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Atrial pacing is indicated for sinus node dysfunction (SND) after Fontan surgery; preferred lead implantation technique is debated. We compare outcomes of transvenous (TV) and epicardial (Epi) atrial lead implants in this population.Retrospective review of Fontan patients undergoing atrial lead implant between 1992 and 2007. Demographics, lead performance data, and outcomes were analyzed.78 patients had 90 leads implanted: 25 via TV route and 65 via Epi route. Median follow-up was 1.6 years (TV) and 3.6 years (Epi). TV leads were implanted in older patients (23.1 vs 9.3 years, P < 0.001) and at longer intervals after Fontan (15.2 vs 4.9 years, P < 0.001). Pacing indication for most TV leads was SND, while Epi leads were also indicated for atrioventricular block. Acute complication rates were similar (8% TV vs 19% Epi, P = 0.23), but median hospital stay was shorter for TV (2 vs 5 days, P = 0.03). Thrombus was observed in five patients (two in TV; three in Epi), but no thromboembolic events were observed. Mean lead survival was similar (TV 9.9 vs Epi 7.8 years, P = NS). Energy threshold was lower at implant for TV leads (0.9 vs 2.2 μJ, P = 0.049), but similar at follow-up (1.2 vs 2.6 μJ, P = 0.35). Atrial sensing was unchanged over time for TV (2.2 to 2.1 mV, P = NS), but decreased for Epi (3.3 to 2.5 mV, P = 0.02).Compared to epicardial leads, transvenous atrial pacing leads may be placed in Fontan patients with lower procedural morbidity and equivalent expectation of lead performance and longevity.