It has been suggested in previous studies, that inflammatory bowel disease can induce hepatic vein thrombosis. However, the main weakness of those studies was the lack of extensive screening of prothrombotic factors. We report an unusual association of severe inflammatory bowel disease, hepatic vein thrombosis and latent platelet proliferation disorder. Early treatment with heparin and cyclosporin administered intravenously induce a remission of intestinal disease and total disappearance of hepatic vein thrombosis. Extensive screening excluded the classical causes of hepatic vein thrombosis, inherited coagulation disorders and latent polycythemia by culture of erythroid progenitors without added erythropoietin. However, using recent bone marrow culture conditions, we observed spontaneous colony formation of megakaryocyte progenitors revealing latent thrombocythemia. In summary, progress in the diagnosis of haemostasis disorders, will probably confirm that one or more additional predisposing prothrombotic factors are needed to the development of hepatic vein thrombosis in inflammatory bowel disease. This hypothesis could explain the scarcity of this complication in inflammatory bowel disease. Moreover, this case-report suggests that administration of heparin at the onset of the thrombosis may induce a complete regression of the thrombus in hepatic veins.