Objective: Persistent infection with carcinogenic human papillomavirus (HPV) causes cervical intraepithelial neoplasia (CIN) which, is commonly treated using the loop electrical excision procedure (LEEP). We investigated the factors that associate with the persistency of HPV after LEEP in patients with CIN. Methods: We retrospectively analyzed 860 CIN patients who underwent LEEP. All patients had high-risk HPV (HR-HPV) testing using Hybrid Capture II system. HPV persistency, defined as HPV DNA being present before and 6 months after LEEP, was evaluated. Cervical tissues specimens were collected at the time of LEEP. CD8+ and CD138+ expression were detected by immunohistochemistry and IFN-γ expression was detected by RT-PCR. Results: The HPV persistency rate was 33.3% (286/860). Univariate analysis showed that HPV clearance rate after LEEP in the patients with CIN was higher when patients were younger (Rs=-0.109, P=0.011), lesions with HSIL (Rs=0.141, P<0.001), lesions involving the glands (X2=12.145, P<0.001) and contraception been used (P=0.001). Persistent HPV infection was more likely to occur when the pretreatment viral load was high (RLU/positive control >100, P=0.027). Patients with persistent HR-HPV infection had lower numbers of CD8+ cells (P=0.022), higher numbers of CD138+ cells (P=0.035) and lower levels of IFN-γ. Conclusion: Age, LSIL, condom contraception used and local immune status are significantly related to HR-HPV persistency after LEEP.