People with metabolic syndrome (MetS) are at increased risk of type 2 diabetes and cardiovascular diseases, and often have increased triglyceride, reduced high-density lipoprotein cholesterol (HDL-C) and sometimes moderately increased low-density lipoprotein cholesterol (LDL-C) levels. Lifestyle intervention is critical for treating MetS, while pharmacotherapy of dyslipidemia in MetS remains controversial. Considering the specific lipid profile in MetS, fibrates are typically used as first-line treatment. Nevertheless, first-line therapy should be directed towards LDL-C, even in people with MetS, because of the evidence that lowering LDL-C has cardioprotective effects. Non-HDL-C is considered to be an alternative treatment target for people with moderately or severely elevated triglyceride (> or =200mg/dl). Statins improve lipid profiles principally by lowering LDL-C and may exert anti-inflammatory and anti-atherothrombogenic effects, which ameliorate the fundamental pathophysiology of MetS. Fibrates also have pleiotropic effects that improve cardiometabolic risk factors, including insulin resistance, although they do not have clear cardioprotective effects. Omega-3 fatty acids, niacin, pioglitazone and anti-obesity drugs are also candidates for the treatment of dyslipidemia and other complications in MetS. Another question is whether statins in combination with fibrates or other lipid-lowering drugs has greater cardioprotective properties than monotherapy. In this article, we discuss several issues in the pharmacotherapy of MetS.