Conserving healthy wildlife populations requires an understanding of the factors which affect infection patterns. Stress, particularly if chronic or severe, may impair immune function and influence disease susceptibility and severity. This is particularly concerning in endangered species which may be more susceptible to the impacts of stress and disease for various reasons including low abundance limiting the population’s capacity to adapt and restricted range preventing dispersal away from stressors. In this multidisciplinary study, we used parallel stress physiology (faecal glucocorticoid metabolites), immunology (phagocytosis flow cytometry) and parasitology analyses (faecal flotation for intestinal helminths, immunofluorescence for Giardia and Cryptosporidium spp. and PCR for Trypanosoma spp. ofhaemoparasites) to investigate the relationship between stress, immunocompetence and infection in a critically endangered marsupial, the woylie or brush-tailed bettong (Bettongia penicillata). Woylies, once numerous and widespread across Australia, have declined by 90% since the 1990s and only two indigenous populations remain in the southwest corner of Western Australia. It has been suggested that stress, immunosuppression and infectious disease may be acting synergistically to contribute to the species’ decline. We predict that woylies experiencing a higher level of physiological stress will demonstrate compromised immune function and higher prevalence and intensity of parasite infection. We explore implications for the future of the species and wildlife conservation.