In the present study, effectiveness of topical vidarabine or subsequent 5-fluorouracil (5-FU) administration was examined against persistent genital human papillomavirus (HPV) infection after local surgery. Thirty patients underwent local eradication treatment of uterine cervical intra-epithelial neoplasia (CIN) and stage Ia1 uterine cervical cancers. HPV typing was performed by PCR-RFLP analysis. HPV infection was detected pre-operatively in 29 of 30 patients. Of these, HPV was still present in the 20 patients within two months after the therapy. Topical administration of vidarabine or subsequent 5-FU once a week for four weeks was performed to the post-operative persistent HPV-positive cases. HPV infection was abolished in 1 of 10 (10%) with topical vidarabine, and in 2 of 4 vidarabine-resistant cases (50%) with topical 5-FU. Topical vidarabine or 5-FU treatment is beneficial for HPV-positive cases after local surgical excision.