Several studies have demonstrated an association between variation in the apolipoprotein (apo) B gene, principally as detected by the XbaI and EcoRI restriction fragment length polymorphisms (RFLPs), and lipoprotein levels or cardiovascular disease. We have examined the frequency of the EcoRI and XbaI RFLPs of the apoB gene in 95 white Type 2 diabetic patients aged between 45 and 80 years in order to ascertain whether variation in this gene may be influencing the development of Type 2 diabetes and associated atherosclerosis through obesity. Neither of the two RFLPs had a significant association with clinically defined cardiovascular disease or with body mass index in our sample. However, while XbaI displayed no association with circulating levels of lipids, lipoproteins or apolipoproteins, the presence of the rare (R2) alele of EcoRI (absence of cutting site) was associated with significantly higher levels of circulating triglycerides. Furthermore, the EcoRI R2 allele was over-represented in the diabetic sample when compared to a healthy control group. Our findings support previous studies which have shown an effect of variation at the apoB gene on circulating lipid levels; additionally, variation in this gene may contribute to the development of Type 2 diabetes mellitus.