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The aim of this study was to determine the prevalence and treated status of congenital heart disease (CHD) in elementary schoolchildren and facilitate the long-term planning of health care, resource allocation, and development of targeted primary prevention strategies. From November 2011 to November 2012, 540,574 schoolchildren from 449 elementary schools were screened for CHD by trained doctors in Dongguan City. The schoolchildren who were suspected to have CHD were referred to a pediatric cardiologist and/or an echocardiographist for complete evaluation. Of them, 214,634 (39.7%) were local children and 325,940 (60.3%) were migrant children. The total prevalence of CHD was 2.14‰, and there was a significant difference (p <0.05) of the CHD prevalence between local (1.97‰) and migrant children (2.26‰). The treatment rates of CHD in local children and in migrant children were 63.51% and 47.21%, respectively (p <0.01). The commonest CHD was ventricular septal defect (43.13%), followed by atrial septal defect (25.84%) and patent ductus arteriosus (12.79%). With respect to gender, CHD was equally distributed between men and women. In conclusion, social, economic, and environmental risk factors that affect health of migrant children with CHD call for more attention from health policy makers and researchers in contemporary China. Efforts should be made to increase public health investment, establish health care manage system for children from migrant families, and increase the parents' awareness of preventing the CHD. [ABSTRACT FROM AUTHOR]