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New space exploration missions are currently being designed to take humanity beyond low Earth orbit (LEO) to cis-lunar space, the lunar surface, and eventually to Mars. These missions carry increased risks due to a number of factors, including distance from Earth, exposure to deep space hazards, reduced capacity and ability to resupply and evacuate, and increased communication delays. As distance from Earth grows and mission length increases, a growing proportion of mission risk can be attributed to the “human system.” Almost twenty years ago, the Institute of Medicine in the United States recommended the early and complete integration of the human system into the spacecraft and mission design process to mitigate this increased risk inherent in exploration missions. Exploration missions will require increasing levels of crew self-sufficiency that will challenge the current operational paradigms established in LEO. Enabling progressive Earth independence requires management of the increasingly complex interactions among spacecraft systems and integration of all the data and functions that affect human health and performance into one coordinated system –the Crew Health and Performance (CHP) system. This system is a critical spacecraft system that is analogous to other systems such as propulsion, guidance and navigation, or avionics. Design and integration of the CHP system requires the evidence-based merger of typically disparate disciplines such as medicine, human factors, and life support system design, using systems engineering (SE) practices. SE provides traceability of spacecraft requirements and enables reliable and repeatable trade space analysis of the many competing options for hardware and software to be included in the mission architecture. The approach described here enables spacecraft and mission designers to align the scope of a CHP system with mission specific requirements, decrease risk to the crew, and increase the probability of mission success.