We here report a case of subacute Budd-Chiari syndrome (BCS) related to Factor V Leiden (FVL) mutation in the presence of visceral leishmaniasis. A 17-year-old man was admitted to hospital because of abdominal pain, pretibial edema and fever. The clinical picture of BCS had been developed within several months. BCS was diagnosed by radiographic examination. On DNA analysis, a heterozygote Arg506Gln mutation in the factor V gene was found. Histological examination of the bone marrow showed intracellular leishmania amastigotes. Despite appropriate treatment patient's clinical condition deteriorated rapidly and died with multiorgan failure. FVL mutation is the most common procoagulant disorder and account for many cases of BCS. This case report demonstrates that in addition to duration and severity of the disease accompanying conditions including infections are prognostically significant for the outcome of this potentially lethal disease.