The International AIDS Vaccine Initiative (IAVI) is one of a number of Product Development Partnerships created to bridge the gap between scientific and technological potential and the needs of low income populations in low and middle income countries. Specifically IAVI is focused on creating a preventative vaccine for HIV/AIDS. Whilst the remit of IAVI is to create new science, technology and products, its work necessarily involves a wide range of stakeholders and different constituencies in industrially developing and developed countries. Its capacity building activities relate to strengthening the ability to conduct clinical trials and are broad based, spanning scientific and technological capacity through to organisational, advocacy and broader development capabilities. The aim of this study was to deepen IAVI's understanding of how it contributes to capacity building activities in East Africa (Uganda, Kenya and Rwanda), spanning scientific and technological capacity through to organisational, advocacy and broader development capabilities. IAVI's mission to develop an HIV vaccine has become increasingly connected to wider health systems strengthening, through its clinical research activities in East Africa. Since it began its operations in the region, IAVI has made a significant contribution to training interventions to support scientific excellence and good clinical practice and invested in infrastructure and laboratories at Clinical Research Centres in East Africa. Although clear challenges still exist with ensuring sustained investment, accessing marginalized populations and demonstrating progress in capacity building, the experiences of IAVI to date suggest that substantial progress is being made towards wider health systems strengthening in the region.