Metabolic diseases are the second largest indication for LT in children after BA. There are limited data on the long-term post-transplant outcome in this unique group of patients. Therefore, our aim was to assess post-liver transplant outcomes and to evaluate risk factors for mortality and graft loss in children with metabolic disorders in comparison to those with non-metabolic diagnoses. We reviewed all patients enrolled in the SPLIT registry. Between 1995 and 2008, 446 of 2997 (14.9%) children enrolled in SPLIT underwent liver transplant for metabolic diseases. One-yr and five-yr patient survival for children with metabolic diseases was 94.6% and 88.9% and for those with other diseases 90.7% and 86.1% (log-rank p = 0.05), respectively. One-yr and five-yr graft survival for children with metabolic disorders was 90.8% and 83.8%, and for those with other diseases 85.4% and 78.0% (log-rank p = 0.005), respectively. Children with metabolic diseases were less likely to experience gastrointestinal complications (5.6% vs. 10.7%, p = 0.001), portal vein thrombosis (2.9% vs. 5.2%, p = 0.04), and reoperations within 30 days post-transplant (33.4% vs. 37.8%, p = 0.05) than those with other indications. In conclusion, children who underwent liver transplant for metabolic disease had similarly excellent patient survival as, and better graft survival than, those who received a liver allograft for other indications.