The mortality rate for cervical cancer (CC) in Northern Argentina is three times higher than the average for the country (7.8 deaths/100,000 women). We determined the prevalence and genotype distribution of human papillomavirus (HPV) in 227 sexually active women of the native Pilagá community in Formosa, Argentina. We also conducted an HPV-16 variant analysis and studied several community factors that might play a role in viral entry and infection. Endo and exocervical samples were tested for HPV DNA with MY09/11-PCR or with GP5+/6+-PCR. HPV was detected in 46.7% of the samples and 21 different types were found; the most frequent being HPV-16 (19.4%), -6 and -18 (5.3%), -58 (3.5%) and -31 and -33 (3.1%). In relation to HPV-16 variants, 68.2% were European and 31.8% Asian-American. Among the cofactors analyzed only disposal of hu man excreta to the open air (P=0.01) was significantly associated with HPV infection. Our prevalence estimates clearly show that Pilagá women are highly exposed to or infected with high risk HPV types and therefore are at a high risk of developing precancerous lesions and eventually CC at the population level.