Background In Brazil malaria is most frequent in the Amazon region, mainly in the Amazonas state, where it is found the most proportion of indigenous people of the whole country. It is remarkable publications about malaria in the Amazon, although information on malaria in indigenous populations is still poorly explored. Objective Identify factors associated with malaria in indigenous populations. Methods Cross-sectional study of positive cases of malaria in the state of Amazonas, Brazil, from 2007 to 2016. Secondary data were obtained from the Epidemiological Surveillance Information System for Malaria and from the Mortality Information System, both from Brazil. To tackle with race missing data, cases with no race fulfilled were classified according to the probable location where infection occurred. This way, was imputed indigenous race for those which the probable infection location was indigenous village (aldeia). Variables tested with race were: sex, age, schooling, microscope surveillance slide type, parasitic infection species, parasitemia level, and timeliness of treatment. Multivariate logistic regression was used. Results A total of 1,055,852 cases of malaria were notified in the state of Amazonas. Among the factors that associate malaria and indigenous peoples, the most significant were sex, children and high levels of parasitemia. The magnitude of Plasmodium vivax infection is higher than