BACKGROUND: Children who have unhealthy lifestyles are predisposed to develop hypertension, dyslipidemia and other complications. The epidemic of obesity is also affecting children with congenital heart disease. The aim of this study is to estimate the prevalence of obesity and describe associated risk factors, including family history in children with congenital heart disease. METHODS: A cross-sectional study with 316 children and adolescents with congenital heart disease seen in an outpatient clinic of a reference hospital. Collected sociodemographic data included family history of chronic disease, dietary habits, laboratory tests (total cholesterol, HDL and LDL/cholesterol, triglycerides, fasting glucose, CRP, hematocrit and hemoglobin), and anthropometric assessment. Anthropometric data of the caregivers was self-reported. RESULTS: The prevalence of excess weight was 26.9%. Altered levels of total cholesterol were observed in 46.9%, of HDL in 32.7%, LDL in 23.6% and of triglycerides levels in 20.0%. A higher frequency of family history of obesity (42.6%; p = 0.001), dyslipidemia (48.1%; p = <0.001), diabetes (47.4%; p = 0.002), hypertension (39.2%; p = 0.006) and ischemic disease (43.7%; p = 0.023), as well as significantly higher values of triglycerides (p = 0.017), glycemia (p = 0.004) and C-reactive protein (p = 0.002) were observed among patients with excess weight. CONCLUSION: The presence of modifiable risk factors and the variables associated to excess weight in this population was similar to that described in the literature for children without congenital disease. As these children already present the risks associated to heart disease, it is particularly important to promote a healthy lifestyle in this group.