Background: Otitis media (OM) is the most common paediatric illness for which antibiotics are prescribed. In Australian Aboriginal children OM is frequently asymptomatic and starts at a younger age, is more common and more likely to result in hearing loss than in non-Aboriginal children. Absent transient evoked otoacoustic emissions (TEOAEs) may predict subsequent risk of OM. Methods: 100 Aboriginal and 180 non-Aboriginal children in a semi-arid zone of Western Australia were followed regularly from birth to age 2 years. Tympanometry was conducted at routine field follow-up from age 3 months. Routine clinical examination by an ENT specialist was to be done 3 times and hearing assessment by an audiologist twice. TEOAEs were measured at ages <1 and 1-2 months. Cox proportional hazards model was used to investigate the association between absent TEOAEs and subsequent risk of OM. Results: At routine ENT specialist clinics, OM was detected in 55% of 184 examinations in Aboriginal children and 26% of 392 examinations in non-Aboriginal children; peak prevalence was 72% at age 5-9 months in Aboriginal children and 40% at 10-14 months in non-Aboriginal children. Moderate-severe hearing loss was present in 32% of 47 Aboriginal children and 7% of 120 non-Aboriginal children aged 12 months or more. TEOAE responses were present in 90% (46/51) of Aboriginal children and 99% (120/121) of non-Aboriginal children aged <1 month and in 62% (21/ 34) and 93% (108/116), respectively, in Aboriginal and non-Aboriginal children at age 1-2 months. Aboriginal children who failed TEOAE at age 1-2 months were 2.6 times more likely to develop OM subsequently than those who passed. Overall prevalence of type B tympanograms at field follow-up was 50% (n = 78) in Aboriginal children and 20% (n = 95) in non-Aboriginal children. Conclusion: The burden of middle ear disease is high in all children, but particularly in Aboriginal children, one-third of whom suffer from moderate-severe hearing loss. In view of the frequently silent nature of OM, every opportunity must be taken to screen for OM. Measurement of TEOAEs at age 1-2 months to identify children at risk of developing OM should be evaluated in a routine health service setting.