| Animal welfare monitoring protocols currently used by the Australian livestock export industry rely on the use of input measures relating to environment, resources and management, and outputs relating to morbidity and mortality. More recently, animal behavioural outcomes have been recognised as important indicators of welfare for animals in all livestock production systems. Our research project has created a system for recording the welfare conditions of cattle and sheep in the Australian livestock export supply chain. We used a suite of easily defined and universally understood measures to explore the links between environmental and management conditions and the health and behavioural outcomes for cattle and sheep during the live export process. Four consignments of cattle and three consignments of sheep were assessed at different stages of the export supply chain by a pen side observer. Measurements were taken in Australian pre-export facilities, at multiple times of the day on each day during the sea voyage, and in destination feedlots and quarantine centres. The protocol has proven to successfully record behavioural changes as animals become habituated to intensive management practices during the export process. Links between behaviour and health outcomes with changing environmental conditions and resource access were also detected. Preliminary data analysis aims to determine how many animals constitute a representative sample, and the sampling frequency required to provide accurate insight into the welfare of the whole consignment. Our data have indicated that, during a sea voyage, assessments must be made from different lines of livestock and from areas of the ship that differ in environmental conditions or resource access. Multiple daily sampling is required to show patterns of appropriate activity and resting behaviour, as well as responses to changing conditions such as heat and respite periods. Decisions about the impacts of management and environmental conditions, the suitability of livestock and the regulation of industry, can be better informed by taking a whole of supply chain approach to assessing and reporting on animal-based outcomes for live sheep and cattle exported from Australia.