Purpose. Cholestatic liver injury is associated with a high production of free radicals. The pathogenesis of liver injury in biliary atresia (BA) patients is largely undefined. The goal of the present study was to clarify the oxidative damage and the changes in antioxidant enzyme activities that occur during the development of BA and after liver transplantation (LT). Methods. We enrolled BA patients and control subjects and collected their clinical information. The activities of antioxidant enzymes in BA patients before LT (BA group) and after LT (LT group) were analyzed. Results. The number of mitochondrial DNA copies had increased in the LT group compared with the BA group. Similarly, the activity of glutathione peroxidase had increased in the LT group compared with the BA group. The level of glutathione was higher in the LT group than in the BA group. Malondialdehyde levels were decreased in the LT group compared with the BA group. Conclusions. These data indicate that LT is associated with increased antioxidant enzyme activities and decreased malondialdehyde levels in BA patients. The manipulation of mitochondria-associated antioxidative activity might be an important future management strategy for BA.