In the present study, we evaluated the influence of lipoprotein lipase (LPL) and apolipoprotein (apo) E polymorphisms on lipid concentrations of 178 Greek men of similar age with coronary heart disease (CHD), but varying body mass index (BMI).Patients were divided according to their BMI (in kg/m²) into three groups: lean (BMI = 20-24.9), overweight (BMI = 25-29.9), and obese (BMI ≥ 30). Polymorphisms of LPL (HindIII, S447X) and apo E (ε2, ε3, ε4), and lipid parameters were studied.There was a negative correlation between BMI and high-density lipoprotein cholesterol (HDL-C) concentration (r = -0.272, p < 0.001), as has already been described. Lean homozygotes for the HindIII(+) allele had higher HDL-C levels compared to lean homozygotes for the HindIII(-) allele (p = 0.012). No correlation was found between S447X or apo E polymorphisms and BMI or plasma lipids in any group. Overweight men with the ε3/ε3 and SS genotypes had higher triglycerides concentration compared with overweight men with ε3/ε3 and SX (p = 0.002).The HindIII polymorphism alone may influence HDL-C concentration in lean men, in contrast to S447X alone, which has no influence on any lipid parameters. However, the S447X and apo E polymorphisms may have a synergetic effect and alter plasma triglyceride concentration in overweight men.