The scope for health genomics research in Africa is rapidly expanding, and standardisation of sample and data collection and processing can facilitate much larger study sizes through collaborative networks, and meta-analyses with greater statistical power to identify aetiological factors. The global health benefits that can result from data sharing and meta-analysis for health conditions are indisputable, and exploring the diversity and depth of African genomes can improve the health care provided to Africans as well as informing the identification of aetiological variants in rest-of-world populations. In the enthusiastic pursuit of such sample and data sharing and re-use, however, the preferences, permissions and wishes of the participants who provide those resources for research should be unambiguously understood, faithfully recorded and rigorously upheld. To do so in a systematic way can ensure participant protection, and can also facilitate sample and data reuse and meta-analysis through standardised approaches to recording and storing individual participants’ consents and dissents. Here, we present a framework for tiered consent for health genome research in Africa which we believe can capture the choices of participants accurately in a standardised way. We describe information that should be shared with participants, the different tiers of consent and how they might be explained to participants, and provide a generic template for participant information and tiered consent questions that can be re-purposed for specific studies. We also propose a schema for storing tiered consent data and describe a flexible approach for mapping individual consents to data use ontologies as they become available or evolve.