The European grayling Thymallus thymallus is widely distributed in Austria, occurring in all eight rural provinces. However, in recent years, an increasing number of studies report severe declines in population sizes. Since 1997, the grayling has had the status of an endangered species in Austria. In 1997 the multidisciplinary research programme ‘Local Adaptation, Threat, and Conservation of European Grayling’ has carried out three projects in Upper Austria, Salzburg, and Carinthia. Research has included repeated electro-fishing in selected stretches of eight rivers and the collection of data on habitat characteristics, fish species composition, population abundance and size distribution, growth and body condition, as well reproductive timing, and migratory activities of grayling. Furthermore, genetic and morphological variation among grayling populations has been studied as well as the number, habitat use and feeding activity of cormorants. Evidence is provided for the existence of distinct negative effects caused by single factors or combinations of factors on grayling stocks in each of the river stretches studied.