) than those with DM2 + CP (23.5%) (odds ratio [OR] = .58, 95% confidence interval [CI]: . 35‐.94, P = .022). Likewise, the CC allele was significantly more frequent among healthy individuals (11.6%) than those with DM2 + CP (2.6%) (OR = .17, 95% CI: .03‐.79, P = .015). Conclusion The results suggest that the presence of these variants could lead to a lower susceptibility to DM2 and CP. No other significant differences among groups were found for the other SNP investigated.