Remote and rural Australian Aboriginal children achieve lower standards of numeracy and literacy than their non-Aboriginal peers. The reasons are complex, but extraordinarily high rates of conductive hearing loss (> 50%) are, in part, responsible for poor classroom success. In addition to the burden of acute bacterial respiratory illness (highest rates of invasive pneumococcal disease in the literature), chronic disease affects virtually every young child. In the Aboriginal community studied, otitis media commenced within 3 months of birth for all infants, progressed to chronic suppurative otitis media in 60% and did not resolve throughout early childhood. Our findings, supported by mathematical modelling, show that the vicious cycle of endemic chronic otitis media is perpetuated by high carriage rates of multiple species and multiple types of respiratory bacterial pathogens, by high cross-infection rates and thus, by early age of pathogen acquisition and prolonged carriage. Long-term damage to respiratory mucosa, possibly linked to later chronic bronchitis and bronchiectasis, follows a constant series of infections by each of the concurrently held pathogens, without periods of recovery. Overcrowding and poor hygiene promote this vicious cycle. Medical and social options for intervention are limited by poor resources, low expectations for health and a complex biology that includes antibiotic resistant pneumococci.