Rust diseases have caused significant losses to Australian cereal crops, and continue to pose a serious threat. Because Australian cereal crop yields are generally low, genetic resistance remains the most economical means of rust control. Resistant cultivars also contribute significantly to reducing over-summer rust survival. A policy of releasing only rust resistant wheats in northern New South Wales and Queensland has resulted in industry-wide protection from rust in this region for the past 40 years. The Australian Cereal Rust Control Program conducts annual pathogenicity surveys for all cereal rust pathogens, undertakes genetic research to identify and characterize new sources of resistance, and provides a germplasm screening and enhancement service to all Australian cereal breeding groups. These three activities are interdependent, and are closely integrated with particular emphasis on linking pathology and genetics to ensure breeding outcomes. Recent changes in the wheat rust pathogens, including the development of virulences for Yr17, Lr24, Lr37 and Sr38 resistance genes, and the introduction of a new pathotype of the wheat stripe rust pathogen, have provided new and significant challenges for wheat rust resistance breeding. Similar challenges exist in breeding barley and oats for rust resistance. Examples are discussed to illustrate the ways in which rust isolates are providing information that can be used in breeding for rust resistance. In future, as more markers linked to durable rust resistance sources become available, it is likely that the use of marker-assisted selection will become more common-place in rust resistance breeding.