In the presence of the uterus, it is rare that vaginal intraepithelial neoplasia (VAIN) alone exists. We described our experience with a case in which VAIN3 was found in the vaginal fornix without lesions in the uterine cervix. She had cervical intraepithelial neoplasm (CIN) 1 several years ago. After that, it disappeared. However, high-grade squamous intraepithelial lesion persisted cytologically. After hysterectomy was performed, VAIN3 was found in the vaginal fornix. CIN was not found in the cervix. We are apt to suspect endocervical lesions when Papanicolau (Pap) smear shows abnormalities and colposcopy fails to identify columnar epithelium. However, we need to keep in mind that the vaginal fornix may have a lesion. It may be difficult to assess the vaginal fornix in young women because of a large cervix. The presence of VAIN should also be considered when cytological abnormalities persist on Pap smears.