BACKGROUND CHD is the leading cause of morbidity and mortality in the developed world, while reports from India looking into the burden of the disease have been variable depending on the age group of subjects studied and the methodology involved. We were interested to find the prevalence and pattern of the disease in this north eastern Indian state of Manipur, which has a unique geographical and racial composition. MATERIALS AND METHODS This is a community based, prospective, cross sectional study where each and every child aged 5-15 years from randomly selected schools of Manipur were examined by 2D colour Doppler Echocardiography and physically as well, where the examiners were blinded, and the findings were noted independent of each other. The anthropometric parameters, clinical details and echocardiography findings were all recorded. RESULTS Of the 3600 children examined, 47 cases of CHD were detected, giving echocardiographic prevalence of 13 per 1000 where BAV (44%) was found as the commonest lesion followed by VSD (17%) and ASD (14%). Clinically detectable lesion was found in 21 subjects (VSD -8, ASD-7, PS-3, PDA -1, AVSD-1, BAV-1 with AR). Of the clinically detectable CHD, VSD was the commonest followed by ASD. In the subclinical CHD category, 20 cases of BAV, 4 cases of mild MVP without MR, 1 case of apical LV discompacta, 1 case of IASA were detected. CONCLUSION The echocardiography prevalence of congenital heart disease in school going children of Manipur is 13/1000. This highest ever reported prevalence of CHD in children is most probably related to the use of the highly sensitive investigative tool of Echocardiography in each subject of our study resulting in detection of clinically silent lesions.