The Global Fund to Fight AIDS, Tuberculosis and Malaria has played an important role in financing the response to HIV/AIDS and tuberculosis (TB) in Indonesia. As part of a series of case studies, we assessed the nature and extent of integration of Global Fund portfolios into the national HIV and TB programmes, integration of the HIV and TB programmes within the general health system, and system-wide effects of Global Fund support on the health care system in Indonesia. The study relied on a literature review and interviews with 22 key informants using the Systemic Rapid Assessment Toolkit and thematic analysis. Global Fund programmes in Indonesia are highly vertical and centralized, in contrast with the decentralized nature of the Indonesian health system. Consequently, there is more integration of all functions at local levels than centrally. There is a high level of integration of planning of Global Fund HIV and TB portfolios into the National AIDS and TB programmes and some limited integration of these programmes with other disease programmes, through joint working groups. Other synergies include strengthening of stewardship and governance and increased staff recruitment encouraged by incentive payments and training. Monitoring and evaluation functions of the Global Fund programmes are not integrated with the disease programmes, with parallel indicators and reporting systems. System-wide effects include greater awareness of governance and stewardship in response to the temporary suspension of Global Fund funding in 2008, and increased awareness of the need to integrate programme planning, financing and service delivery. Global Fund investment has freed up resources for other programmes, particularly at local levels. However, this may hinder a robust exit strategy from Global Fund funding. Furthermore, Global Fund monetary incentives may result in staff shifting into HIV and TB programmes.