The restricted distribution of Johne's disease in Australia resulted in States implementing regulatory controls for many years to try to stop the spread of infection to free areas and herds. This has contributed to the virtual absence of paratuberculosis in northern and western Australia. National zoning for Johne's disease, introduced in 1999, formally recognised the differential distribution of infection and should strengthen regional control. At the same time zoning permits more appropriate controls in infected areas and cattle enterprises than are required in protected and free zones. A new national approach to the control of cattle (C) types of M. paratuberculosis is being developed by Animal Health Australia in conjunction with industry and government stakeholders. Within the infected areas of south-eastern Australia the dairy industry is focussing more on reducing contamination of farm and product and improving management of replacement heifers. It appears that the beef industry in Australia has very little disease but some infected breeder herds have distributed the infection with sales of bulls and female breeders. Different risk-based strategies are being developed in both industries to allow trading of live cattle while still aiming to reduce the spread of paratuberculosis to non-infected herds and regions. The occurrence of C types of M. paratuberculosis in alpaca and goats in Australia has diminished but outbreaks in deer herds in the past 2 years are presenting new challenges.