Primary hyperlipidemia, characterized by hypertriacylglycerolemia and/or hypercholesterolemia, is considered to be one of the most important risk factors for atherosclerosis and coronary heart disease. This study was performed by using polymerase chain reaction and restriction fragment length polymorphism analysis. We measured lipids and cholesteryl ester transfer protein (CETP) activity in primary hyperlipidemic and normolipidemic subjects, with and without Taq1B polymorphism. Genotype distribution and allelic frequencies of polymorphism were determined and compared in both groups. Our results showed that plasma CETP activity was significantly higher in primary hyperlipidemia than in controls (p = 0.001). Plasma lipids were also remarkably increased in primary hyperlipidemic subjects. In both patient and control groups, individuals with B1B1 and B1B2 genotypes had higher plasma CETP activity, lower total cholesterol, lower high-density lipoprotein cholesterol and higher triacylglycerol than those with the B2B2 genotype. The values of low-density lipoprotein cholesterol were significantly increased in primary hyperlipidemic patients with the B2B2 genotype. The genotype and allelic frequencies for this polymorphism differed significantly between primary hyperlipidemic patients and controls (p = 0.022 and p = 0.039, respectively). Taq1B polymorphism of the CETP gene was associated with changes in lipid profile and plasma CETP activity in the selected population.