Vaginal intraepithelial neoplasia (VaIN) always diagnosed through coloscopy accidentally when the cervical cancer screening was abnormal. A precise estimate of the detection rate of cervical cancer screening for VaIN is limited. This study to investigated the characteristics and screening history of VaIN, and compared the sensitivity of cytology and human papillomavirus tests on the cervix against vaginal and cervical high-grade squamous intraepithelial lesion (HSIL) or cancer. A total of 1200 patients with definitive histopathologic diagnoses of VaIN were included in this study. Among them, 22.5% were diagnosed with VaIN2+, and 50.4% were concomitant with cervical lesions. The median age of VaIN2+ patients was 41.5 years old , while VaIN1 reported a median age of 53 years old , p＜0.001. This study reported that VaIN was significantly and positively correlated with cervical lesions (r=0.387). The high-risk human papillomavirus (hr-HPV) detection rate was 88.5% (883/998) in VaIN and 95.4% in VaIN2+. HPV 16 was the most prevalent HPV type in VaIN2+, which accounted for 54.5%, followed by HPV58 (17.0%), HPV52 (14.8%), HPV51 (11.4%), and HPV18 (10.2%). The sensitivity of hr-HPV and cytology tests on the cervix for detecting VaIN2+ was 95.0% and 84.9%, respectively. Both tests were not significantly different from detecting CIN2+. When the cervical cancer screening is abnormal and referring to colposcopy, acetic acid and Lugol’s iodine need to cover the whole vaginal mucosa as well as the fornix, attention need to be paid for the abnormal images of vagina in order to find VaIN.