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Abstract Background It is now 25 years since the adoption of the Agreement on Trade-Related Aspects of Intellectual Property Rights (TRIPS) and the same concerns raised during its negotiations such as high prices of medicines, market exclusivity and delayed market entry for generics remain relevant as highlighted recently by the Ebola and COVID-19 pandemics. The World Health Organization’s (WHO) mandate to work on the interface between intellectual property, innovation and access to medicine has been continually reinforced and extended to include providing support to countries on the implementation of TRIPS flexibilities in collaboration with stakeholders. This study analyses the role of intellectual property on access to medicines in the African Region. Methods We analyze patent data from the African Regional Intellectual Property Organization (ARIPO) and Organisation Africaine de la Propriété Intellectuelle (OAPI) to provide a situational analysis of patenting activity and trends. We also review legislation to assess how TRIPS flexibilities are implemented in countries. Results Patenting was low for African countries. Only South Africa and Cameroon appeared in the list of top ten originator countries for ARIPO and OAPI respectively. Main diseases covered by African patents were HIV/AIDS, cardiovascular diseases, cancers and tumors. Majority countries have legislation allowing for compulsory licensing and parallel importation of medicines, while the least legislated flexibilities were explicit exemption of pharmaceutical products from patentable subject matter, new or second use of patented pharmaceutical products, imposition of limits to patent term extension and test data protection. Thirty-nine countries have applied TRIPS flexibilities, with the most common being compulsory licensing and least developed country transition provisions. Conclusions Opportunities exist for WHO to work with ARIPO and OAPI to support countries in reviewing their legislation to be more responsive to public health needs.