Cholesteryl ester transfer protein (CETP) plays a key role in lipid metabolism. Thus, variations in the CETP gene may be clinically relevant. Newly started atorvastatin users (n=212) were genotyped for CETP genetic variants (TaqIB and I405V). Homozygotes for B1 allele of TaqIB polymorphism had lower plasma high density lipoprotein cholesterol (HDL-C) compared with B1B2 or B2B2 genotypes (p=0.03, for each). Homozygotes for I allele of I405V polymorphism had lower plasma HDL-C compared with IV or VV genotypes (p=0.001, for each). In the whole population, the B1 carriers increased HDL-C levels by 4% after atorvastatin treatment, compared with B2 carriers, where a 4% decrease occurred (p=0.03). Also homozygotes for B1 allele decreased triglyceride levels to a lesser, though not significant, degree compared to B1B2 or B2B2 genotypes. CETP TaqIB or I405V polymorphisms seem to modify the lipid lowering response to atorvastatin treatment. This knowledge may help design more effective hypolipidaemic treatment.