A semiquantitative nasopharyngeal culture was found to be sensitive and specific in predicting middle ear pathogens in children with acute bacterial otitis media. In nasopharyngeal specimens with growth of at least 1,000 colonies, the tympanocentesis isolate was present and was either the predominant isolate or accounted for 50% of growth in 16 of 16 children. Data suggest that virulence of nasopharyngeal organisms plays a role in the pathogenesis of acute otitis media. Qualitative differences were found in the nasopharyngeal flora of children with bacterial otitis media as compared with children with clinical otitis media and sterile tympanocentesis cultures, children with uncomplicated upper respiratory illness, and healthy children. Abundant growth of Haemophilus influenzae (greater than or equal to 50% total colony count) was associated with children with bacterial otitis media, and abundant Branhamella catarrhalis was associated with the others (P less than or equal to 0.01). Abundant growth of Streptococcus pneumoniae occurred frequently and regardless of clinical category. Antibiotic treatment of children with otitis media resulted in rapid quantitative and qualitative changes in nasopharyngeal flora.