Aims: Genetic variation at the apolipoprotein E (apoE) locus is an important determinant of plasma lipids. The aim of the present study was to evaluate the association between apolipoprotein E genotype and plasma lipid levels among a rural black population in South Africa. Methods: Lipid levels and apoE genotypes were studied in 505 volunteer subjects (363 women, 142 men) resident in the Dikgale demographic surveillance site. Results: Allele frequencies were found to be 0.190 for e2, 0.518 for e3, and 0.293 for e4, indicating a relatively low frequency of the e3 allele and a high frequency of the e4 allele. To determine the effect of apoE polymorphism on lipid levels three groups were formed: namely e2-, e3-, and e4-expressing groups. A significant effect of the apoE genotype on total cholesterol, low-density lipoprotein cholesterol (LDL-C), highdensity lipoprotein cholesterol (HDL-C)/Total cholesterol (TC) ratio, and triglycerides was observed. LDL-C was significantly lower and the HDL-C/TC ratio was significantly higher in the e2 group compared with the e3 and e4 groups. Triglyceride levels were significantly higher in the e2 group than in the e3 group. Conclusions: With the unfavourable apoE allele distribution, and the lifestyle changes taking place in rural South African populations, preventive strategies need to be developed to limit a potential epidemic of cardiovascular disease in the black population of South Africa.