This study aimed to characterize the impact of race on morbidity and mortality after hospital discharge from neonatal congenital heart surgery. A retrospective chart review examined all the neonates who underwent neonatal heart surgery from January 2005 to June 2006 at The Children’s Hospital of Philadelphia. After risk adjustment for the type of surgery using the Risk Adjustment for Congenital Heart Surgery 1 (RACHS-1) method, the association of race with mortality after hospital discharge was assessed using Fisher’s exact test for statistical analysis. A cross-sectional telephone survey of surviving patients also was conducted to examine the association of race and social factors with adverse events (admissions or reinterventions). Mortality status was known for 201 of the 217 patients screened. The mortality rate after discharge was 8 %, with a higher mortality rate for nonwhite patients (14 %) than for white patients (4 %) (p = 0.01). After risk adjustment, this effect was limited to nonwhite patients with less complex heart disease (RACHS-1 categories 1–3; 17 vs 2 %, respectively; p = 0.01). The survey completion rate was 54 %. In this cohort, race also was independently associated with adverse events among patients with less complex heart disease (RACHS-1 categories 1–3; nonwhites 53 % vs whites 25 %; p = 0.046). Among the patients with less complex heart disease, the nonwhite patients had a significantly higher risk of morbidity and mortality after hospital discharge than the white patients.