We studied the long-term survival and rejection episodes of paediatric heart transplant recipients. We included all paediatric patients (≤18 years) who underwent heart transplantation during 1991-2014 in Finland. Data were obtained retrospectively from a paediatric cardiac surgery database. Patient status was received from the Finnish population registry. All patients underwent yearly routine postoperative endomyocardial biopsies and coronary angiographies. Between 1991 and 2014, 68 heart transplantations were performed. The early mortality (<30 days after surgery) rate was 10% and follow-up coverage was 100%. The 10- and 15-year survival rates for all patients were 68% (95% confidence internal, CI, 56-80%) and 65% (95% CI 53-78%), respectively, including early mortality. The 1-year survival rate was 100% when excluding early operative mortality. Indications for heart transplantation were cardiomyopathy in 57% and cardiac malformations in 43% of patients, with similar long-term survival between the groups. During 23 years of follow-up, 43 patients (70%) had at least one rejection episode and 17 patients (29%) at least a grade 1 coronary artery vasculopathy finding. Patients with early rejection episodes (<3 months) had a higher incidence of late rejection episodes (P = 0.025). Older age at operation was a significant risk factor for the development of coronary artery vasculopathy (hazard ratio 1.1, 95% CI 1.0-1.3, P = 0.012). First-year survival was excellent. Asymptomatic rejection episodes were common among patients. Early rejection episodes are a risk factor for late rejection episodes and show a trend towards an increased risk of late death. Coronary artery vasculopathy remains a major challenge for late graft survival.