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To identify the prevalence, causes, risk factors, and outcomes associated with extubation failure following first stage single ventricle reconstruction surgery.Retrospective cohort analysis of neonates who underwent a first stage single ventricle reconstruction operation. Extubation failure was defined as endotracheal reintubation within 48 hours of first extubation attempt.The Royal Children’s Hospital, Melbourne.Data were collected for all infants who underwent a Norwood or Damus-Kaye-Stansel procedure between 2005 and 2014 at our institution.None.Extubation failure occurred in 23 of 137 neonates (16.8%; 95% CI, 11.0–24.1%) who underwent a trial of extubation. Overall, 42 patients (30.7%) were extubated to room air, 88 (64.2%) to nasal continuous positive airway pressure, and seven (5.1%) to high-flow nasal cannulae, though there was no major difference in extubation failure rates between these three groups (p = 0.37). The median time to reintubation was 16.7 hours (interquartile range, 3.2–35.2), and male infants failed extubation more frequently (63.2% vs 87.0%; p = 0.02), although age, gestation, weight, cardiac diagnosis (hypoplastic left heart syndrome vs other single ventricle conditions), shunt type (modified Blalock-Taussig vs right ventricle-pulmonary artery shunt), intraoperative perfusion times, preextubation mechanical ventilation duration, preextubation acid-base status, and postoperative fluid balance were not related to extubation outcome. Infants who failed extubation had a higher intensive care mortality (19.4% vs 3.5%; p = 0.03) and in-hospital mortality (30.4% vs 6.1%; p < 0.001).There is a high prevalence of extubation failure following first stage single ventricle reconstruction, and this is associated with considerably worse patient outcomes. The high prevalence and also the wide variation in rates of extubation failure in reported literature provide with an opportunity for implementation of quality assurance activities to minimize this complication and improve outcomes.