Few epidemiological studies of middle ear disease have been conducted in Aboriginal and Torres Strait Islander populations, yet the disease is common and causes hearing impairment and poorer educational outcomes. The objective of this study is to identify factors associated with abnormal middle ear appearance, a proxy for middle ear disease. Aboriginal and Torres Strait Islander children aged 0-14 years receiving a Child Health Check (CHC) at an urban Indigenous Health Service, Brisbane, Australia were recruited from 2007 to 2010. Mixed-effects models were used to explore associations of 10 recognised risk factors with abnormal middle ear appearance at the time of the CHC. Ethical approval and community support for the project were obtained. Four hundred and fifty-three children were included and 54% were male. Participants were Aboriginal (92%), Torres Strait Islander (2%) or both (6%). Abnormal middle ear appearance was observed in 26 (6%) children and was significantly associated with previous ear infection (odds ratio (OR), 8.8; 95% confidence interval (CI), 3.2-24.0) and households with eight or more people (OR, 3.8; 95% CI, 1.1-14.1) in the imputed multivariable mixed-effects model. No significant associations were found for the other recognised risk factors investigated. Overcrowding should continue to be a core focus for communities and policy makers in reducing middle ear disease and its consequences in Aboriginal and Torres Strait Islander peoples.