Abstract: Objective To study the prevalence of short stature among primary and secondary school students in Chongqing municipality and to provide evidences for intervention.Methods Body height was measured among 54743 primary and secondary school students of 6-18 years old selected with stratified cluster random sampling from 9 districts with different economic development level in Chongqing municipality.Results The overall prevalence of short stature among the students was 6.10% and at a high level according to the standard national criterion.Significantly higher short stature prevalence was observed among the rural students compared with that among the urban students(7.90% vs.4.20%, P<0.01) and among the students from the districts with low and moderate economic development level compared to that among the students from the districts with high economic development level(7.80% and 7.60% vs.3.10%, P<0.001);no gender difference in short statue prevalence was found among the students(P>0.05).The prevalence of short statue increased with the increment of age among the students and the increased prevalence was especially obvious among the students aged 12 years.Conclusion The results suggest that developing local criterion for short statue screening and intervention on short statue should be promoted among primary and secondary school students in Chongqing municipality.