OBJECTIVES: To identify stakeholder perceptions of sponsored clinical trials in a publically funded New Zealand hospital, and then to identify the similarities and differences in perceptions across these stakeholder groups.  The stakeholders are: 1) participants involved in clinical trials; 2) management and the multidisciplinary team; 3) the larger South Auckland community; 4) government and decision makers; and 5) the pharmaceutical industry  METHODS: We use purposive sampling to select representatives of the stakeholder groups, which provides 109 respondents.  We gather data using focus groups, in-depth interviews, telephone interviews and surveys. RESULTS: Many of the respondents represent more than one stakeholder group.  While there is consensus across the stakeholders on some costs and benefits such as developing safe medicines and collecting useful data there are marked differences in perceptions in other areas, such as those indicated below.  Most stakeholders perceive the risk of adverse reactions as the greatest cost to trial participants but the participants themselves do not regard this as significant. Pharmaceutical representatives, management and the multidisciplinary team feel that gaining access to new medicines motivates people to participate in a trial.  Trial participants feel that the support is more important to them than the medication. Most researchers and staff believe trial involvement increases their job satisfaction, motivation, knowledge and skills  while a few  have concerns  that sponsor control leads to the loss of their flexibility and independence Generally there is a perception that New Zealand based clinical trials assist in the process of obtaining registration and subsidisation of new drugs in New Zealand. However, this perception may be erroneous as location of trials is apparently not considered in the drug registration process. CONCLUSIONS: We find that most stakeholders are satisfied with the conduct of clinical trials in New Zealand and they believe the benefits outweigh the costs.