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We have determined the haplotypes of the factor IX gene for 95 Indians from 5 Brazilian Amazon tribes: Wayampf, Wayana-Apalaf, Kayapo, Arara, and Yanomami. Eight polymorphisms linked to the factor IX gene were investigated: MseI (at 5', nt —698), BamHI (at 5', nt —561), DdeI (intron 1), BamHI (intron 2), XmnI (intron 3), Taql (intron 4), Mspl (intron 4), and Hhal (at 3', ~ 8 kb). The results of the haplotype distribution and the allele frequencies for each of the factor IX gene polymorphisms in Amerindians were similar to the results reported for Asian populations but differed from results for other ethnic groups. Only five haplotypes were identified within the entire Amerindian study population, and the haplotype distribution was significantly different among the five tribes, with one (Arara) to four (Wayampf) haplotypes being found per tribe. These findings indicate a significant heterogeneity among the Indian tribes and contrast with the homogeneous distribution of the /?-globin gene cluster haplotypes but agree with our recent findings on the distribution of a-globin gene cluster haplotypes and the allele frequencies for six VNTRs in the same Amerindian tribes. Our data represent the first study of factor IX-associated polymorphisms in Amerindian populations and emphasizes the applicability of these genetic markers for population and human evolution studies.