Biotechnology and genomic innovation are seen as increasingly important for achieving public health goals in Africa. In particular, vaccines based on advances in genomic technology are deemed vital in the fight against HIV/AIDS. Public-Private Partnerships (PPPs) provide a collaborative mechanism to ensure these vaccines are developed when the private sector lacks incentives to develop these products. These partnerships provide new mechanisms for transferring the knowledge required to ensure vaccine development occurs as quickly and efficiently as possible. One such accine partnership is the South African AIDS Vaccine Initiative (SAAVI). This has been successful in ensuring 'value added' (benefit gained by taking part) is created for those involved particularly in the area of intangible value added determinants of collaboration and knowledge capacity. This paper outlines the results of a case study of SAAVI and argues that it provides evidence of a need to strengthen our understanding of the linkage between wider conceptual 'systems' of innovation and health. In particular, it espouses the usefulness of 'Systems of Innovation' thinking as a means to ensure that more specific focus is placed on process outputs such as collaboration and knowledge capacity. This will ensure that necessary knowledge flow is transferred between those working in the vaccine project for more efficient and effective operations. The research also raises questions about the possibility of such case studies highlighting areas of attention that need addressing if greater linkage is to occur between innovation and health at a wider health research policy level.