Association between high density lipoprotein (HDL) cholesterol concentration and restriction fragment length polymorphisms at the cholesteryl ester transfer protein (CETP) gene locus was studied in a random population-based cohort of 526 Caucasian subjects (259 men, mean age 50.9 years, and 267 women, mean age 51.8 years). HDL cholesterol concentration was adjusted for age, body mass index, alcohol consumption, smoking and plasma triglyceride and low density lipoprotein cholesterol levels. In females, the HDL cholesterol levels were associated with TaqIB polymorphism (1.46 mmol/l in the B1B1 genotype, 1.56 mmol/l in B1B2 and 1.72 mmol/l in B2B2, P = 0.0001 for the trend). In contrast, this was not observed in men (1.24, 1.20, 1.27 mmol/l, NS). The association was seen even in women who were current smokers (1.41, 1.56, 1.75 mmol/l, n = 72, P = 0.007), but not in male smokers (1.26, 1.19, 1.14 mmol/l, n = 102, NS). In male non-smokers the association was weak (1.22, 1.20, 1.32 mmol/l, n = 157, P = 0.05). In postmenopausal women not receiving hormone replacement therapy (n = 108), the association continued to be present, although weaker (1.50, 1.58, 1.70 mmol/l, P = 0.06). CETP activity (n = 101) tended to be lower in subjects with the B2B2 genotype. In conclusion, a clear-cut sex difference was observed in the genotype effect on plasma HDL cholesterol levels. The slight attenuation of the gene dosage effect after menopause suggests that the gender difference may be, at least in part, due to sex hormones. A genetic subgroup (men with the B2B2 genotype) particularly susceptible to the HDL cholesterol decreasing effect of smoking could be demonstrated.