OBJECTIVE To develop the reference on height among children and adolescents aged 7 to 18 years of Chinese Han ethnicity in different administrative districts of China and to use this height reference for screening stunting. Results from the national screening program were compared with the WHO references. METHODS Data from the Chinese National Survey on Students Constitution and Health in 2005 was used to develop the height references through LMS method. RESULTS Differences among the references on height for children and adolescents in different districts (I-IV) were remarkable. The highest was seen in the Second Districts while the lowest was seen in the First Districts among those at the age of 18, with differences as 3.18 cm for boys and 2.92 cm for girls. The heights from the inland were shorter than that of the WHO references, with the differences ranging from 0.31 cm to 5.07 cm for boys, and from 0.98 cm to 4.22 cm for girls. The prevalence rates of stunting were 2.22%, 2.29%, 5.25%, respectively according to local references, national references and the WHO references. CONCLUSIONS Universal height references from the whole nation could not discriminate the variations caused by geographic conditions and hereditary factors related to socio-economic situations. Height references should be developed locally, to evaluate height levels of the areas.