Australian wildlife can be hosts to a variety of different infectious agents that are of significance to the wildlife themselves, or of significance to other animals or to people who are in contact with wildlife. Recently we have studied pathogens in a range of different wildlife species, particularly native birds and marsupials. Many of these studies are in collaboration with veterinarians from Zoos Victoria, or with other wildlife veterinarians. Some of our most recent work has focussed on pathogens (Salmonella, Campylobacter, Chlamydia, herpesviruses and other viruses) present in Australian native birds presenting to Healesville Sanctuary, as well as pathogens (Chlamydia, Koala Retrovirus, herpesviruses) present in different populations of Victorian koalas. Ongoing work is focussed on zoonotic and other pathogens present in possums in Melbourne and surrounds, as well infectious agents in bent-wing bats. This work helps to characterise risks to wildlife and also to veterinarians, wildlife carers and other people who are in contact with wildlife. Our work has revealed that most zoonotic pathogens are present at a low prevalence but other pathogens are present at a very high prevalence. Examining the phylogenetic relationships between pathogens present in wildlife and other species provides information about potential transmission events. Our work has revealed evidence supporting complex interspecies transmission of beak and feather disease virus in Australian birds, and evidence supporting livestock-wildlife transmission of Chlamydia pecorum in Victorian koalas. Understanding the transmission of these pathogens ultimately facilitates the implementation of appropriate control measures.