Objective To explore the correlation between different stages of Periodontal disease and genetic variation of HLA-DP gene.Methods A Case-control study was conducted to collect 159 patients with Periodontal disease and 169 healthy controls.Taqman PCR was used to detect the HLA-DP gene locus typing of subjects,and to compare the correlation between Periodontal disease and HLA-DP gene genetic variation.Results The distribution of HLA-DP gene rs3077 and rs9277535 genotypes in the Han population was consistent with Hardy Weinberg's law of genetic balance(P>0.05).The distribution of rs9277535 GG genotype in the healthy control group was significantly higher than that in the Periodontal disease group(χ2=7.56,P=0.02).Multivariate Logistic regression analysis showed that both the heterozygous genotype GA and the mutant genotype AA at rs9277535 locus increased the risk of Periodontal disease(P<0.05).The Haplotype analysis showed that the distribution proportion of AA Haplotype in Periodontal disease patients was significantly higher than that in the healthy control group(OR=0.52,95% CI:0.36~0.78).The results showed that the distribution of rs3077 and rs9277535 loci polymorphism in patients with Periodontal disease in different stages was statistically different(P<0.05).Conclusion Genetic variation of HLA-DP gene is associated with the risk of Periodontal disease and may affect its pathogenesis.