Congenital Heart Diseases (CHD) are among the leading causes of morbidity and mortality associated with congenital malformations among children. Not knowing the risk profile of CHD among children in Uganda impedes development of effective prevention interventions. In this hospital based unmatched case-control study we examined risk factors for all types of CHD among 179 pair of case and control children aged 0-10 years old at Mulago National Referral Hospital. Odds ratios and their corresponding 95% confidence intervals were calculated using multivariate logistic regression. Low birth weight (adjusted OR: 3.15, 95% CI 1.48 -6.69), high birth order ≥5 th birth order (adjusted OR: 3.69 (1.10 -12.54), maternal febrile illness during pregnancy, maternal and paternal alcohol consumption, and paternal socio-economic status were associated with CHD. Family history of CHD, maternal education level, maternal chronic illness, and paternal education level were not associated with CHD. The results suggest: low birth weight, high birth order, and maternal febrile illness during pregnancy, parental alcohol use and paternal socio-economic status as dominant risk factors for CHD among children. Rigorous implementation of public health policies and strategies targeting prevention of febrile illness during pregnancy, maternal malnutrition, parental alcohol consumption, delivery of high number of children per woman, might be important in reducing the burden of CHD among children in Uganda.