Weak and dysfunctional health systems in low-income countries, particularly in sub-Saharan Africa, are recognised as major obstacles to attaining the health-related Millennium Development Goals by 2015. Some progress is being made towards achieving the targets of Millennium Development Goal 6 for tuberculosis (TB), HIV/AIDS and malaria, with the achievements largely resulting from clearly defined strategies and intervention delivery systems combined with large amounts of external funding. This article is divided into four main sections. The first highlights the crucial elements that are needed in low-income countries in sub-Saharan Africa to deliver good quality health care through general health systems. The second discusses the main characteristics of infectious disease and TB control programmes. The third illustrates how TB control and other infectious disease programmes can help to strengthen these components, particularly in human resources; infrastructure; procurement and distribution; monitoring, evaluation and supervision; leadership and stewardship. The fourth and final section looks at progress made to date at the international level in terms of policy and guidelines, with some specific suggestions about this might be moved forward at the national level. For TB and other infectious disease programmes to drive broad improvements in health care systems and patient care, the lessons that have been learnt must be consciously applied to the broader health system, and sufficient financial input and the engagement of all players are essential.