Aims To examine factors related to excess mortality in a cohort of adults with congenital heart disease (CHD). Methods and results We conducted a survival analysis using prospective data of 3311 adults with CHD [ 50.5% males, median age at entry 22.5 years (IQR 18-39), median follow-up time 10.5 years (IQR: 4.4-18)]. Survival status of each patient was further verified by cross checking with the Spanish National Death Index. During a total follow-up of 37608 person-years, 336 (10%) patients died. Annual death rate was 0.89% and standardized mortality ratio (SMR) 2.64 [95% confidence interval (CI) 2.3-3.0; P < 0.001]. Median age at death estimated by left-truncated Kaplan-Meier method was 75.1 years (95% CI 73-77). Survival was reduced compared with the general population whatever their level of complexity, repair status, or underlying CHD. Independent risk factors for excess mortality, including cyanosis, univentricular physiology, genetic disorders, ventricular dysfunction, residual haemodynamic lesions and acquired late complications, among others, were identified by left-truncated Cox regression model. SMR was 5.22 (95% CI 4.5-6.0; P< 0.001) and median age at death 55.6 years (95% CI 50-61) for 996 patients (30%) with at least one risk factor. In contrast, SMR was 1.14 (95% CI 0.91.5; P=0.19) and median age at death 83.7 years (95% CI 82-87) in 2315 patients (70%) with no risk factors. Conclusions Clinical parameters, such as anatomical features, haemodynamic sequelae, or acquired complications, were independent predictors of excess mortality in adults with CHD. Survival of individuals with no risk factors did not differ from the reference population.