Objective: Although earlier a feared complication of congenital cardiac surgery, the incidence of heart-block and sinus node dysfunction has been lowered to 1-4% due to improved surgical techniques and better anatomical understanding of the cardiac conduction system. Development of feasible pacemaker technologies has further lowered mortality and morbidity. However, pacemaker implantation in paediatric patients is in itself associated with significant morbidity due to pacemaker system failure and replacement. The aim of the present study was to examine prognostic factors of mortality, failure of systems and timing of implantation after surgery in post-surgical pacemaker patients. Methods: We carried out a historical prospective follow-up analysis of all patients (age less than 18 years) who underwent pacemaker implantation due to post-surgical heart-block or sinus node dysfunction in the period 1981-2002 at our institution. Data was extracted from the Danish Pacemaker Register and hospital records. Kaplan-Meier survival time estimates and Cox proportional hazards analysis (Relative Risk, RR) were used to identify prognostic factors. Results: High RACHS score (RR, 16.57), low age at implantation (RR, 0.22), low age at operation (RR, 0.06) and epicardial lead (RR, 0.18) were significant predictors for early mortality. Similarly, high RACHS score (RR, 4.84), low age at implantation (RR, 0.32), low age operation (RR, 0.38) and epicardial lead (RR, 0.40) were significant predictors failure of 1st pacemaker system. Conclusions: We identified a number of prognostic factors of patient mortality and failure of systems. One factor, high RACHS score, was previously shown to predict mortality and length of ICU stay in paediatric cardiac surgery; however, this study is the first to show a correlation between RACHS score and mortality as well as failure of pacemaker systems. This may have future implications for preoperative risk stratification of patients and counselling of parents to patients with congenital heart disease.