A point mutation in the factor V Leiden gene is the most common hereditary thrombophilic state and an important risk factor for Budd-Chiari syndrome. We report on a patient with Budd-Chiari syndrome secondary to factor V Leiden mutation, who underwent successful liver transplantation. Following liver transplantation, his thrombophilic state was corrected and he did not require anticoagulation therapy. There has been no recurrent venous thrombosis for 14 months after transplantation. Although his activated protein C sensitivity was normal, showing the normalization of protein C-factor V interaction, PCR analysis demonstrated that heterozygosity for factor V Leiden mutation was still present. We suggest checking resistance to activated protein C, rather than PCR analysis of factor V Leiden mutation in patients with Budd-Chiari syndrome after liver transplantation; the presence of the second does not effect clinical outcome.