We investigated using haplotype analysis whether genetic variation of the apo B gene is associated with a higher risk for coronary heart disease in a Brazilian population. Ins/Del, XbaI, and EcoRI polymorphic sites of the apolipoprotein B (apo B) gene were studied in 67 patients with CHD and in 67 age-matched healthy individuals selected from a population of Brazilians. The allelic frequency of apo B polymorphisms did not differ between the CHD patients and controls. However, a significant linkage disequilibrium was observed between the XbaI site and Ins/Del polymorphism of the apo B gene in CHD individuals (chi2, P < 0.01). The simultaneous presence of the rare X+ and Del alleles (X+Del haplotype) in males of CHD group was associated with significantly higher serum levels of total cholesterol (P < 0.01), triglycerides (P < 0.05), and LDL-cholesterol (P < 0.05), and with a higher TC/HDL-C ratio (P < 0.05). These data indicate that a single haplotype, X+Del, within the apo B gene exerts an impact on lipid metabolism and may contribute to the susceptibility to development of CHD in males from a population of Brazilians.