Introduction: This article describes the use and effectiveness of the participatory action research (PAR) framework to better understand community members' perceptions and risks of pandemic influenza. In 2009, the H1N1 influenza pandemic affected Indigenous populations more than non-Indigenous populations in Oceania and the Americas. Higher prevalence of comorbidities (diabetes, obesity, asthma and chronic obstructive pulmonary disease) as well as pregnancy in Indigenous communities may have contributed to the higher risks of severe disease. Social disparity, institutionalised racism within health services and differences in access to culturally safe health services have also been reported as contributors to disadvantage and delayed appropriate treatment. Methods: Given these factors and the subsequent impact they had on Australian Aboriginal and Torres Strait Islander communities, the authors set out to ensure that the Australian national, state and territory pandemic plans adequately reflected the risk status of Aboriginal and Torres Strait Islander peoples and promoted meaningful engagement with communities to mitigate this risk. A national study explored the views of Aboriginal and Torres Strait Islander people and their experiences with H1N1 and used a qualitative PAR framework that was effective in gaining deep understandings from participants. Aboriginal and Torres Strait Islander community-controlled organisations and health services were involved in the implementation, interpretation and monitoring of this project. Results: As a result, important features of the implementation of this PAR framework with Aboriginal and Torres Strait Islander communities and organisations emerged. These features included the importance of working in a multidisciplinary team with Aboriginal and Torres Strait Islander researchers; the complexities and importance of obtaining multi-site human research ethics approval processes; the importance and value of building the research capacity of both experienced and novice researchers in PAR; the need to use localised sampling protocols; and the process of undertaking a collective research process and enacting action research and feedback. Conclusions: The most effective responses of this project were embedded in pre-existing relationships with individuals within organisations that had been established over a long period of time between Aboriginal medical services and investigators; however, research relationships established specifically for the purposes of the project were less successful because of changes in personnel and organisational support. The participatory approach used in this study has the potential to be applied to vulnerable populations in other countries.