Background and aim: Cholesteryl ester transfer protein (CETP) plays pivotal role in HDL metabolism and in reverse cholesterol transport (RCT) pathway. CETP gene variants such as -629C/A that affect HDL cholesterol directly modulates CETP gene tranh1ional activity. This study was aimed to determine influence of -629C/A polymorphism of CETP in statin effects with regard to plasma HDL cholesterol levels. Methods: In this deh1ive-analytical study 196 adult patients with LDL-C more than 120mg/dL were divided into two groups base on lovastatin and atorvastatin using. Lipid profile was measured in all subjects before and after treatment and -629C/A polymorphism of CETP promoter was studied using polymerase chain reaction/restriction fragment length polymorphism method. Data were compared with paired t-test and ANOVA in SPSS software. Results: Cholesterol was decreased and HDL was increased in AA genotype more than other genotypes by lovastatin but ApoA1 was increased in CC genotype. ApoA1 also was increased in CC genotype more than AA or AC genotypes by atorvastatin. Conclusion: In CC genotype lovastatin and specially atorvastatin increased ApoA1 in HDL particles more than other genotypes. Therefore treatment with lovastatin and atorvastatin is more effective in patients with CC genotype for raising HDL particles activity