Background and Purpose— Previous studies have shown regional and temporal variations in epidemiological features of moyamoya disease, but population-based studies in regions other than Japan are limited. We investigated the incidence and patients characteristics of moyamoya disease during 12 years in Taiwan using claims databases of a universal health insurance system. Methods— From the inpatient databases of the Taiwan National Health Insurance program, we identified subjects who had an initial hospitalization with moyamoya disease and had been underwent cerebral angiography as incidence cases during 2000 to 2011. The incidence and the patient characteristics were described by age and time periods of the hospitalization. Results— During the 12-year period, 422 patients were identified, representing an annual incidence of 0.15 per 100 000 person-years. Adults exhibited an upward trend in incidence with an incidence rate ratio of 1.74 (95% confidence interval [1.17–2.58]) in years 2010 to 2011 comparing with years 2000 to 2001. However, children had a decreased incidence except a slightly increase in the last 2 years. Compared with patients hospitalized during 2000 to 2005, patients identified during 2006 to 2011 had greater women-to-men ratio (1.7 versus 1.1, P =0.048). Children were more likely to have comorbid epilepsy than were adult patients (25.0% versus 3.4%, P =0.002). Hemorrhagic stroke was rare among pediatric patients but presented more frequently in adults. However, ischemic stroke was more prevalent in both groups. Conclusions— The incidence of moyamoya disease has increased in adults but not in children from 2000 to 2011 in Taiwan. Sex ratio and comorbid conditions differed by age and study period.