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BACKGROUND Knowledge about the disease itself can be important for self-care in patients with several problems and comprehends information about the diagnosis up to the most important clinical implications. OBJECTIVE To identify the level of knowledge of children and adolescents with congenital heart disease (CHD) about their illness, and to analyze the association between the level of knowledge and the practice of physical activity. METHODS Cross-sectional study with 335 patients with CHD, aged 8 to 13 years, followed at a referral pediatric cardiology service in Southern Brazil. Patients were interviewed regarding their knowledge about CHD and a review of medical records was performed to obtain details on heart disease and procedures. A significance level p<0.05 was used. RESULTS More than 50% of the children and adolescents did not know how to say the name of their disease or explain it. After adjusted OR (AOR), cyanotic patients in comparison to acyanotic ones (AOR: 2.29; 95%CI: 1.76-6.71; p = 0.019); children with lower level of schooling (AOR: 2.20; 95%CI: 1.81-5.86; p = 0.025); and those who did not practice physical activity (AOR: 1.88; 95%CI: 1.09-3.45; p = 0.011) showed potential for incorrect answers or did not know their disease. CONCLUSION Cyanotic children and adolescents, with a lower level of schooling and who did not practice physical activity, had little knowledge about their disease. It is necessary to develop educational intervention strategies to increase knowledge and change behavior in physical activity promotion, according to the CHD complexity. (Arq Bras Cardiol. 2020; 114(5):786-792).