We made a study of the prevalence of human papillomavirus (HPV) and cervix lesions in an Amazonian Bora native population (Bn) and compared it with the prevalence in an urban population in Iquitos (Iq). We also examined the distribution of HPV types among abnormal cervical smears in the Iq population. Swabs and cytologies were collected from 472 females. DNA consensus PCR, followed by direct sequencing, were used to determinate the HPV types in the swabs. Cytologies were classified based on the lesion grade. HPV prevalence was 43.9% in Iq and 35.4% in Bn. Cervix lesion prevalence was 20.0% in Iq and 0.3% in Bn. The frequency of high-risk HPV types among HPV+ females was 71.9% in Iq and 56.3% in Bn. The frequencies of low-risk and undetermined risk HPV types were 19.3/6.3% (Iq/ Bn) and 12.3/37.5% (Iq/Bn), respectively. In lesIq (women seeking cytological services with a previous cervix lesion diagnosis) the prevalence of HPV, was 72.9%. The incidence of carcinoma and high-grade squamous intraepithelial cervix lesions in lesIq were 31.2 and 18.8%, respectively. The Bn population had a lower incidence of high-risk HPV and cervix lesions. The high-risk strain HPV16 was significantly more frequent in Iq compared with Bn. lesIq high-risk HPVs were more frequent in high-grade squamous intraepithelial lesions and carcinoma. High-risk HPV16 prevalence was significantly higher than the prevalence of the other high-risk HPVs, especially in the high-grade squamous intraepithelial lesions and carcinoma.