BACKGROUND: Cervical cancer is the second most common cancer and cause of cancer-related death for women worldwide. The aims of this study were to investigate the prevalence of cervical neoplasia and examine factors associated with high-grade cervical squamous intraepithelial lesions (HSIL) among women taking part in a cervical cancer screening program in Beijing. METHODS: Women aged 25-65 years were screened using the ThinPrep cytologic test and gynecologic examination. Univariate and multivariate logistic regressions were conducted to investigate factors associated with HSIL. RESULTS: Among 728,704 women screened, the prevalence of cervical intraepithelial neoplasia (CIN) I, II, III was 50.2, 34.0, and 36.4 per 100,000, respectively. Prevalence of cervical cancer was 12.2 per 100,000. Risk factors for HSIL included being in age group of 46-55 years (adjusted odds ratio [aOR] = 1.15, 95% CI: 1.07-1.44, compared with the 25-35 age group), bleeding after intercourse (aOR = 2.08, 95% CI: 1.40-3.10), and presence of trichomonas vaginalis infection (aOR = 2.62, 95% CI: 1.35-5.07), cervical inflammation (aOR = 4.22, 95% CI: 3.39-5.26), and genital warts (aOR = 3.89, 95% CI: 2.54-7.70). High education level (college and above compared with junior middle school or lower) was found to be protective (aOR = 0.79, 95% CI: 0.37-0.90). CONCLUSIONS: The prevalence of cervical neoplasia is relatively high in Beijing. Women aged 46-55 years, those with a lower education level, those reporting bleeding after intercourse, and those affected by Trichomonas vaginalis infection, cervical inflammation and genital warts are at higher risk for HSIL. Particular efforts should be made to ensure these women are included in cervical cancer screening programs.