The objective of this study was to explore the effect of insurance type on mortality for congenital heart surgery. We performed a population-based retrospective cohort study using hospital discharge abstract data from five states in 1992 and 1996. The outcome measure was risk-adjusted in-hospital mortality. Cases of pediatric congenital heart surgery were identified and placed into six risk categories using the Risk Adjustment in Congenital Heart Surgery method. Multivariate analyses were used to determine the effect of insurance type on risk-adjusted mortality; regional effects were explored. Using standardized mortality ratios, institutions were grouped by outcome; within and between group differences were examined. Of 11,636 cases, 9656 (83%) were placed in a risk group for analysis. In 1996, children with Medicaid had a higher risk of death than those with commercial or managed care in both unadjusted (p = 0.002) and adjusted (p < 0.001) analyses. Overall mortality rates decreased between 1992 and 1996 (p = 0.001). However, improvement was not consistent among insurance groups. Differences were present within and between low, average, and high-mortality hospitals, suggesting that the adverse effect of Medicaid may be due to both differential referral and other differences in care among patients treated at similar institutions. Children with Medicaid insurance have a higher risk of dying after congenital heart surgery than those with commercial and some managed care insurance. Barriers to access go beyond differences in referral patterns.