As part of a series of case studies on the interactions between programmes supported by the Global Fund to Fight AIDS, Tuberculosis and Malaria and health systems, we assessed the extent of integration of national HIV, tuberculosis (TB) and malaria programmes with the general health system, the integration of the Global Fund-portfolios within the national disease programmes, and system-wide effects on the health system in Thailand. The study relied on a literature review and 34 interviews with key stakeholders using the Systemic Rapid Assessment Toolkit and thematic analysis. In Thailand, the HIV, TB and malaria programmes' structures and functions are well established in the general health care system, with the Department for Disease Control and the Ministry of Public Health's network of health providers at sub-national levels as the main responsible organizations for stewardship and governance, service delivery, monitoring and evaluation, planning, and to some extent, demand generation. Civil society groups are active in certain areas, particularly in demand generation for HIV/AIDS. Overall, the Global Fund-supported programmes were almost fully integrated and coordinated with the general health system. The extent of integration varied across disease portfolios because of different number of actors and the nature of programme activities. There were also specific requirements by Global Fund that limit integration for some health system functions namely financing and monitoring and evaluation. From the view of stakeholders in Thailand, the Global Fund has contributed significantly to the three diseases, particularly HIV/AIDS. Financial support from the early Global Fund rounds was particularly helpful to the disease programmes during the time of major structural change in the MoPH. It also promoted collaborative networks of stakeholders, especially civil societies. However, the impacts on the overall health system, which is relatively well developed, are seen as minimal. One major contribution is the establishment of a health service system for neglected population groups. No specific negative impacts on the health system were raised.