This report focuses on changes in the nasopharyngeal bacterial flora before and after administration of antimicrobial agents in 172 cases of acute upper respiratory infection in patients aged 6 years or younger. The antimicrobial agents administered were amoxicillin (AMPC) (34%), clavulanic acid/amoxicillin compound (11%), cefditren pivoxil (CDTR-PI) (43%), and others (12%). Changes in nasopharyngeal bacterial flora were investigated with reexaminations conducted after 2–5 days (day 2–5 subgroup), 6–10 days (day 6–10 subgroup), and 11 days and thereafter. There was a significant reduction in the Streptococcus pneumoniae detected in the group administered AMPC (AMPC group) in the day 2–5 subgroup and the day 6–10 subgroup. There was also a significant decrease in H. influenzae in the group administered CDTR-PI (CDTR-PI group) in the day 2–5 subgroup. From this it was inferred that for the most part significant changes in infectious nasopharyngeal bacteria occurred in the day 2–5 subgroups. However, a significant improvement in the degree of inflammation, as indicated by leukocyte infiltration images for the AMPC group, was observed in the day 2–5 subgroup, and for the CDTR-PI group in the day 6–10 subgroup. On the other hand, in both the antimicrobial agent groups, S. pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis were newly detected at reexamination. Furthermore, a difference in the incidence of these bacteria was observed between the 2 antimicrobial agent groups. It was suggested that such phenomena related to the survival of resistant strains or a recurrence otitis media.