The aims of this study were to determine reference norms for a fat-free mass index (FFMI) and fat mass index (FMI) in a large population of healthy children in Japan, to observe differences in these values in three age groups between ages three and eleven, and to develop percentile distributions for these parameters. Five hundred twenty-two boys and six hundred forty-nine girls with a wide spectrum of stature, body mass, and body composition underwent bioelectrical impedance analysis (BIA) for the determination of fat-free mass (FFM) and fat mass (FM). Both FFM and FM were divided by stature² to give FFMI and FMI, as described previously. Normal FFMI and FMI were defined within the range of the 25th to 75th percentile of age- and gender-specific data in this study. The reference norms for FFMI (3–11 yrs) were 12.7–13.4 kg/m² in boys and 12.0–13.0 kg/m² in girls. A modest increase in boys was observed with an age increase; otherwise, there were no marked age differences in FFMI for the children as a whole. The reference norms for FMI were 2.8–3.6 kg/m² in boys and 3.2–3.8 kg/m² in girls. For each 3-year category (i.e., ages 3–5, 6–8 and 9–11 yrs.), FMI progressively increased by an average of 28.6% in boys and 18.8% in girls, compared to an increase in BMI of 11.0 and 11.3% respectively. FFMI and FMI are appropriate for many purposes, and have the advantage of expressing both aspects of body composition in common units. In conclusion, the data presented as percentiles can serve as reference in comparing a child's body composition to that of healthy children of the same age and gender. The reference standards should be appropriate for almost all children in the Japan for whom stature, body mass, and body composition can be measured satisfactorily. However, a more sophisticated approach is ultimately required for evaluating body composition. This article is a preliminary attempt to promote future research in the area of childhood body composition.