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The competing needs of maintaining productivity within abattoirs, and maintaining high standards of animal welfare, provide fertile grounds for applied research in animal behavior. However, there are challenges involved in capturing useful behavioral data from the supply chain (from paddock to processing plant). The challenges identified in this report are based on a review of the scientific literature as well as field study observations. This article describes those challenges as they relate to collecting behavioral data on livestock-herding dogs, humans and livestock as they interact in abattoirs, and provides insights and recommendations for others embarking on animal studies in confined spaces, as well as in commercial settings. Direct observation of livestock behavior permits animal-welfare assessments and evaluations of the efficacy of operations in unfamiliar and high-pressure contexts, such as abattoirs. This brief report summarizes the factors that must be considered when undertaking in situ studies in abattoirs. There is merit in passive behavioral data-collection using video-recording equipment. However, the potential for hardware issues and sampling difficulties must be anticipated and addressed. Future research directions and recommendations to avoid such issues are discussed. This information will be highly beneficial to future abattoir studies focusing on efficiency and animal welfare at commercial abattoirs. Furthermore, it may also be relevant to any analyses involving large cohorts of animals in a confined environment.