Background: The tong elimination half-life of azithromycin allows subinhibitory serum and epithelial Lining fluid (ELF) concentrations over a period of several weeks post treatment, which may have an impact on the emergence of macrolide resistance. In this prospective, open-label, randomized study, four macrolides and the azalide azithromycin were studied for their Likelihood to promote resistance in the oral flora of children with respiratory tract infections. Patients and Methods: Children were randomly assigned to receive azithromycin, clarithromycin, erythromycin, roxithromycin and josamycin. Throat swabs were obtained prior to treatment and weekly for 6 weeks. Minimum inhibitory concentrations (MICs) for resistant strains were assessed by E-test and National Committee for Clinical Laboratory Standards (NCCLS) broth microdilution. Results: One week post treatment, up to 90% of children harbored macrolide-resistant strains in their oral flora. Except for azithromycin, the percentage of patients colonized by resistant organisms decreased to a rate of 17% for clarithromycin (10/60), erythromycin (2/12) and josamycin (2/12) and 33% for roxithromycin (4/12) after 6 weeks. In the azithromycin group, 85% (51/60) of patients were colonized by macrolide-resistant organisms after 6 weeks, 11.6% (7/60) of children suffered from reinfection. Conclusion: Azithromycin therapy appears to put selective pressure on the infective and native flora of children, promoting the carriage of macrolide-resistant strains.