In this study the frequencies of the genotypes of four restriction fragment length polymorphisms in the apolipoprotein B gene (XbaI, EcoRI, PvuII and MspI) are compared between groups of normolipidaemic and diet resistant hypercholesterolaemic individuals as possible markers for the influence of this gene on plasma cholesterol levels. In the first part of the study genotypes of all four markers were determined in 92 normolipidaemic (mean cholesterol 5.6 + 0.8 mmol/l) and 79 diet resistant hypercholesterolaemic (mean cholesterol 7.8 + 0.7 mmol/l) individuals seen in a local health centre screening programme for coronary heart disease risk factors. No significant difference was seen in the frequencies of the EcoRI and PvuII genotypes between the two groups. There was significant enrichment of both the XbaI X2 (presence of cutting site) allelic frequency and of the MspI M1M2 (M2 absence of cutting site, rarer allele) genotype frequency in the hypercholesterolaemic group. In the second part of the study an independent larger group of individuals, seen in a multicentre screening programme across the city of Glasgow, were genotyped for the two potentially significant polymorphic sites (XbaI and MspI). From this second screening programme 188 age matched normolipidaemic males (mean cholesterol 5.0 +/- 0.8 mmol/l) were compared with 186 males who were still hypercholesterolaemic (mean 8.2 +/- 0.6 mmol/l) after three months dietary intervention. The hypercholesterolaemic individuals in this second study did not show a significant enrichment of the XbaI X2 allele but again showed a highly significant enrichment of the MspI M1M2 genotype. This genetic effect may relate directly to the charge change from arginine to glutamine at amino acid 3611 caused by the MspI mutation or to an as yet unknown functionally significant mutation in linkage disequilibrium with this site.