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Two DNA polymorphisms, insertion/deletion (insldel) and Xbal, of the apolipoprotein B (APOB) gene and their relationships with serum lipoprotein and lipid levels were examined in two Nigerian populations from Benin (/? = 828) and Sokoto (n = 394). Allele frequencies for both polymorphisms were comparable between the two populations, and genotype frequencies conformed to Hardy-Weinberg equilibrium expectations. Because lipid profiles are affected by many known sex differences, males and females were analyzed separately. Analysis of variance was performed to test equality of means of quantitative traits across genotypes; the dependent variables were first adjusted by stepwise linear regression for environmental covariates in both populations. Plasma apoB and HDL2 cholesterol levels varied significantly between insldel genotypes in Benin males (p = 0.05) and Sokoto males (p = 0.02), respectively. No significant variation between Xbal genotypes was observed for any lipid trait in either population. Combining the insldel and Xfral polymorphisms to form haplotypes revealed significant linkage disequilibrium in both the Benin (p < 0.0001) and Sokoto (p < 0.001) populations. Analysis of the two-site haplotype showed a significant effect on serum lipoprotein (a) levels in Benin females (p < 0.04) and on HDL2 cholesterol among Sokoto males (p = 0.01). The haplotype explained 4% of the adjusted phenotypic variation in lipoprotein (a) levels in Benin females and 8.5% of the adjusted phenotypic variation in HDL2 cholesterol levels in Sokoto males. These data indicate that the insldel and Xbal polymorphisms in the APOB gene affect interindividual variation in serum lipoprotein and lipid levels in African populations.