Product Development Public-Private Partnerships (PDPs) are mechanisms used to incentivise health innovation for neglected diseases. PDPs undertaking clinical trial research in developing countries work – collaborate – at the interface of innovation and healthcare activities. Within the literature around innovation systems collaborative activity is deemed to build important organisational processes creating stronger institutions and enabling environments by increasing knowledge exchange. This process capacity building activity is recognised as important in some areas of the international development arena within which health related PDPs work. Using qualitative research methods this thesis studies the International AIDS Vaccine Initiative (IAVI) in Kenya to consider how partnership collaborative activity occurs, the interaction created between healthcare and innovation and, what capacity building results. This is an interdisciplinary study that mixes innovation systems thinking with an ethnographic/ anthropological rationale. The Kenyan IAVI partnership takes multiple forms. It is an ‘effective’ partnership acknowledging benefits gained within unequal power relations making it impossible to also be a ‘true’ partnership. The partnership has characteristics of an innovation system because actors are conduits of knowledge. Collaborative activity creates knowledge exchange producing ‘process capacity’. This less tangible, knowledge based, and organisational related capacity takes place within the partnership but is not overtly recognised as important. Focusing on process capacity highlights the linkages between innovation and healthcare activities. It also highlights the importance of considering AIDS vaccine research activities in a holistic, systemic manner. Understanding the partnership requires recognition of activities and multiple relations across time and space. The Kenyan IAVI partnership is not simply the result of international (macro) level discourse and storylines regarding the need to incentivise product development. Recognising this complexity moves beyond value laden notions of partnership towards understanding what is required to strengthen developing country health and innovation.