"This paper begins by shedding light on the dominant types of internal migration in SSA, and in particular rural-urban migration as reported in previous national censuses; thereafter, it analyses urbanisation in the region, comparing the phenomenon in the four sub-regions of SSA; and finally, it examines health challenges especially in urban areas where communicable diseases are rampant and from which urbanites move back to their rural origins once they reach the terminal stage of ill-health. In the discussion, the paper interrogates the policies being adopted to handle migration-urbanisation-health inter-linkages rather than concentrating on anyone of the three thereby only partially solving the puzzle. The paper is of immense importance for SSA governments in their efforts to meet the Millennium Development Goals(MDGs) which relate to these three phenomena: rural poverty which triggers rural-urban migration, in the process leading to translocation of rural population to urban areas; urbanisation which creates an environment for creating employment opportunities and thus alleviating poverty; and the concentration of health challenges such as the three scourges(HIV/AIDS, TB and malaria) which threaten urban lifestyles. Moreover, it raises issues which should attract multi-disciplinary research on the three issues that are largely discipline-free."