Background: Childhood/adolescent obesity and stunting are associated with heightened risk of metabolic syndrome. Understanding the prevalence and patterns of stunting, the emergence of overweight/obesity in children and adolescents and the concomitant risk for metabolic syndrome is of critical importance for public health policy. Aim: To investigate the prevalence of overweight, obesity and stunting in school children and adolescents aged 6–19 years in Beijing and to compare the differences in screening rates by national and international references. Subjects and methods: School children aged 6–19 years in Xuanwu, Haidian and Fangshan district were selected. Overweight and obesity in the children was screened for using the International Obesity Task-force (IOTF) and Chinese standards. Stunting was defined as height-for-ageZ-score (HAZ) less than −2 using the 2009 Chinese standards and 2007 WHO reference. Results: A total of 99 482 children were included in this survey. The prevalences of overweight and obesity are 17.7% and 14.4% in the Chinese standard, but they are 18.1% and 8.6% in the IOTF standard; there were significant differences between the prevalences of these two standards (p < 0.01). The prevalences of overweight/obesity in boys are all significantly higher than that of girls in every age-group (p < 0.05). Overall there was stunting in 2630 children and adolescents (2.6%) according to the Chinese standards, with 2.8% in boys, higher than the 2.5% of girls (p < 0.01). According to WHO standards, there was stunting in 1201 children and adolescents (1.2%) with 1.1% in boys and 1.3% in girls (p < 0.05). The prevalence of stunting in urban areas was 1.3%, which is significantly lower than that of suburban areas, at 3.9% (p < 0.01). Conclusion: The prevalence of overweight/obesity in children and adolescents aged 6–19 years in Beijing was close to western countries, which should be highly valued when considering public health policies and the problem of growth stunting should not be ignored. [ABSTRACT FROM PUBLISHER]