Objectives: The objective of this study was to identify the factors associated with the percentage of body fat and bone mineral density (BMD). Methods: 886 students of the 4, 5, 6th grade were sampled from 6 elementary schools in Daejeon city from May to June 2005. Participants completed the questionnaire on socio-demographic factors, eating habits and physical activities, and had the measurements of body composition, BMD, height and weight. T-test, one-way ANOVA and ANCOVA were used to compare body composition and BMD among groups defined by study factors. Multiple regression analysis was used to determine the factors related with percentage of fat and BMD in each sex. Results: When adjusting age, height, weight and family income, the amount of food intake and regular exercise including the days of exercise per week and the daily exercise duration were significantly associated with percentage of fat in boys, but not in girls. When adjusting the same variables, regular exercise, the days of exercise per week and the daily exercise duration were positively associated with BMD in both sexes. Conclusion: Regular exercise with one or more days per week were the common factor to decrease percentage of fat and increase BMD in school children. This showed that regular exercise program could improve the body composition of school children.