Recent studies demonstrated that low-density lipoprotein-tryglyceride (LDL-TG) may represent another marker of cardiovascular risks. We therefore measured LDL-TG including the low-density lipoprotein (LDL) subclass distribution and investigated the association between LDL-TG subclass profile and the clustering of metabolic syndrome (MetS) components and insulin resistance in Japanese children. The study included 237 schoolchildren (boys 115, girls 122). Four subclasses of low-density lipoprotein-tryglyceride (large, medium, small, and very small) was quantified using high-performance liquid chromatography. Total LDL-TG and TG levels in LDL subclasses were evaluated among four MetS component groups; non-abdominal obesity, abdominal obesity, pre-MetS, and MetS. Total LDL-TG (P = 0.0003, P = 0.0175) and triglyceride levels in LDL subclasses were significantly different among four MetS component groups (large: P = 0.0002, P = 0.0084; medium: P = 0.0009, P = 0.0491; small: P =0.0025, P = 0.0509; very small: P = 0.0808, P = 0.0228; boys and girls, respectively). Total LDL-TG (r = 0.411, P < 0.0001, r = 0.378. P < 0.0001) and triglyceride levels in LDL subclasses correlated positively with the homeostasis model of assessment ratio (large: r = 0.396, P < 0.0001, r = 0.346, P < 0.0001; medium: r = 0.274, P = 0.0030, r = 0.228, P = 0.0115; small: r = 0.342, P = 0.0002, r = 0.292, P = 0.0011; very small: r = 0.385, P < 0.0001, r = 0.426, P < 0.0001, boys and girls, respectively). Subclass distribution of LDL-TG was significantly associated with the clustering of MetS components in both sexes, and insulin resistance is a significant determinant of LDL-TG in all LDL subclasses. Lipoprotein-tryglyceride subclass analysis, rather than LDL-C, may provide a precise evaluation for cardiovascular disease risks in children with MetS.