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The clinical features suggest that genetic factors may have a strong influence on susceptibility to aggressive periodontitis. The aim of this study was to investigate the association of vitamin D receptor gene polymorphisms with generalized aggressive periodontitis in Chinese patients.A restriction fragment length polymorphism (RFLP) for 10,438,141 C to T (rs1544410, BsmI), 10,382,063 A to G (rs731236, TaqI), 10,382,143 C to A (rs7975232, ApaI) and 10,416,201 A to G (rs2228570, FokI) of vitamin D receptor gene was analysed by polymerase chain reaction, followed by digestion with restriction enzymes and gel electrophoresis. The genotypes of 51 generalized aggressive periodontitis patients and 53 periodontally healthy control subjects were analysed. The genotypic and allelic frequencies of each polymorphism site for the patients and control subjects were compared.The distribution of vitamin D receptor FokI genotypes and alleles between the two groups was significantly different (p = 0.043 and p = 0.012, respectively). The F allele seemed to increase the susceptibility of aggressive periodontitis (odds ratio = 2.02, 95% confidence interval = 1.16–3.50) in Chinese patients. There was no significant difference in the genotype distribution or the allele frequencies of vitamin D receptor BsmI, ApaI and TaqI between two groups.The study indicates that FokI polymorphism of vitamin D receptor gene might be associated with generalized aggressive periodontitis in Chinese patients. In addition, the carriage of F allele increases the risk of developing generalized aggressive periodontitis.