BACKGROUND: Despite progressive health policy, disease burdens in South Africa remain patterned by deeply entrenched social inequalities. Accounting for the relationships between context, health and risk can provide important information for equitable service delivery. The aims of the research were to initiate a participatory research process with communities in a low income setting and produce evidence of practical relevance. METHODS: We initiated a participatory action research (PAR) process in the Agincourt health and socio-demographic surveillance site (HDSS) in rural north-east South Africa. Three village-based discussion groups were convened and consulted about conditions to examine, one of which was under-5 mortality. A series of discussions followed in which routine HDSS data were presented and participants' subjective perspectives were elicited and systematized into collective forms of knowledge using ranking, diagramming and participatory photography. The process concluded with a priority setting exercise. Visual and narrative data were thematically analyzed to complement the participants' analysis. RESULTS: A range of social and structural root causes of under-5 mortality were identified: poverty, unemployment, inadequate housing, unsafe environments and shortages of clean water. Despite these constraints, single mothers were often viewed as negligent. A series of mid-level contributory factors in clinics were also identified: overcrowding, poor staffing, delays in treatment and shortages of medications. In a similar sense, pronounced blame and negativity were directed toward clinic nurses in spite of the systems constraints identified. Actions to address these issues were prioritized as: expanding clinics, improving accountability and responsiveness of health workers, improving employment, providing clean water, and expanding community engagement for health promotion. CONCLUSIONS: We initiated a PAR process to gain local knowledge and prioritize actions. The process was acceptable to those involved, and there was willingness and commitment to continue. The study provided a basis from which to gain support to develop fuller forms of participatory research in this setting. The next steps are to build deeper involvement of participants in the process, expand to include the perspectives of those most marginalized, and engage in the health system at different levels to move toward an ongoing process of action and learning from action.