The resource based view (RBV) of the firm has drawn attention to the role of human resources in building innovative capacity within firms. In ‘high technology’ firms scientific capability is a critical factor in achieving international competitiveness. Science, however, is a costly business and many firms are entering into cross sector R&D partnerships in order to gain access to leading edge scientific capability. The Australian Cooperative Research Centres (CRC) program is typical of the ways many governments are seeking to promote such cross-sector R&D collaboration. Scientists are key resources in these organisational arrangements. However, there is only fragmentary information available about why and when scientists choose to work in these cross-sector organisations rather than others, nor the impact of changing funding regimes on their career choices. Similarly, there has been little research into the impact of such partnerships and career choices on the organisations in which scientists work. This paper presents some findings from two new ARC funded studies in Australia designed to investigate the careers of scientists and the organisational and career implications of participation in cross sector R&D collaboration. One of our findings is that CRCs may not endure as long term ‘hybrid’ organisational arrangements as some observers have suggested, but rather remain as transitional structure influencing the partners involved and the careers of scientists. This has important implications for the managers of CRCs as well as those responsible for partner organisations.