We studied pediatric liver transplantation for metabolic disease in a large national cohort to determine whether smaller studies suggesting a survival advantage for these recipients could be corroborated. We also hoped to determine whether higher survival rates in recipients with metabolic disease are associated with lack of structural liver disease, and to evaluate these recipients' risk factors for mortality. Data from the Scientific Registry of Transplant Recipients were used to analyze nationwide results (1990-99) of pediatric liver transplantation for patients with biliary atresia and metabolic disease. Adjusted patient survival rates for children with metabolic disease at 1 and 5 years were 94% and 92%, respectively, - significantly higher than for recipients with biliary atresia (90% and 86%) (p = 0.008). Cox regression models identified recipient black race [relative risk (RR) = 5.1] and simultaneous transplantation of other organs (RR = 3.2) as significant risk factors for mortality in the metabolic group. Adjusted survival rates for metabolic patients with structural and nonstructural liver diseases were similar to each other at both 1 and 5 years. Children with metabolic disease had significantly higher adjusted short- and long-term post-transplant survival rates than those with biliary atresia. Structural disease was not a risk factor for worse outcomes.