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Background Budd-Chiari syndrome (BCS) is a rare heterogeneous liver disease characterized by obstruction of the hepatic venous outflow tract. The incidence of BCS is so low that it is difficult to detect in general practice and difficult to include within the scope of routine diagnosis. The clinical manifestations of BCS are not specific; hence, BCS tends to be misdiagnosed. Case summary We report the case of a 33-year-old Chinese woman who presented with progressive distension in the upper abdomen. She was initially misdiagnosed with liver cirrhosis (LC) due to abnormalities on an upper abdominal computed tomography scan. Although she was taking standard anti-cirrhosis therapy, her symptoms did not improve. Magnetic resonance imaging showed caudate lobe hypertrophy; and dilated lumbar and hemiazygos veins. Venography revealed membranous obstruction of the inferior vena cava owing to congenital vascular malformation. A definitive diagnosis of BCS was made. Balloon angioplasty was performed to recanalize the obstructed inferior vena cava and the patient's symptoms were completely resolved. Conclusion BCS lacks specific clinical features and can eventually lead to LC. Clinicians and radiologists must carefully differentiate BCS from LC. Correct diagnosis and timely treatment are vital to the patient's health.