Focusing on the problem of pharmaceutical R&D for drugs and vaccines against neglected diseases in developing countries, this article argues that the effectiveness of global health partnerships potentially lies in their capacity to address the problem of dual market failures: on a first level they may tackle the poverty induced lack of effective demand for health products which impedes the creation of market-financed innovative products. On a second level, they may help overcoming hold-up problems and underinvestment induced by the complexity of neglected diseases R&D. Yet, organizing transactions within a partnership is not a panacea against these problems: a crucial determinant of success is proper ownership structures. They need to respond to (i) the degree to which the respective parties value the partnership outcome, (ii) the relative importance of the investment of the parties, and (iii) the nature of the partnership outcome. The argument developed in the analysis is built on an integrated framework combining insights from incomplete contracting theory and public goods economics. It is supported by a preliminary statistical analysis of 17 GHPs.