The microbiology of bacterial pathogens attributable to acute otitis media(AOM) and otitis media with effusion (OME) have therapeutic and prognostic implications for the treatment of middle ear disease in infancy. Healthy newborns (n=306) were enrolled shortly after birth and followed monthly until 6 mos. of age, and then at 8, 10, 12, 15, 18, 21, and 24 mos. Nasopharyngeal(NP) cultures were taken using sterile technique, following ear examinations and medical information collected at scheduled visits. Bacteria most often isolated in OM infections included streptococcus pneumoniae (SP),Haemophilus influenzae (NTHI) and Moraxella catarrhalis(MC). At 3 mos., roughly 30% of the cohort carried one or more bacterial pathogens, which increases to 42% by 6 mos. Carriage rates remained stable, thereafter, through 12 mos. of age. Cumulative acquisition rates were highest for MC, with 30% of the cohort colonized at 3 mos. and 70% colonized at 12 mos. of age. Only 15% of the cohort were colonized with SP organisms at 3 mos., but rates increases exponentially to 54% at 12 mos. Less than 10% of the cohort were colonized by NTHI at 3 mos., with colonization increasing to 33% at 12 mos. of age. Bacterial pathogens were associated, but not significantly, with first episodes of AMO in infancy. A significant association, (p<.01) however, was found between colonization with one or more bacterial pathogens and recurrent episodes of AOM. Similar associations were found between bacterial pathogen carriage rates and chronic otitis media with effusion.