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<p>Abstract</p> <p>Background</p> <p>Acute otitis media with perforation (AOMwiP) affects 40% of remote Indigenous children during the first 18 months of life. <it>Streptococcus pneumoniae</it>, <it>Haemophilus influenzae </it>and <it>Moraxella catarrhalis </it>are the primary bacterial pathogens of otitis media and their loads predict clinical ear state. Our hypothesis is that antecedent respiratory viral infection increases bacterial density and progression to perforation.</p> <p>Methods</p> <p>A total of 366 nasopharyngeal swabs from 114 Indigenous children were retrospectively examined. A panel of 17 respiratory viruses was screened by PCR, and densities of <it>S. pneumoniae, H. influenzae </it>and <it>M. catarrhalis </it>were estimated by quantitative real time PCR. Data are reported by clinical ear state.</p> <p>Results</p> <p><it>M. catarrhalis </it>(96%), <it>H. influenzae </it>(91%), <it>S. pneumoniae </it>(89%) and respiratory viruses (59%) were common; including rhinovirus (HRV) (38%), polyomavirus (HPyV) (14%), adenovirus (HAdV) (13%), bocavirus (HBoV) (8%) and coronavirus (HCoV) (4%). Geometric mean bacterial loads were significantly higher in children with acute otitis media (AOM) compared to children without evidence of otitis media. Children infected with HAdV were 3 times more likely (p < 0.001) to have AOM with or without perforation.</p> <p>Conclusion</p> <p>This study confirms a positive association between nasopharyngeal bacterial load and clinical ear state, exacerbated by respiratory viruses, in Indigenous children. HAdV was independently associated with acute ear states.</p>