Cholesteryl ester transfer protein (CETP) transfers cholesteryl ester from high-density lipoprotein (HDL) to very low-density lipoprotein (VLDL), low-density lipoprotein (LDL) and chylomicron in exchange for triglycerides. Two CETP genetic variation and four polymorphisms are investigated by polymerase chain reaction (PCR) and restriction enzyme digestion in a population of Taiwan. The results show that a very rare variation frequency is found for CETP intron 14 splice site G-->A change. The population shows a predominant 405Ile allele (61%), 442Asp (97.7%), intron 1Taq1B(+) G allele (52%), intron 8 Msp1(-) A allele (89%) and intron 9 EcoN1(-) T allele (59.2%) in the control group. Patients with coronary heart disease (CHD) have more CETP EcoN1(+/+) GG genotype (25.3%) than the controls (13.6%) (P=0.049). The intron 1 Taq1B(-) A allele is associated with a high HDL cholesterol and apoA1 level, the EcoN1(+) G allele with a low apoA1 level and the 442Gly with both high total cholesterol and LDL cholesterol levels. Paradoxically, the 442Gly is also present with a higher frequency (5.2%) in HDL cholesterol > or =65 mg/dl group than that in the general population (2.3%) (P=0.04).