Objective To investigate the possibility of human papillomavirus late 1 (HPV-L1) protein detection in predicting the prognosis of cervical intraepithelial neoplasia (CIN). Methods (1)Through immunocytochemical method to detect expression of HPV-L1 protein in diagnosis of CIN before treatment. (2) Through hybridization and gene chip technology to detect expression of high-risk human papilloma virus (HR-HPV) in diagnosis of CIN after treatment for twelve months. Results (1) Comparing the three treatment methods in CIN patients, HR-HPV infection sustained no significant difference (P > 0.05). (2) The positive expression rate of HPV-L1 protein was 75.00% in CINⅠand 36.13%in CINⅡ~Ⅲbefore treatment, with statistically significant (P<0.05). (3) Persistent infection rate of HR-HPV was 5.97%in HPV-L1 positive expression group after treatment for twelve months and 19%in HPV-L1 negative expression group. The difference between the two was statistically significant (P<0.05). (4) The expression of HPV-L1 capsid protein before treatment had a negative relationship with HR-HPV persistent infection after 12 months of treatment. Conclusion Detection of HPV-L1 protein before treatment can predict the prognosis of CIN which had been treated.