The factors underlying poor child health in remote Australian Indigenous (Aboriginal and Torres Strait Islander) communities are complex. There is a lack of consistent and reliable information that allows: (i) the identification of priorities or areas of particular need at household and community levels; (ii) monitoring progress over time; and (iii) the assessment of the impact of interventions. This paper describes the process and methods used to identify the factors that underlie high rates of poor child health in remote Aboriginal communities in the Northern Territory (NT). This work has led to the development of indicators and tools suitable for use within a continuous quality improvement programme. Indigenous and non-Indigenous individuals from a range of disciplines and backgrounds participated in study activities. This allowed for a range of perspectives, including scientific, lay and Aboriginal perspectives, to be accommodated and reflected in study outcomes and outputs. Study participants identified a wide range of physical and social factors that they believe underlies poor child health in remote Aboriginal community contexts in the NT. The approach taken in this study provides some confidence that the indicators developed will be seen as meaningful and appropriate by the residents of remote communities and key stakeholders. Two tools have been developed and are now in use in the practice setting. One assesses social determinants of health at the community level, for example water supply, food supply. The second applies to individual households and assesses the social and environmental indicators that are recognized as placing children at greater risk of poor health and development outcomes.