Human T cell lymphotropic virus type II (HTLV-II) infection is endemic in a number of indigenous populations in North, Central, and South America. In the present study we have employed serological and molecular methods to identify HTLV-II infection in Indian communities in the Amazon region of Brazil. Sera (1324) from 25 different Indian communities were analyzed by ELISA and Western blot. One hundred and four samples (7.8%) from a number of culturally distinct and geographically unrelated populations were found to have reactivities consistent with HTLV-II infection. Of these, 67 were from the Kayapo Indian communities, which had an overall seroprevalence rate of greater than 30%. In addition, high seroprevalence rates were observed in three other communities, the Munduruku, Arara do Laranjal and the Tyrio, suggesting that there are additional foci of endemic infection in the Amazon region. In the Kayapo, seroprevalence rates tended to increase with age, supporting the importance of sexual transmission of the virus, and family studies demonstrated that vertical transmission is also an important route of infection. Restriction fragment length polymorphism (RFLP) and nucleotide sequence analysis of a region of the env gene demonstrated that the Kayapo are infected with the HTLV-IIa subtype. Moreover, nucleotide sequence analysis of the LTR demonstrated that this belonged to a distinct HTLV-IIa phylogenetic group. The identification of HTLV-IIa in the Kayapo is, as far as we are aware, the first identified endemic focus of infection by this subtype of HTLV-II in the Americas.