A transdisciplinary pilot study with Australia's livestock industries is bringing multiple stakeholders together as equal partners, to examine the complex problems around animal disease management. These problems include disease surveillance and on-farm biosecurity practices. The pilot groups are established in industries susceptible to foot and mouth disease, namely dairy and beef cattle, pork, sheep and goats. The Agricultural Innovation Systems framework is being evaluated to determine its effectiveness as a tool to improve partnerships between stakeholders. These stakeholders include livestock producers (farmers), private and government veterinarians, local council representatives, and industry personal including from saleyards and abattoirs. Stimulation of innovative solutions to issues arising from conflicting priorities and limited resources around animal disease management are also expected. Using a participatory communication approach, the impact of the pilot on trust and relationships is being evaluated. The sustainability of the Agricultural Innovation Systems approach to address complex issues around animal health management is also being assessed. The aim of the study is to strengthen Australia's preparedness for an emergency animal disease outbreak, such as Foot and Mouth Disease.