It is generally recognised that poor living conditions and poor hygiene underlie the high burden of infection experienced by Indigenous (Aboriginal and Torres Strait Islander) children living in remote communities. There has been little research on this topic. Taking an ecological approach, our study aimed to identify the key factors contributing to poor hygiene in one remote Aboriginal community and to determine appropriate approaches for improving hygiene and reducing the burden of infection among children. Key findings include that multifaceted interventions are required to ensure that household water and sanitation technology are functional, hygiene behaviour change is achieved and environments that enable good hygiene behaviour are created. Many of the factors contributing to the problem of poor living conditions and poor hygiene in these communities are outside the control of the health system. Intersectoral collaboration and action is required to identify acceptable, effective and sustainable solutions.