Background Based on published results from a training set, EPB41L3 and JAM3 gene methylation status had favorite results compared with high-risk human papillomavirus (hrHPV) testing. This validation trial evaluated the DNA methylation status and genotyping of hrHPV in unselected patients with gynecologic diseases.Methods This study enrolled all patients in the study center from June 1, 2019 to September 1, 2019. Liquid-based samples were collected from cervical swabs for methylation assays and hrHPV testing one day before surgery. The primary endpoint was the diagnostic accuracies of DNA methylation and hrHPV genotyping for cervical intraepithelial neoplasia (CIN) 2 or more severe lesions (CIN2+).Results In total, 307 patients were included in the final analysis, with a median age of 46 years. The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the methylation assay for CIN2+ were 68.7%, 96.7%, 0.933 and 0.712, respectively, and the methylation assay achieved similar diagnostic accuracies to those in the training set and to hrHPV testing. Even in patients with negative hrHPV results, DNA methylation was significantly able to identify CIN2+ (odds ratio 39.857, 95% confidence interval 7.137-222.577). The methylation assay was sensitive for CIN2/3 and cervical squamous cell carcinoma without residual lesions and was not positive in this context.Conclusion For the diagnosis of cervical adenocarcinoma, methylation assessment, hrHPV testing and their combination had favorable results in all subtypes.