This study examines the legitimation of power and knowledge in the struggle of public health and health care agencies in the Lower Congo region of the Democratic Republic of Congo to vanquish chronic tropical diseases. Of particular interest is the creation of alternative institutions following the collapse of state sponsored structures and supply lines in the 1980s and 1990s, and the process by which such alternative structures are legitimized. A review of legitimation theory suggests that new paradigms are required to assess the nature and efficacy of diverse non-state institutions within a fluid global neo-liberal context. The paper argues that these new or newly adapted post-state institutional arrangements, born in the crisis of state failure, may be effective in the lessening of the disease burden that weighs on the region to the extent that they are able to muster the legitimacy of the populace, the professions, the national society, and the wider international community. I thus hope to shed light on the paradox of persistent tropical diseases - e. g., malaria, sleeping sickness, and schistosomiasis, as well as seasonal grippe, typhoid fever, tuberculosis and HIV/AIDS - as endemic or seasonal scourges, despite their being understood by local specialists, with known treatments and public health measures to control them.