This study investigated the prevalence and risk factors for genital infection with HPV in women from rural and urban areas in two different regions of the Eastern Brazilian Amazon. A cross-sectional survey was performed in Pap screening programs, with a total sample of 444 women (233 urban and 211 rural). Uterine cervical swabs were collected for the detection of HPV DNA with the established PCR assay using MY09-MY11. All volunteers answered an epidemiological questionnaire. Bivariate and multivariate logistic regression analyses were performed to identify risk factors associated with HPV infection. Overall prevalence of HPV infection was 14.6% (15% in urban women and 14.2% in rural). The only factor associated with HPV was marital status in the 13-25-year-old rural population, with higher HPV prevalence among single and divorced women and widows. The findings indicate the need for risk factor control strategies targeted specifically to women in rural and urban areas.