This report describes a case of Abernethy malformation associated with hepatopulmonary syndrome, which was resolved after shunt ligation. The clinical course indicated that hepatopulmonary syndrome can develop in Abernethy malformation in which liver function and portal pressure is normal, and liver transplantation is not the exclusive therapy for hepatopulmonary syndrome. The levels of endotoxin and endothelin 1 in the shunt blood were high, whereas those of tumor necrosis factor alpha and interleukin-1beta were within reference range. Although pathogenesis of hepatopulmonary syndrome remains unknown, the findings in this case suggest that bacterial translocation as well as elevated endothelin 1 may play a causal role in development of hepatopulmonary syndrome.