This study proposed the optimum design values for the biological clean room system observing the regulations of Hazard Analysis Critical Control Point (HACCP). Even though the standard for industrial clean room system has been well established, the basis for biological food clean room system is the first stage. In order to prevent the contaminations in advance for food storages, processes, and distributions, the criterion of Hazard Analysis Critical Control Point is positively required. This study also suggested the possible ways of how to avoid the hazardous contaminations.