OBJECTIVE Evaluation of serum lipoprotein profiles including triglyceride (TG)-rich lipoprotein, that is, intermediate-density lipoprotein (IDL), very low-density lipoprotein (VLDL), and chylomicron (CM) remnant is important to manage coronary heart disease (CHD) risk. The purpose of this study was to investigate CHD or cardiovascular disease (CVD) risk scores with cholesterol levels of six fractionated lipoprotein classes {high-density lipoprotein [HDL], low-density lipoprotein [LDL], IDL, VLDL, CM including CM remnant, and lipoprotein (a) [Lp (a)]} in Japanese healthy men. METHODS The present study enrolled 161 healthy men without any medications. Lipoprotein profiles (fractionated lipoprotein cholesterol levels) were measured by anion-exchange high-performance liquid chromatography (AEX-HPLC) method and were compared with age, estimated glomerular filtration rate (eGFR), and three risk scores, that is, NIPPON DATA, Hisayama risk predicting model, and Suita score. RESULTS Levels of LDL-cholesterol (C), VLDL-C, and CM-C significantly differed with age, while values of HDL-C, IDL-C, and Lp(a)-C were not different. The eGFR inversely correlated with LDL-C, IDL-C, VLDL-C, and CM-C. In a stepwise multiple logistic regression analysis, VLDL-C only correlated independently with eGFR. Three risk scores significantly correlated with CM-C. CONCLUSIONS These results suggested that VLDL-C concentration contributes to an increased risk at early stages of renal dysfunction, and CM-C may serve as a marker for estimating CHD risk in Japanese healthy men.