Abstract Background Patients with congenital heart disease (CHD) form a high-risk niche among patients considered at high-risk of infective endocarditis (IE). Their life-long exposure to the risk of IE, starting from birth, necessitates a nuanced approach to both prevention and treatment strategies. However, comprehensive data from an unselected nationwide cohort, including children, are lacking. Purpose This study sets out to compare characteristics and associated outcomes among patients with IE with and without CHD. Methods Using nationwide registries, all Danish patients diagnosed with IE from 1977-2021 were identified and stratified on whether they had a diagnosis of CHD, regardless of its complexity. Characteristics prior to and during admission as well as associated outcomes (i.e., in-hospital mortality, 1-year mortality, and 10-year mortality, and IE recurrence) were compared between groups. Results In total, 14,040 patients were diagnosed with IE from 1977-2021 including 895 (6.4%) with a diagnosis of CHD. Patients with versus without CHD were significantly younger at time of IE diagnosis (median age 38.8 years [IQR 21.2-56.4 years] versus 70.7 years [IQR 58.8-78.9 years], Figure 1) and less comorbid. Patients with versus without CHD were hospitalized due to IE for a similar period of time but more often underwent cardiac surgery during admission (44.9% versus 21.3%). The IE-related bacteremia was significantly different between groups: the most common bacteriemia in relation to IE was Streptococci (29.9%) in patients with CHD and Staphylococcus Aureus (29.9%) in patients without CHD. Patients with CHD were associated with a significantly lower risk of in-hospital mortality (6.4% versus 19.8%), 1-year mortality (10.5% versus 32.4%) and 10-year mortality (21.3% versus 58.7%) compared with those without CHD. The 10-year incidence of IE recurrence was similar among groups (p-value 0.5). Conclusions Patients with CHD who develop IE are distinctive from patients with IE without CHD in terms of characteristics as well as long-term outcomes. Notably, our findings stress a key point: the majority of children and adolescents with IE have a CHD. These unselected findings should help guide future preventive strategies, diagnosis, and management.