In 1175 Japanese school children, insulin resistance (IR) was assessed by the homeostasis model approximation index and obesity by body mass index standard deviation score (obese: BMISD ≥ 2.0). In nonobese children, BMISD was most significantly associated with IR, and with log triglycerides (TG), apoB and LDL size in boys and log TG, LDL size, and HDL-cholesterol in girls as well, even after correctiion for BMISD. In obese children, all lipid-related parameters were significantly associated with IR excepting LDL-cholesterol in boys and LDL size in girls. In multiple regression analysis, log TG and LDL size in nonobese children, and log TG in obese boys, and LDL size in obese girls were independent predictors of IR. Furthermore, IR was significantly higher in children with IIb and IV hyperlipidemia compared with those with normolipidemia and IIa hyperlipidemia. Thus, characterization of lipid phenotypes in children may be important for devising and implementing interventions to prevent coronary heart disease in later life.