BACKGROUND: Preventing and treating obesity during childhood have been recognized as effective strategy to tackle the global epidemic of obesity. School setting is suitable to carry out intervention for childhood obesity. This study was conducted to assess effect of a school-based intervention for overweight children performed on elementary schools in Seoul, 2007. METHODS: "Fitness Class" was a multi-component intervention including education on nutrition, physical activity and behavior modification. It was an intervention for secondary prevention targeting obese children. The intervention was composed of 12 sessions during 1st semester and 2nd semester, respectively. 446 students (276 boys, 170 girls; 2 students from 3rd grade, 188 from 4th grade, 210 from 5th grade, 46 from 6th grade) from 35 elementary schools located in Seoul were included in this study. Body mass index, obesity index and body fat percentage were measured and lifestyle habits were surveyed at baseline and post-intervention. RESULTS: Mean obesity index of participants was 140.0 +/- 14.3% at baseline and 137.0 +/- 14.4% at post-intervention. Mean obesity index of participants was reduced by 3.1 +/- 7.7% (P < 0.001). The prevalence of severe obesity was decreased from 20.2% to 14.8% and the prevalence of moderate obesity was decreased from 61.0% to 54.0% after this intervention. Eating habits, physical activity habits, self-respect and nutrition knowledge were also improved through this intervention. CONCLUSION: "Fitness Class" performed on elementary schools in Seoul in 2007 reduced obesity index of children and also improved eating habits, physical activity habits, self-esteem and nutrition knowledge of children. However, definite effect of this intervention could not be evaluated due to some limitations in program design.