Since 2003 the Austrian Stroke-Unit-Registry has been administered by the Gesundheit Osterreich GmbH. A total of 26 out of the 32 existing Stroke Units in Austria take part in the project, financed by the Federal Ministry of Health and accompanied by a steering group. This paper provides a description of the objectives, organisation, methodology and the data set of the registry. The main objective of the registry is quality assurance and quality improvement of stroke-treatment in stroke units. Therefore, the participating stroke units document their cases using a web-based database. The data are discussed in the steering group and the stroke units get feedback in terms of benchmarking-graphs. The data set follows a modular approach and contains information about stroke, transport, admission to the hospital, stroke unit discharge and the 3-month follow-up. Between 2003 and 2007 about 27,000 cases (containing about 20,000 strokes) were documented in the registry.