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Background: The Fontan operation provides lifesaving palliation for individuals with single ventricle (SV) physiology. Given recent concerns of systemic disease (SD) for patients with a Fontan circulation, we sought to (1) quantify the increase in SD incidence associated with the Fontan circulation; (2) identify the risk factor of SD; (3) assess the association between SD and mortality in patients with a Fontan circulation., Methods: A matched retrospective cohort study design was adopted. From the Quebec Congenital Heart Disease (CHD) Database with up to 35 years of follow-up, patients who survived at least 30 days after the Fontan operation were identified. For each Fontan patient, patients with isolated ventricular septal defect (VSD) with the same sex and age were identified and 20 of them were randomly selected to form the control group. The presence of SD was defined as at least 1 hospitalization due to extra-cardiac complications including liver, respiratory, gastrointestinal or renal disease. Time-to-event analysis including Kaplan-Meier curve analysis and Cox proportional hazard models were conducted to assess the cumulative risk of SD, risk factors of SD, and the association between SD and 10-year mortality., Results: A total of 533 patients with Fontan circulation were identified and matched with 10,280 VSD patients. The cumulative probabilities of SD at 10- and 35-years follow-up were 59.02% and 89.66% in patients with a Fontan circulation, 4 to 7 times of the probabilities in VSD patients (8.68% and 23.34%, respectively; LogRank tests P < .0001). In Fontan patients, cardiovascular complications were associated with a 4.1-fold (95% CI: 3.52-4.88) higher risk of developing SD. Multisystem disease (>1 extra-cardiac organ affected) disease was associated with a 3.38-fold (95%CI: 1.73-6.60) increase in 10-year mortality risk when comparing to the absence of SD., Conclusions: This population-based study demonstrated that patients with a Fontan circulation had increased risk of SD, which in turn led to higher risk of mortality. These findings underscore the need for more systematic surveillance of cardiac and systemic disease for patients after Fontan operation., Competing Interests: Conflict of interest None reported., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)