The Estonian stroke audit analysed the current status of the management of stroke in Estonian hospitals. The aim of the study was to evaluate the following Estonian Stroke Guidelines in the management of stroke to evaluate the quality of medical records and to compare the results with those of the previous stroke audit (2002–2003). Experts of the L. Puusepp Society of Neurologists and Neurosurgeons (ENNS) evaluated 400 medical records from 17 hospitals. The guidelines were followed adequately. Management of stroke was better in hospitals where patients were treated by neurologists. Shortcomings were the high proportion of unclear or incorrect diagnoses, and insufficient documentation in medical records. Compared to the previous audit, the diagnosing and treatment of stroke patients have improved, but there still exist shortcomings in the monitoring and treatment of physiologic parameters and in early rehabilitation of stroke. There is a need for a national stroke strategy. Proposals for improvement of quality of stroke management are presented.