This article describes a probabilistic model that quantifies hazards that arise from Staphylococcus aureus in milk that is sold as pasteurized in the United Kingdom. The model is centered on coupled dynamics for S. aureus populations, staphylococcal enterotoxins, and the concentration of alkaline phosphatase throughout the milk chain. The chain includes farm collection and storage of pooled milk, further pooling for off-farm processing, high temperature short time thermal processing, and possible postprocess contamination. The model is implemented as a Bayesian belief network. The results indicate that milk sold as pasteurized is relatively safe with respect to the hazards associated with S. aureus and that most risk is associated with small scale on-farm processing. An additional analysis of likelihood ratios shows that alkaline phosphatase concentrations in filler tank milk are a good indicator of potential hazards and that these concentrations, in conjunction with other measurements, can be used effectively to discriminate over possible failure modes. The ability to discriminate over potential failure modes can support preemptive actions, such as maintenance or hygiene, which assist with milk chain management and, over extended periods, accumulate to drive improved safety, efficiency, and security.