Abstract: Primary hypertriglyceridemia is considered to be a major risk factor for pancreatitis, atherosclerosis and coronary heart disease. Cholesteryl ester transfer protein gene polymorphisms known to be associated with changes in lipid levels. This study was performed by using polymerase chain reaction and restriction fragment length polymorphisms. Genotype distribution and allelic frequencies of polymorphism were determined and compared in primary hypertriglyceridemic and normotriglyceridemic subjects. The results showed that plasma cholesteryl ester transfer protein activity was significantly higher in primary hypertriglyceridemia than in controls (p = 0.001). In this study all individuals with B2B2 genotype had lower plasma cholesteryl ester transfer protein activity, higher high-density lipoprotein than B1B1 and B1B2 genotypes, whereas triglyceride was significantly decreased in this genotype. The genotype and allelic frequencies for this polymorphism differed significantly between primary hypertriglyceridemic patients and controls (p = 0.014 and p = 0.027, respectively). In both groups, CETP Taq 1B polymorphism (presence of B2 allele) correlated significantly with HDL-C (r = 0.207 and 0.300 in control and patient groups, respectively) and CETP activity (r = -0.193 for controls and r = -0.132 for patients). Taq 1B polymorphism of cholesteryl ester transfer protein gene was associated with changes in lipids profile and plasma cholesteryl ester transfer protein activity in the selected population.