Community participation in program decision-making and implementation is an ideal that community and academic stakeholders aspire to in participatory research. This ideal, however, can be difficult to achieve. We describe lessons learned about community participation from a quasi-experimental trial aimed at reducing the uptake of smoking among pre-adolescents in a community with a high percentage of Maori and Pacific Island people. The intervention involves students, parents, school teachers and management, extended families and members of the wider community. A total of approximately 4000 students (and their parents) of four urban Auckland schools were enrolled in the study over 3 years. The intervention is carried out through collaborations between public health professionals, academic institutions and school personnel. In order to enhance community participation, we conclude that (i) time commitment is needed to establish long-term ongoing relationships through face-to-face communication, (ii) research team members should ideally share similar cultural and ethnic backgrounds to the target audience and have in-depth understanding of and experience in the community milieu and (iii) collaborative partnerships between academic institutions and public health services are necessary to create strength and cohesion, and assist with clear articulation of the research project mission and objectives.