Genetic polymorphism of apolipoprotein (apo) E has been demonstrated to be associated with hyperlipoproteinemia (HLP). There are few reports on this association in Japan. Thus, in this study, we have examined the apo E allele frequencies in normolipidemia (n = 129), non-familial hypercholesterolemic (FH) type IIa HLP (n = 40), non-FH type IIb HLP (n = 35), type III HLP (n = 17), type IV HLP (n = 59), type V HLP (n = 19) and heterozygous FH (n = 51) in Japan, and compared these frequencies between normolipidemia, and different types of HLP and FH. The frequency of the epsilon 4 allele was significantly higher in type IIa (18.7%), IIb (21.4%) and V (29.0%) HLP and FH (16.6%) than in normolipidemia (8.9%), whereas the frequency of the epsilon 2 allele was significantly higher in type III (70.6%) and IV (11.0%) HLP than in normolipidemia (3.1%). These results indicate that the epsilon 4 allele is associated with non-FH hypercholesterolemia (type IIa and IIb HLP), type V HLP and FH, whereas the epsilon 2 allele is associated not only with type III HLP but also with type IV HLP.