OBJECTIVE To determine the prevalence of human papillomavirus (HPV) using polymerase chain reaction (PCR) in women with abnormal cytology results. METHODS A prospective study of 215 women with abnormal cytology results referred consecutively to the cervical pathology clinic was carried out. A second cervical cytology using the Bethesda System was performed on all the patients to confirm the initial diagnosis, as well as to test for the presence of HPV by PCR and a colposcopy and punch biopsy in cases presenting with an abnormal pattern on colposcopy. The sensivitiy, specificity, and positive and negative predictive value (PPV and NPV) were calculated using 2 x 2 tables. RESULTS The women aged 35 years or younger presented a higher percentage of HPV infection (85.6%) than the women over 35 years of age (54%). The highest percentage of women with a positive result for HPV was found in those with a cytological high-grade squamous intraepithelial lesion (HSIL) (85.5%), as compared with 47.4% of the women with a cytological low-grade squamous intraepithelial lesion (LSIL). HPV infection has a high negative predictive value (93.2% of cases) and a high sensitivity (93.5%) for the detection of HSIL by biopsy, although the specificity and positive predictive value were low, 51.5% and 52.1%, respectively. CONCLUSIONS Patients with cytological HSIL have a high prevalence of HPV infection.