Worldwide, innovation policy is perceived to be at the heart of economic growth and global competitiveness, and nations invest vast amounts of money to give effect to innovation. Higher education institutions, in partnership with industry, are expected to play a key role in supporting the national system of innovation and developing the nation's global competitiveness. This paper draws on the audit of higher education-industry partnerships conducted by the Human Sciences Research Council (HSRC) of South Africa during 2002–03. It plots the South African government's programme of incentives for industry-higher education partnerships through two funding programmes: the Technology and Human Resources for Industry Programme (THRIP) and the Innovation Fund. It argues that, notwithstanding considerable outputs, such as publications, patents/artefacts and the involvement of postgraduate students, it is vital that the incentivization of higher education-industry partnerships is managed in such a way that past relations of inequality among higher education institutions and in the broader society are not reproduced.