The agarose gel electrophoresis and differential staining system is an easy and quick method for analyzing the serum lipid composition of each lipoprotein fraction. It has been reported in adults that measured values obtained by this method strongly correlated with those obtained by ultracentrifugation. The aim of this study was to examine the clinical application of this method for children, in comparison with the ultracentrifugation method. The subjects were sixteen hyperlipidemic and twenty-five normolipidemic children, aged from two to eighteen years old. Cholesterol (C) and triglyceride (TG) levels were determined in serum very low density lipoprotein (VLDL), low density lipoprotein (LDL), and high density lipoprotein (HDL) fractions by both methods. Correlation coefficients between the two methods for cholesterol levels were 0.937 (HDL), 0.983 (LDL) and 0.837 (VLDL), and for triglyceride levels were 0.735 (HDL), 0.621 (LDL) and 0.964 (VLDL). We confirmed the clinical application of this method to evaluate the lipoprotein lipid profile in children as well as in adults.