The highly pathogenic avian influenza (HPAI) epidemic throughout Europe required submission of numerous wild birds to diagnostic institutes for investigation. From October 2005 to late 2006, the Austrian Reference Laboratory for Avian Influenza at the AGES received about 5,000 wild bird carcasses for examination and H5N1 testing. A total of 400 carcasses including 369 wild birds were processed for further pathomorphological investigations after having been tested for HPAI by real time RT-PCR. Real time RT-PCR revealed that all investigated birds tested negative for the influenza A viral genome. Furthermore, routine histopathology on formaldehyde-fixed and paraffin-embedded tissue samples and HE staining were performed. Special staining was applied to some samples to confirm any suspected changes. The pathomorphological findings were classified into the following main categories: Organic changes: inflammatory changes: hepatitis (219), enteritis (205), pneumonia (107), tracheitis (40), nephritis (17), myocarditis (9), serositis (7), meningoencephalitis (6), pancreatitis (5) and splenitis (4); degenerative changes: hepatic fatty degeneration (57) and tubulonephrosis (9); intra- and extracellular deposition: hepatic siderosis (114), pulmonary anthracosis (58), amyloidosis (15) and renal tubular concrements (4). General etiology: trauma (177), bacterial infection (89) (2 of which were diagnosed as mycobacteriosis, the rest unclassified), parasitic infestation (24, including protozoan  and metazoan  parasites), mycosis (8), starvation (43) and poisoning (2, suspicion of ethylene-glycol poisoning). In this study, trauma and starvation accounted for 60 % of the mortality; these can most likely be linked to the very cold weather conditions and possibly to the increased movements of birds in search of food. Pulmonary anthracosis seems to be an indicator of environmental pollution. No pathomorphological changes typical for lead poisoning were recorded. The detected infectious diseases caused by various pathogens played an important role in the wild bird mortalities. These diseases need to be considered for further detailed epidemiological analysis and study.