To assess resistance rates among respiratory tract pathogens and antimicrobial usage of children in Iceland and Lithuania, and to correlate usage patterns with resistance rates, nasopharyngeal swabs were taken from healthy children attending day-care centres in Reykjavik (n = 6) and Vilnius (n = 13), and cultured for pneumococci, Haemophilus influenzae and Moraxella catarrhalis. Information about recent antimicrobial use was obtained by a questionnaire. 50% and 51% carried pneumococci, 59% and 67% carried H. influenzae and 60% and 46% carried M. catarrhalis, in Reykjavik (n = 297) and Vilnius (n = 508), respectively. The prevalence of penicillin non-susceptible pneumococci was 11% in Reykjavik (mainly serotype 6B) and 5% in Vilnius (mainly 23F). At the time of sampling 3% of the children in Reykjavik and 8% in Vilnius were receiving antimicrobials. Children carrying penicillin non-susceptible pneumococci had used antimicrobials more frequently in the preceding month and this was significant for the Icelandic children (p < 0.0002). Antimicrobial use was more common in Vilnius than in Reykjavik, yet antimicrobial resistance was more common in Reykjavik. Resistance rates cannot be predicted only on the basis of recent antimicrobial use.