We report a common DNA polymorphism of the apolipoprotein E (apoE) gene detected with the enzyme HpaI. In an individual who is heterozygous for the polymorphism, two hybridising fragments of DNA, one of 50 kb (the H1 allele) and one of 20 kb (the H2 allele) are detected. In 54 controls the frequency of the rare allele is 0.38 (PIC value 0.36). We have also studied the frequency of the polymorphism in normolipidaemic and hyperlipidaemic individuals whose apo E protein typing is known. In 39 individuals with type III hyperlipidaemia and the apo E phenotype E2E2, the frequency of the H2 allele is 0.97. In contrast, the frequency of the H2 allele in normolipidaemic individuals with the E2E2 phenotype is closer to that found in the general population. Possible explanations for this are discussed.