Collaborative research activities are increasingly being used across health-care settings and are viewed as a positive way to achieve mutual outcomes. However, interagency or intersectoral research programmes are not without problems. They are, at best, challenging and complex activities that require enormous commitment of resources, expertise and insight from all stakeholders. This paper uses the example of an actual collaborative research project to illustrate factors that can impair collaboration and in turn negatively impact on intersectoral research outcomes. It is anticipated that an honest description of those events and issues that adversely affected the programme presented here, and examination of the associated literature, will serve as a guide to others embarking on similar collaborative endeavours. This paper does not attempt to provide a full review of the comprehensive range of literature about collaboration and collaborative research; rather, it presents some key themes identified as having the potential to impact on the success of collaborative research projects. Key themes acknowledged by the authors as influencing the progress of the research project highlighted here are communication, environment, politics and power, and organizational culture.