A key feature of government interventions in support of national innovation in recent decades has been investment in cross sector R&D programs. One of the mechanisms for such action has been the institutionalisation of collaboration through the creation of cooperative research centres. In Australia the cooperative research centres (CRCs) program has become one of the nation’s biggest single budget S&T investment strategy. This has led to increasing efforts to evaluate the program in terms of its overall objectives, the objectives of individual centres and individual centre research programs. However, the institutional objectives of the partners involved in CRCs tend to have been ignored in the process. An important question is: to what extent is participation in CRCs impinging (either positively or negatively) on the partners separate (and potentially conflicting) objectives? Typical R&D evaluation processes for cross sector R&D programs, in Australia and elsewhere, focus mainly on the objectives of the program – not the institutional partners. Yet for them, participation carries with it elements of risk. This includes organisational as well as financial risk. This paper focuses on the risks experienced by one category of partner in the Australian CRC program: the universities. Data are presented on the 62 CRCs that comprise the Australian CRC program collected over the past 10 years (since the program commenced). Outcomes from the CRC program over the past ten years are assessed in the context of the broader institutional objectives and expectations in the Australian higher education environment. Our analysis suggests that there are important ‘risk’ factors for universities involved in CRC participation. There are important S&T policy implications that follow. It will be important to take these issues into account in evaluation mechanisms and processes for assessing the full impact of government funded ‘cross-sector’ collaborative R&D programs.