Macrolide-resistant Mycoplasma pneumoniae is emerging in several countries, and it is mainly observed in children. To our knowledge, we conducted the first multicenter prospective epidemiological study of macrolide-resistant M. pneumoniae in order to investigate regional differences in the susceptibility of macrolide-resistant M. pneumoniae to antibacterial agents. The in vitro activities of 11 antimicrobial agents against macrolide-resistant M. pneumoniae isolates from 5 different areas of Japan were investigated. Among 190 M. pneumoniae isolates from pediatric patients, 124 (65.2%) isolates showed macrolide resistance and possessed an A2063G transition in domain V of the 23S rRNA. These isolates showed high resistance to erythromycin, clarithromycin, and azithromycin with minimum inhibitory concentrations (MICs) ≥ 16 μg/ml. Conversely, quinolones such as garenoxacin, moxifloxacin, tosufloxacin, and levofloxacin exhibited potent antimycoplasmal activity. No regional differences were observed with respect to the MICs among the 5 areas in Japan.