Abstract Aim The central aim of this paper is to localize areas of endemism of the vascular plant flora in the Eastern Alps. Moreover, causes for location and limits of the areas of endemism are assessed. Location The study area includes the Eastern European Alps and adjacent lowland areas. Methods Analyses were based on 288 vascular plant taxa endemic to the study region, scored in 115 operational geographic units, which were predominantly mountain ranges. For each of these units, number of endemic taxa, range down weighted endemism, environmental variables, elevation of the last glacial maximum ice sheet, and elevation of the snowline during the last glacial maximum, were estimated. To evaluate the relationships between the geographical areas, the presence/absence matrix of endemics in areas was used to calculate phenograms and cladograms. Values from the range down weighted endemism superimposed on phenograms and cladograms were used to indicate areas of endemism. Linear regressions between richness in endemism and environmental as well as palaeo-environmental variables were used to infer causes of the observed patterns of endemism. Results The endemic taxa of the Eastern Alps show a very uneven distribution, the majority being confined to one or few mountain ranges. High levels of endemism are found in the southern, southeastern, easternmost, and northeastern Eastern Alps. Trees obtained from phenetic and cladistic methods were largely congruent. Seven areas of endemism were clearly delimited, all in regions that are regarded as glacial refugia. Two of them are located on siliceous, four on calcareous bedrock. Not all endemic taxa, however, grow in the areas of endemism. Therefore, enlargement areas are suggested. Linear regression showed a significant correlation between high endemism and low glacial ice cover, but not with other environmental variables. Main conclusions Vicariance resulting from Pleistocene glaciations is the most important factor causing distributional patterns of endemic plants and the formation of areas of endemism. Mapping values of weighted endemism onto trees facilitated delimitation and definition of the areas of endemism. Because of their strong dependence on siliceous bedrock and the resulting disjunct distributional patterns of some taxa in the Southern Alps, the inclusion of a few operational geographic units with high levels of endemism was not supported by the analyses. Despite post-vicariant dispersal that causes problems in analyses of areas of endemism, the circumscription of areas of endemism in the Eastern Alps was possible to a satisfactory extent. Other methodological approaches, however, which include concepts of post-vicariant dispersal and that allow overlap of areas of endemism would be highly useful.