Background: The Fontan operation (FO) has evolved and many centers have demonstrated improved results relative to those from earlier eras. We report a single-institution experience over three decades, describing the outcomes and evaluating risk factors. Methods: Successive patients undergoing primary FO were divided into era I (1984-1994), era II (1995-2004), and era III (2005-2014). Clinical and operative notes were reviewed for demographic, anatomic, and procedure details. End points included early and late mortality and a composite of death, heart transplantation (HTX), or Fontan takedown. Results: A total of 420 patients underwent 18 atriopulmonary connections, 82 lateral tunnels (LT), and 320 extracardiac conduit (EC) Fontan procedures. Forty-six (11%) patients died; early and late mortality were 7.9% and 3.1%, respectively. Eight (1.9%) patients underwent HTX, 11 (2.6%) underwent Fontan conversion to EC, and 1 (0.2%) takedown of EC to bidirectional Glenn shunt. Prevalence of concomitant valve surgery ( P < .001) and pulmonary artery reconstruction ( P < .001) differed over the eras. Preoperative valve regurgitation was associated with likelihood of early mortality (odds ratio [OR] = 3.5, P = .002). Embolic events (OR = 1.9, P = .047), preoperative valve regurgitation (OR = 2.3, P = .029), diagnosis of unbalanced atrioventricular canal defect (OR = 1.14, P = .03), and concomitant valve replacement (OR = 6.9, P = .001) during the FO were associated with increased risk of the composite end point (death, HTX, or takedown). Conclusion: Technical modifications did not result in improved results across eras, due in part to more liberal indications for surgery in the recent years. Valve regurgitation, unbalanced atrioventricular canal, embolic events, or concomitant valve replacement were associated with FO failure.