We analyzed apolipoprotein E (apo E) genotypes of 104 randomly sampled Japanese subjects by using the polymerase chain reaction-restriction fragment length polymorphism method in which the apo E genomic DNA was amplified between bases 2849 and 3071. We compared the results thus obtained with their corresponding phenotypes assessed by isoelectric focusing (IEF). The overall frequencies of the genotypes were as follows: epsilon 2:2.4%, epsilon 3:86.5%, and epsilon 4:11.1%, which are essentially identical to those previously reported when the IEF method has been used. The phenotypes and genotypes were identical in all but five cases. We could not determine the phenotypes of four cases by IEF because of an atypical IEF pattern presumably caused by sialylation. In one other case the phenotype initially did not correlate with its genotype but eventually did after neuraminidase treatment. These results indicate that apo E polymorphism of most Japanese people can be determined by analyzing the apo E genome between bases 2849 and 3071.