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Objective Human papillomavirus (HPV) is known as the causal agent of cervical cancer. The Papanicolaou smear is the most popular screening tool for cervical cancer. Some cytological low grade squamous intraepithelial lesions (LSILs) are in the developmental stage of high grade intraepithelial lesions (HSILs) and cervical cancer metaphases. Our purpose is to disclose the signifi cance of high risk type (HRT) HPV in LSIL. Methods Documentation of 200 cases of cone biopsy at Hallym University Sacred Heart Hospital from February 2006 to February 2008 was reviewed retrospectively. HPV typing with DNA microarray results were found in 20 of the LSIL patients. Chi-square and student-t tests were used in the statistical analysis. Results In the cytological LSIL patients, HRT-HPV positive patients were 16/20 (80%) and one low risk type (LRT) HPV positive patient was 1/20 (5%). In the cytological LSIL patients, postoperative pathological diagnoses were cervical intraepithelial neoplasia 1 (CIN 1) 16/26(61.5%), CIN2 2/26 (7.7%), CIN3 5/26 (19.2%), carcinoma in situ 1/26 (3.8%). Among the 16 HRT-HPV positive patients, there were six that were above HSIL 6/16 (37.5%) in pathologic diagnoses. In the HRT-HPV negative 10 cytologic LSIL patients, there were two that were above HSIL 2/10 (20%) in pathologic diagnoses. HRT-HPV prevalences were not signifi cantly different between LSIL and HSIL. Conclusion In HRT-HPV positive LSIL, the risk of HSIL or cancer of the cervix seems to be increasing. The HPV test is helpful in LSIL patient strategies and should be done in LSIL patients in order to discriminate between the nature and prognosis of cytological LSIL.

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