Introduction Longitudinal sampling of biomaterials using standardised and appropriate methods can elucidate complex questions of disease ecology in the light of the historic characteristics of healthy populations. Wildlife may play an important role as a reservoir of zoonotic diseases and emerging infectious diseases. In 2000, the wildlife management goals of the National Park Hohe Tauern, Austria, were elaborated and the dynamic natural development of wildlife was declared as, a major goal. The aim of this study was to establish a monitoring programme in the Carinthian part of the National Park in order to survey the health status of free-ranging ungulates: chamois (Rupicapra r. rupicapra), red deer (Cervus elaphus hippelaphus), roe deer (Capreolus c. capreolus) and ibex (Capra i. ibex). Methods and Results Park wardens and co-workers were trained in appropriate biomaterial collection methods from harvested animals and in detecting major pathological changes. Emphasis was put on the recognition of potential zoonoses. Tissues from various organs of 122 animals were collected using a defined necropsy protocol and fixed in formaldehyde for subsequent histological examination. Additionally, faecal samples were obtained from 24 animals. Most frequently, histopathological changes were noted in the respiratory system and the gastro-intestinal tract. They were often associated with parasitic infections. In red deer, Dictyocaulus sp. and Protostrongylidae sp. were identified in the observed lung lesions, whereas in the other species, lung lesions were mainly associated with Protostrongylidae sp. In the winter 2003/2004, 5 cases of suppurative bronchopneumonia occurred in chamois. Other frequent histopathological findings included sarcosporidiosis in the heart, sarcoptic mange in the skin, cholangiohepatitis and pyelitis. The lesions are described and discussed with special attention to the species differences, their zoonotic potential, further examinations and the parasitological results. Conclusion Histopathological examinations can only give a limited insight into disease occurrence and dynamics. Nevertheless histopathology is an essential tool in surveying the health status of free-ranging ungulates. This is especially true when combined with additional investigations such as serology and microbiological methods. A great challenge in establishing a successful monitoring programme is to convince the involved persons of the value of collecting biomaterials and to train them in appropriate collection and storage methods. This study provides essential baseline data on the ungulates in the Hohe Tauern National Park which will be essential when evaluating potential disease outbreaks in the future.