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Background Aortic atresia and mitral atresia are predictors of adverse events in early life in patients with hypoplastic left heart syndrome, but it is unclear whether late outcomes are also affected, and whether this impact is related to a small hypertrophied left ventricle (LV) that impairs right ventricle (RV) function. Methods Thirty patients with hypoplastic left heart syndrome surviving with a Fontan procedure were identified. Follow-up echocardiograms were available at birth, before the Fontan procedure, and several years after. Mean follow-up time was 10.9 ± 3.1 years. Measurements included interventricular septum thickness and ventricular length. The LV/RV length ratio at birth was calculated, and its impact on later LV and septal growth was examined. The primary endpoint was a composite of death, transplantation, or Fontan takedown. Results A cutoff LV/RV length ratio of 0.55 was identified: length ratio was 0.55 or less in group A (18 patients) and more than 0.55 in group B (12 patients) The LV/RV length ratio and interventricular septum thickness decreased over time in group A while remaining static in group B. The LV length at birth did not affect late adverse outcomes (hazard ratio 2.7, 95% confidence interval: 0.31 to 23.4, p = 0.37), whereas aortic atresia and mitral atresia were the most potent predictors of death or transplantation or takedown (hazard ratio 8.5, 95% confidence interval: 1.2 to 57.7, p = 0.029). Conclusions Patients with aortic atresia and mitral atresia have worse outcomes even after Fontan independently of a small, thick, hypertrophied LV. The most severely hypoplastic LVs do not grow proportionally as much as the RVs.