Budd-Chiari syndrome and membranous obstruction of the inferior vena cava frequently result in the development of mostly benign hepatic lesions. In cases of membranous obstruction of the inferior vena cava, which is prevalent mostly in the East, these lesions often progress to hepatocellular carcinoma. In contrast, malignant transformation has not yet been recognised in patients with isolated hepatic vein thrombosis. We report the case of a 37-year-old male Caucasian who presented with acute Budd-Chiari syndrome without involvement of the inferior vena cava. Despite porto-caval shunting, a hepatocellular carcinoma developed within several months. Three hepatic lesions were treated by radiofrequency thermal ablation until liver transplantation was performed. This report emphasises the possibility of malignant transformation of regenerative nodules in patients with disturbed hepatic perfusion in general. Physicians must be aware of this when assessing regenerative nodules, especially as no unambiguous predictors for the development of hepatocellular carcinoma have been identified so far.