Background We aimed to determine demographic and clinicopathological predictors for residual disease in women with cervical intraepithelial neoplasia (CIN 2/3) with endocervical cone margin involvement. Methods and findings A cross-sectional study was conducted. The eligible patients were women who underwent hysterectomy as a treatment option after having a positive endocervical margin for CIN 2/3 in cervix conization specimens from 2000 to 2015. The patients were divided into two groups based on the persistence of CIN 2/3 and absence of CIN 2/3 in hysterectomy specimens. Demographic, clinical and histology information were collected in both groups. A total of 80 patients were eligible for the study; 37 (46.3%) had no persistence of CIN 2/3 and 43 (53.7%) had persistence of CIN 2/3 in the hysterectomy specimens. Demographic, clinical, and cone specimen characteristics, and a visible squamocolumnar junction and type of conization were analyzed as possible risk factors for the presence of residual lesions at hysterectomy, and none of these variables were associated with residual disease. Menopausal status was strongly associated with a high risk of persistent residual disease 81.2% (OR 4.9, CI 1.27–18.9), P = 0.014. In the multivariate analysis, only a menopausal status ( P = 0.04) was associated with a high risk of persistent lesions. Conclusion This analysis found that menopausal status exhibited an important association with persistent residual disease. Menopausal women with endocervical margin involvement exhibit a greater than 80% risk of persistent lesions.