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Background: There was no large-scale population survey on the prevalence of short stature in Anhui province yet. To further acquainting the epidemiological character of teenage children short stature in Anhui province, and to provide basis for exploring reasonable intervention measure about children's height, we took this survey on short stature in primary and middle school students of Anhui province., Methods: Twelve thousand nine primary and secondary school students in urban and rural aged from 7 to 18 years were recruited. The comparison of short stature in different genders, regions and age groups was done according to genetic metabolic endocrine group of pediatrics branch in Chinese Medical Association (CMA)., Results: The average detection rate of short stature in primary and middle school students was 3.16% in Anhui province. The detection rate was higher in rural area than in urban area, higher in economic backward area than in economic developed areas., Conclusion: There was no significant difference in detection rate in gender and age.