Subgroup analysis by geographic area (s), control source and periodontitis type, significant correlations between the VDR ApaI periodontitis and variants were found in north China (a vs. A, OR = 0.64, CI = 0.47–0.85; aa vs. AA, OR = 0.48, CI = 0.28–0.82; aa vs. AA + Aa, OR = 0.50, CI = 0.31–0.79). Here, VDR is linked to periodontitis.