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.