BACKGROUND Associations between respiratory viruses and the bacterial pathogens Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis may be important in the pathogenesis of otitis media (OM). However, data on asymptomatic identification rates of respiratory viruses are limited, particularly in Indigenous populations, who suffer a high burden of OM. METHODS We describe the identification of respiratory viruses alone and in combination with pathogenic OM bacteria in 1006 nasopharyngeal aspirates collected from asymptomatic Aboriginal and non-Aboriginal children in a longitudinal community-based cohort study in rural Western Australia. RESULTS Viruses were identified in 42% of samples from Aboriginal and 32% from non-Aboriginal children. Rhinoviruses were the most frequently identified virus with higher identification rates in Aboriginal (23.6%) than non-Aboriginal children (16.5%; P = 0.003). Rhinoviruses were associated with H. influenzae (odds ratio [OR], 2.24; 95% CI, 1.24-4.07 for Aboriginal children) and M. catarrhalis (OR, 1.94; 95% CI, 1.05-3.57 for Aboriginal children). Adenoviruses were positively associated with H. influenzae in Aboriginal children (OR, 3.30; 95% CI, 1.19-9.09) and M. catarrhalis in non-Aboriginal children (OR, 5.75; 95% CI, 1.74-19.23), but negatively associated with S. pneumoniae in Aboriginal children (OR, 0.39; 95% CI, 0.18-0.84). CONCLUSIONS We found a high identification rate of rhinoviruses and adenoviruses in asymptomatic children. The associations between these viruses and OM bacteria have implications for preventive strategies targeted at specific pathogens.