To study the epidemiology of hantavirus infections in Austria, 1215 humans and 596 rodents of different species were tested for the presence of antibodies against Puumala and Hantaan virus. Direct virus identification by polymerase chain reaction in lung tissue of serologically positive rodents was performed to verify antibody results and to determine the genetic identity of viral RNA by phylogenetic analysis of a part of the hantavirus M segment. For 32 of the 37 cases of nephropathia epidemica diagnosed in Austria, the location where transmission took place could be traced to specific areas in the Austrian federal states of Carinthia and Styria. The overall seroprevalence in humans was 1.2% and ranged from 0.02% in Villach, Carinthia, to 0.8% in Korneuburg, Lower Austria, and 1.8% in Wolfsberg, Carinthia. Virus RNA could be amplified from three Clethrionomys glareolus voles collected in Klippitztörl, Carinthia, and from one collected in Ernstbrunn, Lower Austria. The sequences were all identified as Puumala virus by phylogenetic analysis and were found to be most closely related to the western European Puumala viruses from Germany and France. No evidence of the existence of Hantaan-like infections and viruses in Austria was found.