Allele and haplotype frequencies for the T-93G, Hind III, and Pvu II variants of the lipoprotein lipase gene (LPL), and Hpa I and Ava II restriction site polymorphisms (RSP) of the APOE/C-I/C-II gene cluster were determined in 143 individuals from five Brazilian Indian tribes. These results were integrated with those previously reported for APOE. Marked interethnic variability occurs in these sites. A strong linkage disequilibrium was observed between the APOE and APOC-I loci (D' = 0.81; P < 0.00001). Linkage disequilibrium between the Hind III and Pvu II RSPs of the LPL gene was also observed (D' = 1; P < 0.001), but none of these RSPs were in linkage disequilibrium with the T-93G mutation. Considering both loci, heterozygosity was estimated as 0.45, but it was lower in the Xavante and Surui populations, in accordance with the historical and biodemographical data of these Amerindians. The results reported here may have implications for understanding interpopulation differences in lipid levels and coronary heart disease prevalences.