Nasopharyngeal and middle-ear colonization with bacteria and viruses, including Mycoplasma pneumoniae and chlamydiae, was investigated in a survey of 54 children with acute otitis media (AOM) and 201 control children without AOM in Greenland. In total, 98% with AOM and 91% without AOM carried potentially pathogenic bacteria in the nasopharynx. Two or more potentially pathogenic species were carried by 78% with AOM and 57% without AOM. Haemophilus influenzae was found in 92% and 77%, respectively, but only Streptococcus pneumoniae was found significantly more often in the nasopharynx of children with AOM than in age-matched controls (P < .03). The two species were found in 22 of 24 ear-discharge specimens. Nine children (three with AOM) had chlamydiae in the nasopharynx, and seven of them reported rhinitis. Enteroviruses or rhinoviruses were detected in 23 nasopharyngeal specimens from 39 children with AOM, in 13 such specimens from 39 children without AOM (P = .040), and in 4 of 14 ear-discharge specimens. The potentially pathogenic load in the nasopharynx was massive, suggesting an association with the high prevalence of otitis media among children in Greenland.