The association of lipid composition in each lipoprotein fraction with adiponectin level in relation to body fatness was investigated. The subjects were 283 children (144 boys and 139 girls) aged 11.6 years (S.D. 1.5). Cholesterol (C) and triglyceride (TG) levels in each lipoprotein fraction were measured by a combination of agarose gel electrophoresis and differential staining. Adiponectin level was not significantly different between girls and boys. In simple regression analyses, an association of adiponectin level with lipoprotein lipid profile was shown only in girls, and not in boys at all. In girls, very low-density lipoprotein (VLDL)-C, low-density lipoprotein (LDL)-C, VLDL-TG and LDL-TG were negatively correlated with adiponectin level, and high-density lipoprotein (HDL)-C and HDL-C/TG ratio were positively correlated. Multiple regression analyses including adiponectin level and body mass index (BMI) as predictors for the lipoprotein lipid profile demonstrated that adiponectin level was a significant independent predictor of VLDL-TG, LDL-C, LDL-TG, HDL-C and HDL-C/TG ratio. In conclusion, adiponectin level correlates with lipoprotein lipid profile independent of body fatness in adolescent girls.