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AbstractBackground:The present study aimed to quantify the burden of structural heart disease in Nepali children.Methods:We performed a school-based cross-sectional echocardiographic screening study with cluster random sampling among children 5–16 years of age.Results:Between December 2012 and January 2019, 6573 children (mean age 10.6 ± 2.9 years) from 41 randomly selected schools underwent echocardiographic screening. Structural heart disease was detected in 14.0 per 1000 children (95% CI 11.3–17.1) and was congenital in 3.3 per 1000 (95% CI 2.1–5.1) and rheumatic in 10.6 per 1000 (95% CI 8.3–13.4). Rates of rheumatic heart disease were higher among children attending public as compared to private schools (OR 2.8, 95% CI 1.6–5.2, p = 0.0001).Conclusion:Rheumatic heart disease accounted for three out of four cases of structural heart disease and was more common among children attending public as compared to private schools.