In sub-Saharan Africa previous health gains have been reversed and many countries are not on track to achieving the Millennium Development Goals. The reasons are multifaceted but relate fundamentally to poorly functioning health systems and the HIV, AIDS, and tuberculosis epidemics. Although population health can be improved through specific health interventions that target high burden diseases, these interventions must be offered within a functional health system for optimal effectiveness. Schools of Public Health in Africa should respond to the many systemic issues that confound improvements in population level health through reviewing approaches to health professional training that incorporates a public health approach, focusing on health systems research; collaboration, advocacy and networking; and strengthening health systems management. Institutional mechanisms to define joint research agendas and two-way exchanges between universities and national health systems are required.