Among infants with single ventricle congenital heart disease (SVD) requiring Stage I palliation (S1P), the impact of prenatal diagnosis (PD) on outcomes has been variably characterized. We investigated the impact of PD in a large multi-center cohort of survivors of S1P in the National Pediatric Cardiology Quality Improvement Collaborative (NPCQIC) registry. Retrospective analysis of demographic and outcomes data among infants enrolled in the NPCQIC database; eligibility includes SVD requiring S1P and survival to discharge. From 43 contributing surgical centers, 591 infants had data available through time of BDG (519) or interstage death (55). Median gestational age was 39 weeks (31–46), and 66 % had variants of hypoplastic left heart syndrome. PD was made in 445 (75 %), with significant variation by center (p = 0.004). While infants with PD had slightly lower gestational age at birth (p < 0.001), there were no differences in birth weight, the presence of major syndromes or other organ system anomalies. Those without PD were more likely to have atrioventricular valve regurgitation (p = .002), ventricular dysfunction (p = 0.06), and pre-operative risk factors including acidosis (p < 0.001), renal insufficiency (p = 0.007), and shock (p = 0.05). Post-operative ventilation was shorter in the PD group (9 vs. 12 d, p = 0.002). Other early post-operative outcomes, interstage course, and outcomes at BDG were similar between groups. In a large cohort of infants with SVD surviving to hospital discharge after S1P, PD showed significant inter-site variation and was associated with improved pre-operative status and shorter duration of mechanical ventilation. The significance of such associations merits further study.