OBJECTIVE To determine whether atrial-based pacing prevents atrial arrhythmias in adults with congenital heart disease (CHD) compared with ventricular pacing. RESULTS All adult CHD patients from four participating centres with a permanent pacemaker were identified. Patients with permanent atrial arrhythmias at pacemaker implantation and patients who received a pacemaker for treatment of drug-refractory atrial arrhythmias were excluded. The final study population consisted of 211 patients (52% male, 36% complex CHD) who received a first pacemaker for sick sinus dysfunction (n = 82) or atrioventricular block (n = 129) at a median age of 24 years [interquartile range (IQR), 12-34]. A history of atrial arrhythmias at implantation was present in 49 patients (23%). Atrial-based pacing was the initial pacing mode in 139 patients (66%) while the others (34%) received ventricular pacing. During a median follow-up of 13 years (IQR, 7-21), 90 patients (43%) developed an atrial arrhythmia. Multivariate analysis demonstrated no significant effect of atrial-based pacing on subsequent atrial arrhythmias [hazard ratio (HR), 1.53; 95% confidence interval (CI), 0.91-2.56; P = 0.1]. Independent predictors of atrial arrhythmia were history of atrial arrhythmias (HR, 5.55; 95% CI, 3.47-8.89; P< 0.0001), older age (≥18 years) at pacemaker implantation (HR, 2.29; 95% CI, 1.29-4.04; P = 0.005), and complex CHD (HR, 1.57; 95% CI, 1.01-2.45; P = 0.04). CONCLUSIONS In contrast to the general population, atrial-based pacing was not associated with a lower incidence of atrial arrhythmia in adults with CHD.