BACKGROUND The aim of the study was to determine whether human papillomavirus (HPV) L1 capsid protein and the HPV genotype can predict the disease course as prognostic markers for cervical intraepithelial neoplasia 1 (CIN1). METHODS Immunohistochemical staining was performed for HPV L1 capsid protein in 101 women who had been confirmed to have CIN1 by histologic examination and HPV high-risk infection by HPV genotyping. The disease course was analyzed by follow-up histologic examination according to the HPV L1 capsid protein and HPV genotype over a minimum of 12 months. RESULTS The CIN1 regressed spontaneously in 60.4% of the women; most cases of regression occurred within 1 year (90.9% of regression cases). The HPV L1 capsid protein-positive patients had a spontaneous regression rate of 72.7% (48/66) and a rate of persistent disease or progression to higher grade disease of 27.3% (18/66). The HPV L1 capsid protein-negative women had a regression rate of 37.1% (13/35) and a rate of persistent disease or progression of 62.9% (22/35; P < 0.001). The HPV-16-infected patients had a regression rate of 38.6% (17/44) and a rate of persistent disease or progression of 61.4% (27/44), whereas the non-HPV-16-infected patients had a regression rate of 77.2% (44/57) and a rate of persistent disease or progression of 22.8% (13/57; P < 0.001). CONCLUSIONS The HPV L1 protein expression is closely related to spontaneous disease regression, but HPV-16 infection is related to persistent disease or progression to high-grade lesions in patients with CIN1.