This study was undertaken to examine the impact that prenatal diagnosis of congenital heart disease (CHD) has on birth and early neonatal outcomes. The prevalence of prenatally diagnosed CHD has risen over the past decade, but the effect that prenatal diagnosis of CHD has on peripartum decisions remains unclear. No consensus exists on the effect of prenatal diagnosis on neonatal outcomes. Between January 2004 and July 2009, a retrospective chart review of all neonates with CHD admitted to our institution’s neonatal intensive care unit was conducted. Obstetric and postnatal variables were collected. Among the 993 subjects, 678 (68.3 %) had a prenatal diagnosis. A prenatal diagnosis increased the odds of a scheduled delivery [odds ratio (OR) 4.1, 95 % confidence interval (CI) 3.0–5.6] and induction of labor (OR 11.5, 95 % CI 6.6–20.1). Prenatal diagnosis was not significantly associated with cesarean delivery when control was used for maternal age, multiple gestation, and presence of extracardiac anomaly. Mean gestational age had no impact on prenatal diagnosis, but prenatal diagnosis was associated with increased odds of delivery before a gestational age of 39 weeks (OR 1.5, 95 % CI 1.1–1.9) and decreased odds of preoperative intubation (OR 0.5, 95 % CI 0.3–0.6). Prenatal diagnosis did not have an impact on preoperative or predischarge mortality. Prenatal diagnosis was associated with increased odds of a scheduled delivery, birth before a gestational age of 39 weeks, and a decreased need for invasive respiratory support. Prenatal diagnosis of CHD was not associated with preoperative or predischarge mortality.