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Cervical cancer is one of the most common malignancies in women with high morbidity and mortality. Human papillomavirus (HPV) infection is the primary cause of cervical cancer, of which HPV 16 is the predominant. Early detection and effective treatment of cervical precancerous lesions are the key to preventing cervical cancer. Vitamin D receptor (VDR) gene polymorphism is considered to be an important cause of cancer development. Here, we studied the association of VDR polymorphisms (FOKI, BsmI, ApaI, and TaqI) in HPV16-positive cervical intraepithelial neoplasia (CIN)2+ patients. HPV16-positive patients who visited the Colposcopy Clinic of Obstetrics and Gynecology, the Second Hospital of Shanxi Medical University for biopsy due to abnormal HPV and/or Thinprep cytologic test (TCT) from September 1, 2020 to October 1, 2021 were grouped by pathological results. The fasting blood samples were collected and VDR polymorphisms were detected using TaqMan fluorescent probes, and the three sites of BsmI-ApaI-TaqI were subjected to haplotype analysis. FOKI ff genotype ( OR = 2.01 ; 95% CI = 1.12 − 3.59 ; p = 0.019 ) and f allele ( OR = 1.48 ; 95% CI = 1.10 − 1.98 ; p = 0.009 ) were found to be associated with the risk of CIN2+. TaqI Tt genotype ( OR = 2.03 ; 95% CI = 1.20 − 3.43 ; p = 0.008 ), tt genotype ( OR = 2.09 ; 95% CI = 1.09 − 4.02 ; p = 0.028 ), and t allele ( OR = 1.35 ; 95% CI = 1.01 − 1.80 ; p = 0.041 ) were associated with the risk of CIN2+. No haplotype was associated with CIN2+ risk. According to the results, FOKI and TaqI polymorphisms are associated with CIN2+ risk.