The present study was performed to develop regression based prediction equations for fat mass from skinfold thickness in Japanese children, and to investigate the cross-sectional and longitudinal validity of these equations. A total of 127 healthy Japanese prepubertal children aged 6-12 years were randomly separated into two groups: the model development group (54 boys and 44 girls) and the cross-sectional validation group (18 boys and 11 girls). Fat mass was initially determined by using DXA (Hologic Delphi A-QDR whole-body scanner) to provide reference data. Then, fat thickness was measured at triceps and subscapular using an Eiken-type skinfold calipers. Multiple anthropometric and DXA measures were obtained one year later for 28 of the original 127 subjects (longitudinal validation group: 14 boys and 14 girls). Strong significant correlations were observed between total fat mass by DXA measurement and the skinfold thickness × height measures by caliper in the model develop- ment group of boys and girls (R2=0.91-0.92, p<0.01). When these fat mass prediction equations were applied to the cross-sectional and longitudinal validation groups, the measured total fat mass was also very similar to the predicted fat mass. In addition, there were significant correlations between the measured and predicted total fat mass for boys and girls, respectively, although Bland-Altman analysis indicated a bias in cross-sectional valida- tion group. Skinfold-derived prediction equations underestimate for obese children but are generally useful for estimating total fat mass in field research.