Studies on organ-specific autoimmune endocrine disorders showed correlations between disease risks and vitamin D pathways gene variants, such as CYP27B1 rs10877012 and rs4646536, or CYP2R1 rs10741657 single nucleotide polymorphisms. However, previous works presented inconsistent conclusions. Our study aimed at assessing the association of CYP27B1 and CYP2R1 polymorphisms with autoimmune endocrine disorder susceptibility using the meta-analysis method.Case-control studies of the subject of interest were identified from the databases Pubmed, Embase, Cochrane Library, and China National Knowledge Infrastructure. Studies that met inclusion and quality criteria were pooled. Observational outcomes were diagnosis of autoimmune Addison's disease, Graves disease, Hashimoto thyroiditis, or type 1 diabetes mellitus. Statistical analysis was performed using software STATA 16.0.A total of 14 studies involving 12 929 patients (2243 autoimmune Addison disease, 1253 Graves disease, 612 Hashimoto thyroiditis, 8821 type 1 diabetes), and 12 907 healthy control subjects were pooled for meta-analysis. The rs10877012 minor allele A and its homozygote and heterozygote conferred low overall disease risk (OR [odds ratio] = 0.748, 95% CI [confidence interval] 0.620-0.902 in dominant model; OR = 0.709, 95% CI 0.571-0.879 in recessive model; OR = 0.777, 95% CI 0.674-0.895 in the allele model). The population carrying rs4646536 minor allele C and its homozygote and heterozygote showed decreased overall autoimmune endocrine disorders risk (OR = 0.849, 95% CI 0.748-0.963; OR = 0.868, 95% CI 0.790-0.955; OR = 0.915, 95% CI 0.875-0.957 in the dominant, recessive, and allele model, respectively). No significant genetic association was found for rs10741657.Our study suggested CYP27B1 polymorphisms rs10877012 minor allele A and rs4646536 minor allele C were negatively related to susceptibilities of organ-specific autoimmune endocrine diseases.