Background: Governance in the health system is not just a vision, or a model for delivering services, but a key element in planning, implementing and evaluating activities to improve health. The main purpose of this study was to design a pattern for assessing Iran's Health System Governance.
 Methods: The present study was descriptive in terms of purpose, qualitative in terms of application, and qualitative in terms of data type, which was conducted based on thematic analysis and deductive-inductive approach. 14 health system experts were selected through non-random-purposive sampling. To calculate reliability, test-retest reliability and coder reliability were used, which were 70 and 87 %, respectively. Also, Waltz and Basel method was used to assess the content validity of the extracted indices which was 85 %.
 Results: After 6 stages of thematic analysis, 137 basic themes, 15 organizing themes and 5 comprehensive themes (health system accountability, health system participation, health system policy formulation, health system service provision, health system efficiency and quality) were obtained, and finally, a model for assessing the governance of the health system in the Islamic Republic of Iran was designed. Organizational accountability included 7 themes, ethical accountability, 9, and legal accountability included 6 .Financial accountability included 8 basic themes, and efficiency and quality, 10 basic themes. Implementation included 8 themes, comprehensiveness, 4, reporting, 12, and transparency, 6. Structural policy included 23 themes, social inclusion and justice policy, 6, and fiscal policy included 11 basic themes. Medical services included 4 themes, financial services, 7, human services and human rights, 9, and information and technology services included 7 basic themes. In this pattern, participation and policy formulation were considered input, and accountability, efficiency and quality and service delivery were considered output.
 Conclusion: Lack of a clear definition for an appropriate interdepartmental cooperation, Lack of meritocracy, having a guild oriented attitude, conflict of interests, not using a policymaking approach based on a collective evidence and wisdom are among the shortcomings of the current health system governance. In addition, healthcare costs imposed on people are too high.