Background:The value framework governing the health system can guide the policymaking. This study presents a set of values governing the health policies for adopting policies that are in harmony with the ideology of Iran.Methods:This study was conducted in two phases. In the first phase, using the qualitative approach, Shams et al. framework was adopted to identify values. Identification of health-related national documents (nine documents) was performed purposefully. In the next phase, semi-structured interviews on individual experts in the health system were carried out. The key question was “What values and principles govern the health policy system?” Participants included 15 individuals. Both phases were analyzed based on qualitative content analysis.Results:In this study, a taxonomy of values governing policymaking is presented. Results show that equity in different dimensions, comprehensive health and a healthy human being, pioneering in health in the region, and accountability are the most important terminal vaqlues. Individual responsibility, government responsibility for health, endogenous and extrinsic economics, fair access, transparency, efficiency, quality and integrity in the supply, development and fair allocation of public health resources, and professional commitment are the most important instrumental values in Iran. Participants believed that, despite the many higher-order documents available, the health system policymaking was not based on a predetermined value.Conclusions:It is not enough to provide a set of values in upstream documents for implementation. It is necessary to specify the relative weight of the reference values in policymaking and their relation to each other in order to apply them in policymaking.