OBJECTIVE: This study evaluated the effect of the specific human papillomavirus (HPV) genotypes on severity and prognosis in cervical intraepithelial neoplasia (CIN) patients. METHODS: The medical records of 446 patients treated with loop electrosurgical excision procedure (LEEP) were reviewed. The severity of CIN was categorized as CIN1/CIN2 versus CIN3+ including CIN3 and carcinoma in situ (CIS). HPV genotypes were categorized as 1) low risk, 2) intermediate risk, 3) high risk/HPV 16, 4) high risk/HPV 18, and 5) unclassified. Progression was defined as abnormal cytology, including atypical squamous cells, low-grade squamous intraepithelial lesion and high-grade squamous intraepithelial lesion. The margin status and progression free survival (PFS) by HPV genotypes were analyzed in 355 women with three months or more of post-treatment records. RESULTS: CIN3+ was the most common CIN type (67.7%), and high risk/HPV 16 (26.9%) was the most common genotype. Intermediate risk (P < 0.01), high risk/HPV 16 (P < 0.01) and high risk/HPV 18 (P < 0.01) were significantly more common in women with CIN3+ than CIN1/CIN2. Patients with high risk/HPV 18 showed the highest rate of positive margins (P < 0.01). The margin status proved to be the only statistically significant factor affecting PFS. CONCLUSION: The proportion of positive margins was significantly different by HPV genotypes and highest in high risk/HPV 18 group. CIN patients with high risk/HPV 18 need to be more carefully tracked than patients with the other HPV genotypes.