The early postnatal course for a newborn with critical congenital heart disease (CHD) can be negatively impacted if diagnosis is delayed. Despite this, there continues to be inconsistent evidence regarding potential benefits associated with prenatal diagnosis (PND) in neonates who undergo cardiac surgery. The objective of this study was to better define the impact of a PND on pre-operative morbidity by utilizing a large clinical database. Neonates (< 30 days) undergoing heart surgery from 2010 to 2014 and entered in the Society of Thoracic Surgeons Congenital Heart Surgery Database (STS-CHSD) were included. Multivariable logistic regression was used to evaluate the association between PND and a composite measure including nine major pre-operative risk factors. Co-variates were included to adjust for important patient characteristics (e.g., weight-for-age z-score, genetic syndromes, prematurity), case complexity, and center effects. Centers and patients with excess missing data for relevant co-variates were excluded. Included were 12,899 neonates undergoing surgery at 112 centers. Major pre-operative risk factors were present in 34% overall. By univariate analysis, PND was associated with a lower overall prevalence of major pre-operative risk factors. After adjusting for potential confounders, major pre-operative risk factors were less prevalent among neonates with PND compared to neonates without PND (adjusted OR 0.62, 95% CI 0.57-0.68, p < 0.001). A sensitivity analysis excluding neonates with genetic syndromes, non-cardiac anatomic abnormalities, and prematurity demonstrated similar findings (adjusted OR 0.55, 95% CI 0.49-0.61, p < 0.0001). Among neonates with CHD, prenatal diagnosis is associated with significantly lower rates of pre-operative risk factors for cardiac surgery. Further studies are needed to define association of these pre-operative benefits of a PND with longer term clinical outcomes.