Background: There are few contemporary epidemiological data on stroke for Central Europe. We performed a population-based study evaluating the incidence of stroke, stroke types, and ischemic stroke (IS) subtypes in Brno, the second biggest city in the Czech Republic (CR). Methods: Using the National Registry of Hospitalized Patients, and hospital databases, we identified all patients hospitalized with a stroke diagnosis in Brno hospitals in 2011. For Brno residents with validated stroke diagnosis, we calculated (a) the overall incidence of hospitalized stroke, (b) incidence rates for IS, subarachnoid hemorrhage (SAH) and intracerebral hemorrhage (ICH), and (c) incidence rates for IS subtypes. We calculated the average annual age- and sex-standardized incidence (European Standard Population and World Health Organization), to compare our results with other studies. Results: The overall crude incidence of stroke in Brno was 213/100,000 population. The incidence of stroke for stroke types were as follows: SAH, 6.9; ICH, 26.4; and IS, 180 cases per 100,000 population, respectively. The WHO-standardized annual stroke incidence was 107 for all strokes and 88 for IS, 14.4 for ICH, and 5 for SAH. For IS subtypes, the WHO-standardized incidence was large artery atherosclerosis 25.8, cardioembolism 27.8, lacunar 21.6, other determined etiology 6.2, and undetermined etiology 6.5 cases per 100,000 population. Conclusions: The stroke incidence is lower than that previously reported for the CR and Eastern Europe probably reflecting socioeconomic changes in post-communistic countries in the region. These findings could contribute to stroke prevention strategies and influence health policies.