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Genomic research and biobanking has undergone exponential growth in Africa and at the heart of this research is the sharing of biospecimens and associated clinical data amongst researchers in Africa and across the world. While this move towards open science is progressing, there has been a strengthening internationally of data protection regulations that seek to safeguard the rights of data subjects while promoting the movement of data for the benefit of research. In line with this global shift, many jurisdictions in Africa are introducing data protection regulations, but there has been limited consideration of the regulation of data sharing for genomic research and biobanking in Africa. South Africa (SA) is one country that has sought to regulate the international sharing of data and has enacted the Protection of Personal Information Act (POPIA) 2013 that will change the governance and regulation of data in SA, including health research data, once it is in force. To identify and discuss challenges and opportunities in the governance of data sharing for genomic and health research data in SA, a two-day meeting was convened in February 2019 in Cape Town, SA with over 30 participants with expertise in law, ethics, genomics and biobanking science, drawn from academia, industry, and government. This report sets out some of the key challenges identified during the workshop and the opportunities and limitations of the current regulatory framework in SA.