Hypercholesterolemia has been recognized as a significant risk factor for atherosclerosis and coronary artery disease. The aim of this study was to evaluate the prevalence of hypercholesterolemia and the role, if any, of type of dialysis. In 19 hemodialysis (HD) and 20 continuous ambulatory peritoneal dialysis (CAPD) subjects, body weight, body mass index (BMI), arm muscle area (AMA), total cholesterol (C), HDL and LDL fractions, triglycerides, C/HDL ratio, glycosylated hemoglobin, and apolipoproteins AI, AII, B, CII, CIII, and E were evaluated. Hypercholesterolemia was defined as cholesterol greater than 220 mg/dL and LDL greater than 150 mg/dL. Body weight, body mass index, and arm muscle area were higher (p < 0.05) in CAPD as compared with HD; so were total cholesterol, LDL, C/HDL ratio, and glycosylated hemoglobin (Hbalc). Hypercholesterolemia prevalence was 3/19 in HD and 11/20 in CAPD (p < 0.05). A relationship between Hbalc and C/HDL ratio was found in the CAPD group (r = 0.48; p < 0.05). We are greatly concerned about these metabolic effects of CAPD; therefore, we should carefully select patients to be treated by CAPD. Aggressive nutritional and pharmacological treatment for glucose intolerance and hypercholesterolemia in CAPD patients must be performed in order to reduce the incidence of coronary artery disease (CAD).