This study evaluate the effects of the Stroke Unit (SU) in Croatia by comparing the in-hospital case fatality rate in the period before (1995-2000) and after (2001-2006) the implementation of SU and to compare the prevalence of risk factors, such as hypertension, diabetes mellitus (DM), atrial fibrillation (AF) and ischemic heart disease (IHD) among the patients who died. The study was conducted in twelve-year period during which 10,901 stroke patients were admitted to hospital and 1818 of them died. The endpoints were in-hospital case fatality rate and prevalence of risk factors among the patients who died. Before the SU period the case fatality rate was 20.1%, whereas afterwards it decreased significantly to 12.8% (p < 0.001). The relative risk (RR) was 1.57, while the estimate of the odds ratio (OR) showed a 71% increase in chances of death in the pre-SU period. The prevalence of DM, IHD and AF increased significantly, while hypertension was the only risk factor which significantly decreased (p < 0.001). The results showed that the implementation of SU care is associated with a significant reduction of in-hospital case fatality rate of acute stroke patients which strongly suggests that development of the SU network in Croatia should be given priority in the health management.