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Background Childhood obesity has become a health problem in urban areas in China. Intervention to reduce childhood obesity should be of high priority. School-based intervention programmes are needed to deal with the growing prevalence of childhood obesity in China. Methods Five primary schools were selected randomly for this study in the Beijing urban area in China; two were allocated to the intervention group and three to the control group. A total of 2425 children (1029 children in intervention schools and 1396 children in control schools) took part in the study for 3 years. In the intervention group, children and their parents were involved in a programme of nutrition education and physical activity. Control school students followed their usual health and physical education curriculum with no extra intervention. Results After the 3-year intervention, the prevalence of overweight and obesity were significantly lower in the intervention schools than in the control schools (overweight: 9.8% vs. 14.4%, P < 0.01; obesity: 7.9% vs. 13.3%, P < 0.01). The prevalence of overweight and obesity decreased by 26.3% and 32.5% in intervention schools respectively after intervention. The prevalence of overweight and obesity increased in control schools. There was also significant difference in body mass index between intervention and control schools (18.2 ± 2.6 vs. 20.3 ± 3.4, P < 0.01) after intervention. More non-obese children became obese in the control schools (7.0%) than in the intervention schools (2.4%) at end line ( P < 0.01). Among the children who were obese at baseline, 49.2% remained obese at end line in intervention schools while 61.9% remained obese in control schools ( P < 0.01). Conclusions Our study showed that an intervention programme could be feasible in schools in Beijing, China. The prevalence of overweight and obesity was reduced in schoolchildren in Beijing through an intervention focused on nutrition education and physical activity. Overweight and obesity children as well as normal weight children and their parents should be involved in such an intervention programme. [ABSTRACT FROM AUTHOR]