Cattle strains of M paratuberculosis are known to infect cattle, goats and alpaca in south-eastern Australia, where there are also significant numbers of farmed deer. Epidemiological evidence in Australia to date supports the distinction between bovine Johne's disease (BJD) caused by cattle strains and ovine JD (OJD), caused by sheep strains in sheep and goats. The National JD Control Program is coordinated by the Australian Animal Health Council Ltd (AAHC) , working with the livestock industries and with the Commonwealth, State and Territory governments. The Council also brokers industry and government funding for the program. The National Johne's Disease Market Assurance Program for cattle was launched in 1996 as the first of a suite of voluntary national market assurance programs (MAPs) to assess and certify herds as negative for JD. In the following two years, 450 herds achieved an assessed status. MAPs were also developed for alpaca and goats in 1998 (and for sheep in 1997). National standards for state control of JD through zoning, movement controls and procedures in infected and suspect herds have also been developed. National standards and programs have been reviewed and improved. The paper will cover factors affecting development and implementation, uptake of and improvements to national control and assurance programs in Australia.