For more than a decade, community groups, scientific organizations and government agencies have collaborated to repopulate the endangered western barred bandicoot (Perameles bougainville). While initially successful, the unexpected discovery of a papillomatosis and carcinomatosis syndrome in captive and wild populations of P. bougainville exposed a dearth of knowledge regarding their diseases. This dissertation addresses this issue through study of the clinical pathology, immunology, parasitology, and virology of P. bougainville. To facilitate the detection and understanding of diseases in P. bougainville, guidelines for interpreting haematology and clinical chemistry results were developed, including calculated species-specific reference intervals for plasma aspartate transaminase activity (20–283 U/L), haemoglobin (122-165 g/L), haematocrit (0.36-0.49 L/L), total leukocytes (2.9-14.9 x10^9/L), monocytes (0-0.6 x10^9/L), eosinophils (0-0.9 x10^9/L) and total protein (47-63 g/L) estimated by refractometry. P. bougainville immunoglobulin was also fractionated from plasma and inoculated into sheep to derive antiserum for serological screening assays. Arthropods, helminths and protozoa parasitic on P. bougainville were catalogued and Eimeria kanyana n. sp. was formally described. The pathogenic and zoonotic potential of bacteria detected in ticks parasitic on P. bougainville was also considered. The association between bandicoot papillomatosis carcinomatosis virus type 1 (BPCV1) and the western barred bandicoot papillomatosis and carcinomatosis syndrome was investigated using PCR, in situ hybridization and virus isolation. Optimized in situ hybridization techniques demonstrated BPCV1 DNA within keratinocyte and sebocyte nuclei, and BPCV1 mRNA within the cytoplasm. BPCV1 virions were isolated by ultracentrifugation and visualized with negative stain transmission electron microscopy revealing icosahedral, non-enveloped viral capsids ~47 nm in diameter, comparable to viruses classified within Papillomaviridae and Polyomaviridae. A novel virus, tentatively named bandicoot papillomatosis carcinomatosis virus type 2 (BPCV2) was discovered in papillomatous lesions from a southern brown bandicoot (Isoodon obesulus). It had a circular double-stranded DNA genome of 7277 bp, and encoded two papillomavirus-like structural proteins, L1 and L2, and two polyomavirus-like putative transforming proteins, large T antigen and small t antigen. DNA and RNA in situ hybridization confirmed the presence of BPCV2 nucleic acids within lesion biopsies. The discovery of the bandicoot papillomatosis carcinomatosis viruses has provoked reassessment of the established virus taxonomy paradigm, theories of virus-host co-speciation and bandicoot population management strategies.