Collaborative research between universities and pharmaceutical companies is a form of public -private sector partnership that raises important issues of governance and research integrity. The article analyses this from a stakeholder perspective with particular reference to clinical trial collaborations. Constraints and pressures on universities involved in collaborative projects are identified, together with implications for research integrity. A stakeholder systems model is offered as a means of identifying and reconciling disparate stakeholder perspectives, and its organizational justice dimensions enable evaluation of perceptions of fairness in system operation. The article contends incorporation of stakeholder views on system rationale, process and evaluation can enhance effectiveness, social responsibility and stakeholder commitment.