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Background  There is limited evidence regarding the best approaches to helping Indigenous Australians to stop smoking. The composite analysis of the only two smoking cessation randomised controlled trials (RCTs) investigating this suggests that one-on-one extra support delivered by and provided to Indigenous Australians in a primary health care setting appears to be more effective than usual care in encouraging smoking cessation. This paper describes the lessons learnt from one of these studies, the Be Our Ally Beat Smoking (BOABS) Study, and how to develop and implement an integrated smoking cessation program.    Methods  Qualitative study using data collected from multiple documentary sources related to the BOABS Study. As the project neared completion the research team participated in four workshops to review and conduct thematic analyses of these documents.    Results  Challenges we encountered during the relatively complex BOABS Study included recruiting sufficient number of participants; managing the project in two distant locations and ensuring high quality work across both sites; providing appropriate training and support to Aboriginal researchers; significant staff absences, staff shortages and high workforce turnover; determining where and how the project fitted in the clinics and consequent siloing of the Aboriginal researchers relating to the requirements of RCTs; resistance to change, and maintaining organisational commitment and priority for the project. The results of this study also demonstrated the importance of local Aboriginal ownership, commitment, participation and control. This included knowledge of local communities, the flexibility to adapt interventions to local settings and circumstances, and taking sufficient time to allow this to occur.    Conclusions  The keys to the success of the BOABS Study were local development, ownership and participation, worker professional development and support, and operating within a framework of cultural safety. There were difficulties associated with the BOABS Study being an RCT, and many of these are shared with stand-alone programs. Interventions targeted at particular health problems are best integrated with usual primary health care. Research to investigate complex interventions in Indigenous health should not be limited to randomised clinical trials and funding needs to reflect the additional, but necessary, cost of providing for local control of planning and implementation.

Clinical trials in a remote Aboriginal setting: lessons from the BOABS smoking cessation study