Pressure on the world's water supply has directed increasing attention to the use of recycled water in food production and processing. Municipal sewage, unless sufficiently treated, may provide a means by which pathogenic microorganisms enter the food chain through contaminated irrigation or wash water. Australian Guidelines for Water Recycling (AGWR) have been developed using the process of Quantitative Microbial Risk Assessment (QMRA). This process comprises four parts: hazard identification, dose response, exposure assessment, and risk characterisation and results in an output estimate of the burden of disease in a given population over a given period. QMRA may be used as a tool to promote science-based decision making processes, set priorities among different safety problems, identify gaps in scientific knowledge, and to improve control systems and develop guidelines. AGWR (Phase 1) specify a range of indicative treatment processes, exposure reductions and water quality objectives that support a fit-for-purpose approach in relation to using recycled water for non-potable uses. These include livestock drinking water, dairy shed wash down, pasture or fodder crop irrigation and irrigation of food crops (home grown and commercial). This paper discusses the QMRA process and assumptions made in relation to exposure estimates in AGWR guidelines using two case study examples, as well as outlining existing data gaps.