We have examined the association between variation at the apolipoprotein (apo) B gene and apo AI-CIII-AIV gene cluster and within-individual variation in serum cholesterol levels. Annual measurements were available over a period of 5-10 years in a group of 117 male patients with peripheral arterial disease. The overall within-individual coefficient of variation in cholesterol levels over time was 13.9%. For all patients, Restriction Fragment Length Polymorphism (RFLP) genotype at the apo B gene (XbaI and EcoRI) and apo AI-CIII-AIV gene cluster (XmnI, PstI and PvuII-CIII) had previously been determined. At the apo B locus, individuals heterozygous for either the XbaI or EcoRI RFLP showed significantly greater within-individual variability over time compared to individuals of other genotypes. At the apo AI-CIII-AIV gene cluster, individuals homozygous for the common allele of either the PstI or PvuIIA RFLPs showed the greatest within-individual variability over time but there was no difference in this estimate associated with XmnI genotype. Our observations suggest that variation at both the apo B and apo AI-CIII-AIV loci interacts with unidentified environmental factors to determine individual variability in serum cholesterol levels over time.