It has been reported that the long-term outcome for children with metabolic disorders after liver transplantation (LT) is excellent. However, there are several reports citing LT patients with metabolic disorders developing liver dysfunction early after LT. We examined the pathogenesis of liver dysfunction observed after LT in recipients with metabolic disorders at the National Center for Child Health and Development. Of 106 children (aged <18years) with metabolic disorders who underwent LT at our center, 36 patients who underwent liver biopsy within 60days after LT were enrolled. The underlying diseases were urea cycle disorders (14 patients), methylmalonic acidemia (11 cases), Wilson's disease (3 patients), mitochondrial hepatopathy (3 patients), and others (5 patients). The median age was 1year 2months at LT. The reasons for biopsy were liver dysfunction (31 patients) and ascites (5 patients). The main findings of graft liver biopsy were diffuse steatosis (21 patients), rejection (8 patients), infection (3 patients), and others (4 patients). Of 21 patients who received graft biopsy showing steatosis, all the donor livers originally showed no steatosis or only mild steatosis. The liver function improved immediately after biopsy in 18 of 21 patients that showed diffuse steatosis. The major cause of liver dysfunction after LT in recipients with metabolic disorders was steatosis and the risk of rejection was low. It is important to take a liver biopsy and examine the cause of liver dysfunction to avoid administration of excess immunosuppressant, and select the right therapy for recipients with metabolic disorders.