Abstract: Governance is increasingly recognised as being a core determinant of the performance of health care, especially in low-income countries. This project seeks to analyse key factors determining the quality of health governance, with detailed case studies in Tanzania and Tajikistan. Background: Pioneering work by the World Health Organisation (WHO) and others has begun to underline the importance of governance for health care systems. However, there is still a huge need to define what the governance of health systems means, i.e. to elaborate a comprehensive analytical framework that is applied and tested in country case studies. One difficulty is the complex nature of governance systems, which requires an interdisciplinary approach to capture the big picture (e.g. the legal or regulatory framework) as well as health-sector-specific factors (e.g. the burden of disease). The combined expertise and networks in governance, public health and epidemiology of the Basel Institute of Governance and the Swiss Tropical Institute are ideally suited to overcome these problems. The case-studies of Tanzania and Tajikistan will provide valuable information on specific governance problems of two regions that face substantial health challenges. Objective: The main goal of the project is to elaborate, apply and test an interdisciplinary framework to assess the governance of health systems in Tanzania and Tajikistan. The project will, firstly, elaborate a health systems-specific governance framework that has been validated in two countries; secondly, substantially advance the understanding of health systems and allow for better-informed health sector reforms; thirdly, support capacity-building and knowledge-exchange on health systems governance on a national, regional and international level; and lastly provide new empirical data on relevant dimensions of health systems in Tanzania and Tajikistan. Importance: The project is spearheading efforts for a more evidence-based and dynamic understanding of how health systems function in low-income and transition countries. Ultimately, the aim is to contribute to a better understanding of critical governance factors of health systems in general, and to the improvement of health care policies, health care delivery as well as access to health care.