Clinical significance of silent microbleeds is unknown in moyamoya disease. This study was aimed to clarify the incidence, locations, and longitudinal course. This prospective cohort study included 78 nontreated patients with moyamoya disease. The incidence and locations of silent microbleeds were evaluated on T2*-weighted MRI. MR examinations were repeated every 6 or 12 months during a mean follow-up period of 43.1 months. T2*-weighted MRI identified silent microbleeds in 17 (29.3%) of 58 adult patients with moyamoya disease, but in none of 20 pediatric patients. During follow-up periods, de novo silent microbleeds developed in 4 (6.9%) of 58 adult patients. Hemorrhagic stroke occurred in 4 patients (6.9%), all of who had silent microbleeds on initial examination. The presence of silent microbleeds was a significant predictor for subsequent hemorrhagic stroke in adult moyamoya disease (P<0.001). Careful and long-term follow-up of silent microbleeds would be essential to improve their outcome in adult patients with moyamoya disease.