This article summarizes the study design and organization of a multicenter, prospective randomized trial of extracranial-intracranial (EC-IC) bypass for treating adult patients with moyamoya disease who suffered episodes of intracranial bleeding. The Japan Adult Moyamoya Trial will determine whether the combination of EC-IC bypass with risk factor modifications affects the prognosis and the incidence of recurrent bleeding attacks. Direct bypass such as superficial temporal artery-middle cerebral artery anastomosis is essential and indirect bypass procedures alone such as encephalo-duro-arterio-synangiosis or encephalo-myo-synangiosis are not dealt with in this trial. Power calculations are based on an assumption of α=0.05 with an annual event rate of 8% significant morbidity and mortality per year in the non-surgical group and 4% in the surgical group. The study has an 80% rate of accuracy for detection of a 20% difference between the two groups in events in a 5-year follow up.