Many recent studies have shown that Mycoplasma genitalium is among the pathogens responsible for Chlamydia trachomatis-negative nongonococcal urethritis (NGU). A single 1-g dose of azithromycin (AZM) has been recommended for the treatment of NGU, including M. genitalium-positive NGU, irrespective of whether it is positive or negative for Chlamydia trachomatis. The purpose of this study was to determine the minimal inhibitory concentrations of AZM against Mycoplasma genitalium strains, and to assess its clinical efficacy against Mycoplasma genitalium-positive NGU. Seven Mycoplasma genitalium strains were obtained from the American Type Culture Collection, and susceptibility testing of seven antimicrobial agents was performed using a broth microdilution method. Thirty men with M. genitalium-positive NGU were enrolled in this study and treated with a single 1-g dose of AZM. AZM and clarithromycin (CAM) were highly active against M. genitalium strains. Fluoroquinolone activities were moderate, and of the three fluoroquinolones tested, gatifloxacin (GFLX) and sparfloxacin (SPFX) were more active than levofloxacin (LVFX). In 25 of 30 (83.3%) men treated with a single 1-g dose of AZM, M. genitalium was eradicated from first-void urine samples, as determined by polymerase chain reaction. AZM was highly active against M. genitalium, and a single 1-g dose of AZM for M. genitalium-positive NGU was tolerated in Japan. These findings may be helpful in establishing optimal treatment for M. genitalium-positive NGU.