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This study aimed to determine the factors associated with Human Papillomavirus (HPV) persistence in women undergoing cervical excision for pre-invasive lesions, after they have been referred from a primary HPV screening program. A retrospective study design involving patients who were treated at a Cervical Disease Screening and Treatment Unit, in a university hospital setting. After initial treatment, cervical HPV infection status was analyzed at the sixth month, first year and then subsequently after the second year. Totally, 395 patients who were diagnosed with pre-invasive cervical lesions and who subsequently undergone cervical excision were identified. In the first-year visit after cervical excision, HPV 18 was cleared in almost all (95.8%) cases, followed by HPV 16 (69.9%) and other hrHPV types (65.6%). Available data documented that 88.6% of women reached clearance after the two-year follow-up. Univariate analysis revealed a significantly higher proportion of HPV clearance among women who were younger (p = 0.019), premenopausal (p = 0.002), and who had been found to have a negative cytology result on their initial Pap test (p = 0.018). However, only cervical cytology result remained as the independent predictor of HPV persistence on a multivariate logistic regression (OR 0.43; 95% CI 0.21–0.87; p = 0.019). A low risk of HPV persistence was found among every HPV genotype in women undergoing cervical excision for pre-invasive cervical lesions. Initial cervical cytology result was the only independent predictor of HPV clearance during surveillance, which indicates the prognostic value of Pap test in primary HPV screening. • Human papillomavirus (HPV) based screening has been accepted as the most effective strategy for cervical cancer screening. • There has been paucity of data for defining the predictors of HPV persistence in screen-positive cases. • Initial cervical cytology has prognostic value for HPV persistence after treatment of cervical pre-invasive lesions. [ABSTRACT FROM AUTHOR]