The relation between TaqI restriction fragment length polymorphisms (RFLPs) of the cholesteryl ester transfer protein (CETP) gene and plasma lipid and lipoprotein phenotypes was investigated in a sample of Italian and Greek migrants of both sexes, age 40-69 years. Italians display significantly higher mean triglyceride and lower mean high-density lipoprotein (HDL) cholesterol levels than Greeks. Greek females have significantly higher HDL cholesterol than Greek males, and Italian females have significantly higher low-density lipoprotein (LDL), HDL, and total cholesterol than Italian males. The differences in RFLP allele frequencies between the two ethnic groups and sexes are insignificant. Multivariate analyses show that in the Greek sample the TaqI B RFLP of the CETP gene has a highly significant effect on HDL cholesterol levels regardless of sex and that the TaqI A polymorphism has a significant effect on HDL levels in females but modulates LDL cholesterol concentrations in males. Among Italians, with the sexes considered separately or combined, no such effects of the CETP TaqI polymorphisms are detected. Kruskal-Wallis tests detected associations between the TaqI B polymorphism in all Greek samples but not in the Italian samples. Genotype CETP*B2 exhibits significantly higher HDL cholesterol concentrations than either of the other two TaqI B genotypes, but there is no evidence of a dosage effect of the *B2 allele. These data suggest that associations between the CETP gene and lipid phenotypes can be population specific. Further, they suggest that such associations are mediated in some way by gender.