With its primary focus on community health, the public health system focuses on intervention and prevention of disease and injury to protect entire populations. As a federation of city, county and state entities operating independently under a complicated array of local, state and federal laws, public health can best be understood as a complex adaptive system. The dynamic nature of this system and the need for public health agencies to relate and respond to numerous stimuli in terms of new regulations, changing health status, emerging threats and shifting policy, can mask the commonality of underlying business processes performed within the public health sector. Heightened demand for interoperable, adaptive information systems across the broader US health system necessitates the recognition of this commonality and highlights the need for comprehensive analysis and understanding of these core business processes. In turn, this analysis paves the way for public health to apply proven systems engineering techniques to streamline, automate and facilitate those processes. Here, we look at the nature of the public health system and the evolution of a purpose-built methodology for process engineering within public health. We also present a case study based on the application of the methodology to develop requirements for public health laboratory information management systems.