Introduction: Fibromyalgia (FM) is a syndrome of unknown origin characterized by several symptoms, and although its pathogenesis has not been completely elucidated, it seems to be related to inflammatory path-ways and neurochemical changes in the brain. Objective: To evaluate the association between BsmI, ApaI and FokI polymorphisms of the vitamin D receptor (VDR) gene, their polymorphisms, and clinical variables in women with and without FM. Methods: This is a case-control study composed of a group of 53 women with FM and another with 40 women without the disease. The McGill Pain Questionnaire, Fibromyalgia Impact Questionnaire, Pain Visual Analogue Scale and the sit-up test were applied. Real-time PCR was performed to analyze the ApaI and FokI polymorphism. Results: There was a statistical association between race, comorbidity and FM, where 78.4% of the individuals were white and had FM (p < 0.002) and 96.1% had some comorbidity (p < 0.001). Seventy-six point five percent (76.5%) of patients with FM underperformed in the sit-up test (p < 0.001). There was also an association between the genotypic and allele frequencies of the VDR and FM gene Apal and FokI polymorphisms (p < 0.001). In the VDR gene ApaI polymorphism, the CC genotype exhibited a higher frequency in women with FM, the C allele for the Apal polymorphism was 3.33 times more likely, and the FokI polymorphism was 10.9 times more likely to develop FM (p < 0,0001). Conclusion: Women with C allele for ApaI polymorphism are 3.33 times more likely to have FM (95%CI = 1.58-7.02; p = 0.0024), and in FokI polymorphism, the prevalence of T allele is 10.9 times greater (95% CI = 4.76-25.38; p < 0.0001). No significant associations were found in relation to BsmI polymorphism and frequency alleles (p = 0.062 and p = 0.078, respectively).