Background: Coronary heart disease (CHD) is a leading cause of death worldwide and hypertriglyceridemia and hypercholesterolemia are major risk factors for the disease. Considering the role of hyperlipidemia as the underlying cause of cardiovascular mortalities and morbidities, and the limited and conflicting results of studies on CETP gene polymorphisms in Iran, we aimed to study -971 G/A polymorphism of cholesterol ester transfer protein gene in patients with primary hyperlipidemia.Methods: In this case-control study performed in Hamadan University of Medical Sciences (from May 2010 to April 2011), we recruited 200 patients with primary hyperlipidemia (total cholesterol >250 mg/dl and/or triglyceride >200 mg/dl) as the cases and 200 healthy individuals with normal cholesterol and triglyceride as the control group. Gene segments were replicated by polymerase chain reaction (PCR) and -971 G/A polymorphism genotypes were identified by RFLP technique. Subsequently, plasma CETP activity was measured enzymeatically by a kit in a fluorescence spectrometer.Results: The allele and genotype frequencies were not significantly different (P>0.05) between the two groups (in the control group: AA 24%, GA 47% and GG 28.5% and in the case group: AA 18%, GA 51% and GG 31%). In the case group, homozygous individuals with A alleles (AA genotype) had greater cholesterol and HDL-c concentrations than those with other alleles (GG and GA). In both cases and controls, individuals with AA genotype had lower CETP concentrations.Conclusion: We conclude that -971 G/A polymorphism in CETP gene promoter can affect lipid profile and alter CETP activity.