Background This study aimed to evaluate the impact of prenatal diagnosis on parental understanding of congenital heart disease (CHD) in newborns. Methods Consenting parents of newborns with CHD answered questions about the cardiac lesion, surgical repair, follow-up management, risk for CHD in future children, and maternal education before neonatal intensive care unit (NICU) discharge. A total understanding score was calculated (0–10) as the sum of five subscores: physician score, CHD score, surgery score, follow-up score, and reproduction score. Each category was scored as 0 (none correct), 1 (some correct), or 2 (all correct). The prenatal and postnatal diagnoses scores were compared. Results From June 2006 to November 2006, 50 families completed the questionnaire. Of these 50 families, 26 reported a prenatal diagnosis. The mean infant age when the parents were approached was 17.3 ± 13.3 days. The summary understanding score for the entire group was 6.3 ± 2.4 of 10. Multivariate regression analysis demonstrated a difference in scores between prenatal and postnatal diagnosis groups (p = 0.02) when control was used for maternal education. Prenatal diagnosis and maternal education (p < 0.01) had independent effects on the score. Conclusion Prenatal diagnosis increases parental understanding of neonatal CHD. Nevertheless, parental understanding remains suboptimal.