AbstractA total of 231 healthy subjects from a central Javanese population were investigated for the distribution of three apolipoprotein B (apo B) polymorphisms (ins/del,XbaI, andEcoRI), as well as apolipoprotein E (apo E) polymorphism in relation to serum lipid and apolipoprotein concentrations. The frequencies of the rarer alleles (del, 0.09;X+, 0.1; andR−, 0.06) were lower than have been found for some Asian and European populations. Distribution of genotypes was in Hardy‐Weinburg equilibrium for all the polymorphisms. A linkage disequilibrium was observed only between theins/delandXbaI site polymorphisms of apo B (χ42= 25.3;P<0.001) consistent with that observed in some other population studies. No polymorphism of the apo B gene had an association with serum lipid or apolipoprotein concentrations in this population except forXabI, which appeared to be associated with serum TG (as the log transform:R2= 8.3;F= 4.8;P<0.01). The apo E4 allele was found to be associated with significantly higher serum total cholesterol (TC) and low‐density lipoprotein cholesterol (LDLC). Apo E polymorphism explained 5.9% of the sample variance of serum LDLC (F= 5.4;P<0.01). © 1994 Wiley‐