Reliance on market forces can lead to underinvestment in social welfare enhancing innovation. The lack of new medical products in the area of neglected diseases is a case in point. R&D for neglected diseases has increased with new funding and collaborations taking place mainly through product development partnerships (PDPs). PDPs are self-governing, private non-profit R&D organizations. In contrast to push and pull instruments designed to address private-sector R&D underinvestment, PDPs have emerged voluntarily to address this public health challenge. In this study we examine how non-profit R&D collaboration for neglected diseases takes place through PDPs. We find that PDPs act as 'system integrators' that leverage the resources and capabilities of a network of public, philanthropic and private-sector partners. This paper contributes to an understanding of R&D in a non-profit context and highlights the importance of collaboration and non-market institutions for promoting innovation where market failures occur.