Apolipoprotein E plays a very important role in the metabolism of plasma lipoproteins enriched in cholesterol ester. We have studied the structure of this apoprotein in human plasma utilizing high resolution two-dimensional gel electrophoresis. Our studies have revealed a complex array of apo E isoproteins which vary from individual to individual. Six subclasses of apo We have been recognized and designated βII, βIII, βIV, αII, αIII and αIV. We have shown that the basis for this variation is genetic and can be explained by a single locus with three alleles, εII, εIII and εIV. Individuals with the β subclasses, βII, βIII and βIV, are homozygous for the apo E alleles εII, εIII and εIV, respectively. Individuals with the α subclasses, αII, αIII and αIV, are heterozygous for the apo E alleles and have the genotypes εII εIII, εIIIεIV and εIIεIV, respectively. In a study of individuals with type III hyperlipoproteinemia, almost all had the apo E subclass βIV, whereas in the general population, the apo E allele frequencies of εII=11%, εIII=72% and εIV=17% indicate that the apo E subclasses should occur with frequencies of βII=1%, βIII=52%, βIV=3%, αII=16%, αIII=25% and αIV=4%. Thus the apo E subclass βIV may serve as a molecular marker for type III hyperlipoproteinemia, a condition characterized by premature atherosclerosis. The 3% of the population with this apo E subclass may be ideal candidates for a targeted atherosclerosis prevention program.