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Background: The explosion of interest in the human microbiome research was sparked in part by two research initiatives launched in 2008, the European and Chinese-led Metagenomics of the Human Intestinal Tract Consortium and the National Institutes of Health (NIH)-sponsored Human Microbiome Project. The new knowledge provided by these initiatives and others worldwide are transforming our understanding of the pathogenesis of several diseases, including asthma, inflammatory bowel diseases, obesity and Type 1 diabetes, as well as the development of the immune response linked to some vaccines. However, African populations are understudied in these initiatives, and there is no "African Microbiome Initiative". This systematic review aimed to summarize and discuss the state of research on the human microbiome in Africa, including the therapeutic role of the microbiome for the management of certain local diseases. Methods&Materials: Using predefined keywords, we searched in six electronic databases for human microbiome studies conducted in Africa. In addition, to find additional articles, we checked references cited in eligible studies. Two authors independently selected eligible studies published until 30 September 2015. Results: Eighty-nine human microbiome papers were identified from six electronic databases and other sources. There were 80 primary microbiome studies (including Khoi San (n= 1) and Hunter- Gatherers (n= 4)) and 9 nested microbiome studies within existing cohorts. 16S rRNA gene sequencing was the technique most widely used to characterize the microbiota. The main body sites studied were the gut (46%), vagina (25%) and the oral cavity (11%). The diseases targeted were malnutrition (n= 4), HIV/AIDS (n= 7), diarrhoea (n= 4), and periodontitis (n= 5). These microbiome studies were performed in individuals of all ages, with most of the studies being conducted in adults. Kenya, Uganda, South Africa and Nigeria were the sites of the majority of studies; however the principal investigators of most of the studies (87%) were from developed countries. TheUSANIHwasthemainfunding source (25%), followed by the Bill and Melinda Gates Foundation (9%) and the European Commision (8%). Conclusion: More studies of the microbiome including African participants, focusing on endemic diseases and led by African researchers are needed. [ABSTRACT FROM AUTHOR]