A case of noncompaction of the ventricular myocardium in a 24-year-old man with Behçet's disease is reported. Transthoracic echocardiographic examination revealed two cardiac masses in the right atrium, pericardial fluid behind the right atrium and multiple muscular trabeculation in the apical part of the left ventricle. Subsequent transesophageal echocardiography clearly showed two thrombus formations in the right atrium and prominent ventricular trabeculations with deep intertrabecular recesses perfused from the ventricular cavity, which are characteristic findings of ventricular noncompaction. In addition, abdominopelvic computed tomography showed thrombus formation in the inferior vena cava and right iliac vein. These multiple thrombus formations were treated successfully with steroid, immunosuppressive and anticoagulant therapies. This is the first reported case of left ventricular noncompaction in association with Behçet's disease showing pericarditis and multiple thrombus formations in the right atrium, inferior vena cava and right iliac vein.