Congenital heart disease (CHD) increases the risk of infective endocarditis (IE), though the lesion-specific risk and mortality are poorly defined. Using the population-based Quebec CHD database, we sought to describe the predictors of IE and to evaluate if IE was associated with mortality among adult CHD (ACHD) patients without prior valve replacement surgery. We extracted data on ACHD patients with IE and assessed the lesion-specific incidence of IE, risk factors for IE acquisition, and all-cause 1-year mortality. Among 29,866 ACHD patients, 285 (0.95%) developed IE during follow-up period of 378,901 patient-years, from 1988-2010. The highest and lowest lesion-specific incidences of IE were observed with left-sided lesions (1.61/1000 patient-years) and patent ductus arteriosus (0.24/1000 patient-years), respectively. The following predicted the risk of IE acquisition (odds ratio (OR), 95% confidence interval [CI]): cardiac surgery in the previous 6 months (9.07, 3.98–20.67), endocardial cushion defects (6.65, 3.84–11.53), left-sided lesions (5.11, 3.60–7.25), cyanosis at birth (4.82, 3.12–7.46), ventricular septal defect (2.81, 1.87–4.21), diabetes mellitus (1.65, 1.10–2.48), and recent medical interventions (12.52, 5.23–29.97). Twenty-five (8.77%) patients died within 1-year of IE diagnosis, a substantially elevated rate compared to patients without IE (OR 31.07, 95%CI 16.23–59.49). The risk of death following IE diagnosis was similarly elevated among patients with left-sided, cyanotic and other CHD lesions. In conclusion, the risk of IE in ACHD patients is lesion-specific and is greatest in the context of recent medical interventions. IE is associated with increased 1-year mortality, irrespective of broad CHD lesion grouping.