Three apolipoprotein B restriction fragment length polymorphisms (RFLPs) (XbaI, MspI, and EcoRI) and the signal peptide insertion-deletion polymorphism were investigated using the polymerase chain reaction in 140 individuals from 5 Brazilian Indian tribes. All studied markers were polymorphic in this ethnic group. The insertion alíele 5' ßSP*29 at the signal peptide previously observed in Mexican Americans was detected in about 8% of the chromosomes of 2 tribes (Gavião and Zoró), therefore confirming the Amerindian origin of this allele. Negative linkage disequilibrium was observed between alleles at the signal peptide and the EcoRI polymorphism in all tribes. In 3 populations (Gavião, Suruí, and Zoró) a negative disequilibrium was also detected between the insertion-deletion signal peptide markers and the XbaI polymorphism. In the whole sample of Amerindians 14 of the 24 (58%) possible 4-marker extended haplotypes were identified, but only haplotype 2 (5'ßSP*24/*X+/*M+/*E + ) and haplotype 5 (5' ßSP*27/*X-/*M+/* E + ) were shared by all tribes. No associations between plasma lipid levels or body mass index and these polymorphisms were observed in this sample.