Background: Of the children with Down syndrome 40–50% have cardiac defects and the majority of these cardiac defects are amenable to biventricular repair. The outcome of single ventricle palliation is improving; nonetheless, there are limited data on Down syndrome patients with associated high-risk factors undergoing single ventricle palliation. Our aim was to study the outcomes of children with Down syndrome and high-risk factors on the single ventricle palliation pathway. Methods: A retrospective study on all patients with Down syndrome on the single ventricle palliation pathway from 2005 until 2011 was conducted. Operative, clinical, echocardiographic, haemodynamic data, and follow-up data were reviewed. Results: A total of 310 patients underwent at least one single ventricle surgical intervention. Of those, eight patients had Down syndrome, five of which had associated risk factors – low birth weight, high pulmonary vascular resistance, pulmonary vein stenosis, significant atrioventricular valve regurgitation, and extracardiac anomalies. Mortality in the high-risk group was 80% (4/5), compared with 33% (1/3) in the non-high-risk patients. Overall, after a median follow-up period of 138 days (8–576 days), only 37.5% (3/8) of patients were alive. Conclusion: Despite many improvements in the care of single ventricle patients, the fate of those with Down syndrome and associated high-risk factors remains poor. Further multicentre longer-term studies are needed to validate and quantify the cumulative effects of negative prognostic factors in this complex group of patients.