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Abstract Background In developing countries, health information system (HIS) is experiencing more and more difficulties to produce quality data. The lack of reliable health related information makes it difficult to develop effective health policies. In order to understand the organization of HIS in African countries, we undertook a literature review. Methods Our study was conducted using the PubMed and Scopus bibliographic search engines. The inclusion criteria were: (i) all articles published between 2005 and 2019, (ii) articles including in their title the keywords "health", "information", "systems", "system", "africa", "developing countries", "santé", "pays en développement", "Afrique", (iii) articles that are written in English or French, (iv) which deals with organizational and technical issues about HIS in African countries. Results Fourteen retrieved articles out of 2492 were included in the study, of which 13 (92.9%) were qualitative. All of them dealt with issues related to HIS in 12 African countries. All 12 countries (100.0%) had opted for a data warehouse approach to improve their HIS. This approach, supported by the DHIS2 system, has enabled providing reliable data. However, 11 out of the 12 countries (92.0%) frameworks were aligned with funding donors’ strategies and lacked any national strategy. Conclusion This study suggests that the lack of a national health information management strategy will always be a threat to HIS performance in African countries. Ideally, rigorous upstream thinking to strengthen HIS governance should be undertaken by defining and proposing a coherent conceptual framework to analyze and guide the development and integration of digital applications into HIS over the long term.