In the past decade, microbial pathogens have been shown to have a role in asthma pathogenesis, but most studies have focused primarily on viruses. Recent studies on the potential role of bacteria colonization in asthma development have found early postnatal nasopharyngeal colonization with specific bacteria pathogens to be associated with asthma at five years of age. It has also been observed that adult asthmatics have different respiratory colonization patterns, including differences in specific phyla, load and diversity, compared to non-asthmatic controls. However, most such studies have been restricted to a small number of specific bacteria pathogens detected by microbiological culture, and ignored the possible involvement of unexpected organisms. Recent studies using high-throughput sequencing have been restricted to a small sample size and mostly limited to adult subjects. In this study, we performed multiplex sequencing of the V1-3 and V4 variable regions of the 16S rRNA gene on the 454 (Roche) and Illumina platforms. We characterized the bacteria composition of the nasopharyngeal (NP) microbiome in asymptomatic infants during their first year of life. The subjects are part of a community-based cohort study of 263 high allergy-risk children, followed from birth to ten years of age. For each child, we collected “baseline” NP aspirates when the child was healthy, as well as “infection” NP aspirates during each episode of acute respiratory infection. We observed a simple NP microbiome structure in which most communities were dominated by one or two genera such as Corynebacterium, Staphylococcus, Alloiococcus, Streptococcus, Moraxella or Haemophilus. However, the analysis suggests the microbiome is quite dynamic, with community profiles changing over time and dependent on infection status. We are currently investigating the relationship between the infant microbiome and asthma, wheeze, respiratory infection and allergy-related outcomes during childhood.