Equivocal lesions (ASC-US) are common abnormalities in cervical cancer screening exams. HPV testing helps to stratify the risk of progression to high-grade squamous intraepithelial lesions or more (HSIL+). Population-based medical electronic data can be used to evaluate screening recommendations. The study uses routine electronic data from primary health centers to estimate the impact of HPV testing in a 3- and a 5-year risk of HSIL+ after an ASC-US. The study includes data derived from medical electronic information from 85,775 women who first attended a cervical cancer screening visit at the National Health System facilities of Catalonia, Spain, during 2010-11 and followed up to 2015. Included women were aged between 25-65 years old, having at least one follow-up visit, and a cervical cytology of ASC-US (N = 1,647). Women with a first result of low-grade squamous intraepithelial lesions (LSIL) (N = 945) or those with negative cytology (N = 83,183) were included for comparison. Those with a baseline HSIL+ were excluded. Incident HSIL+ was evaluated by means of Kaplan-Meier curves and multivariate regression models. HPV test results were available for 63.4% of women with a baseline ASC-US. Among all ASC-US, 70 incident HSIL+ were identified at 5 years. ASC-US HPV positive women had a high risk of HSIL+ compared to women with negative cytology (adjusted HR = 32.7; 95% CI: 23.6-45.2) and a similar risk to women with baseline LSIL (HR = 29.3; 95% CI: 22.4-38.2), whereas ASC-US HPV negative women had no differential risk to that observed in baseline negative cytology. Women with ASC-US and no HPV test had an average HSIL+ risk (HR = 14.8; 95% CI: 9.7-22.5). Population-based e-medical records derived from primary health care centers allowed monitoring of screening recommendations, providing robust estimates for the study outcomes. This analysis confirms that HPV testing improved risk stratification of ASC-US lesions. The information can be used to improve diagnosis and management of screen detected lesions.