There is currently no large sample data of cytology, high-risk human papillomavirus (hrHPV), and colposcopy results of vaginal intraepithelial neoplasia (VaIN) in women who underwent hysterectomy and those who did not. We aim to explore the values of cytology, hrHPV, and colposcopy reports in detecting VaIN. A retrospective study of women diagnosed with VaIN by colposcopy-directed biopsy was performed at the Obstetrics and Gynecology Hospital of Fudan University, China, between January 1, 2014, and December 31, 2014. A total of 529 cases of VaIN were diagnosed, including 16.1% VaIN2/3 and 83.9% VaIN1. The ratio of VaIN2/3 in VaIN among patients after hysterectomy and with an intact uterus was 35.1% and 12.0%, respectively. The sensitivity of cytology for VaIN2/3 in only, concomitant, and posthysterectomy VaIN was 42.1%, 80.0%, and 80.8%, respectively. The sensitivity of hrHPV and cytology/hrHPV cotesting for VaIN2/3 in patients with an intact uterus versus those after hysterectomy was 93.5% versus 92.3% and 92.0% versus 100.0%, respectively. Notably, 13.3% of the patients with VaIN and 9.7% of the patients with VaIN2/3 underwent hysterectomy for noncervical diseases. The sensitivity of cytology and hrHPV for VaIN is noninferior to that of CIN2+, and thus these methods can help in the early detection of VaIN effectively.