Our objective was to assess risk-adjusted racial and ethnic disparities in mortality following congenital heart surgery. We studied 8483 congenital heart surgical cases from the Kids’ Inpatient Database 2000. Black sub-analysis was performed using predetermined regional categories. For our Hispanic sub-analyses, we categorized Hispanics into state groups according to a state’s predominant Hispanic group: West (Mexican-American), Southeast (Cuban-American), Northeast (Puerto Rican), and Mixed/Heterogeneous. Risk adjustment was performed using the Risk Adjustment for Congenital Heart Surgery method. Multivariate analyses assessed the effect of race/ethnicity and Hispanic state group on mortality and explored the effects of gender, income, insurance type, and region. Black children had a higher risk for death than Whites odds ratio (OR), [1.65; p = 0.003]. Hispanics and the Cuban-American state group showed a trend toward a higher death risk (Hispanic: OR, 1.24; p = 0.16; Southeast Cuban-American: OR 1.55; p = 0.08). Disparities were not influenced by insurance. Among Blacks, disparities were greatest in the Northeast region (OR, 2.25; p = 0.007). After adjusting for gender, income, and region, Blacks (OR, 1.76; p = 0.002) and Hispanics (OR, 1.34; p = 0.05) had a higher death risk. Racial and ethnic disparities in risk-adjusted mortality following congenital heart disease exist for Blacks and Hispanics. These disparities are not due to insurance but are partially explained by gender and region.