The association of genetic markers at the apolipoprotein B gene (APOB) (XbaI, MspI, and EcoRI polymorphisms) and the lipoprotein lipase gene (LPL) (PvuII polymorphism) with coronary artery disease (CAD) and with variation in plasma lipid levels (total cholesterol, high-density lipoprotein cholesterol, and total triglycerides) was studied in 94 male patients with CAD diagnosed by angiography and in 122 unrelated men of Russian descent free of clinical signs of CAD. The frequent allele (M+) of the APOB MspI RFLP was seen more frequently in CAD patients than in control subjects (0.963 vs. 0.898, p < 0.025). No significant differences in allele frequencies were observed for the APOB XbaI and EcoRI polymorphisms or for the LPL PvuII polymorphism. In patients, carriers of the rare allele (E-) of the EcoRI RFLP had higher mean triglyceride levels than homozygotes for E+ (p < 0.05). No significant differences in lipid variables were determined for the other three polymorphisms studied. Analysis of intragenotype variances and the multivariate measure of mean values of lipid concentrations showed that genetic variability within the APOB locus may contribute to a certain extent to the level and variability of serum lipid levels in this Russian population.