Aim: Metabolic syndrome (MS) is associated with dyslipidemia such as hypertriglyceridemia and high-density lipoprotein (HDL) levels. Scavenger receptor BI (SR-BI) is the transmembrane receptor that regulates selective intake of cholesterol esters by the liver and it binds to HDL with high affinity. This study was aimed to determine the effects of SR-BI gen variations upon proatherogenic and antiatherogenic lipid profiles in the patients with metabolic syndrome. Methods: The patient group was consisted of 104 (30–65 years) male subjects who were diagnosed with MS and 100 healthy male subjects were included in control group. DNA was isolated from blood samples. SR-BI gene rs4238001 and rs5888 variants were examined by SNaPshot multiplexing system. SPSS 18 was used for statistical analysis and p < 0.05 considered as statistically significant. Results: It was found that SR-BI gene rs4238001 T allele increased the risk of metabolic syndrome 1.61 fold (p = 0.02). Subjects with TT genotype 2.847 fold increased the risk of metabolic syndrome according to subjects with CC genotype (p = 0.017). Conclusions: SR-BI rs4238001 variation may be related to an increased risk of metabolic syndrome.