We present a 40-year-old female patient with epigastric pain, ascites, and progressive liver failure, caused by Budd-Chiari syndrome (BCS) with thrombotic occlusion of the right and middle hepatic veins. As underlying diseases, essential thrombocythemia and resistance to activated protein C (APC) due to heterozygote factor V Leiden were found. Initial therapy with heparin caused thrombocytopenia (HIT) type II culminating in thrombosis of the last patent left hepatic vein and further deterioration of liver function. The decision against a surgical shunt and liver transplantation by our surgeons on the basis of the risks involved, prompted us to insert a transjugular intrahepatic portosystemic stent-shunt (TIPS). There was no measurable flow signal in the doppler sonography of the portal vein presumably due to thrombosis. A further evaluation with magnetic resonance tomography and angiography was impossible due to movement artefacts. TIPS initially served as a diagnostic tool allowing direct angiography-diagnosed thrombosis of the portal vein, the superior mesenteric and the splenic vein respectively. However, insertion of the TIPS shunt and subsequent fragmentation led to an effective hepatic decompression and full recanalisation of the portal vein. In the present case TIPS simultaneously allowed the diagnosis of portal vein thrombosis and served as rescue therapy of complicated Budd-Chiari syndrome. The potential development of HIT type II should be kept in mind when heparin is given, especially to patients with thrombophilia.