This report describes a case of Budd-Chiari syndrome caused by latent polycythemia vera and factor V Leiden mutation. This syndrome usually occurs due to thrombosis of hepatic veins or membranous obstruction of inferior vena cava. The most common reasons for thrombosis are manifest polycythemia vera and the other prothrombotic conditions. Recently, latent polycythemia vera and factor V Leiden mutation have been reported in increasing frequency. In this report, we aimed to emphasize that all prothrombotic conditions must be evaluated while investigating the etiology of Budd-Chiari syndrome, including latent polycythemia vera and factor V Leiden mutation, and appropriate antithrombotic and surgical therapies must be performed without delay.