Objective To investigate the effects of new macrolides on the infection of mycobacterium chelonei in children and its side effects. Methods The direction, the course of treatment and side effects were analyzed retrospectively in 22 cases with incision infection of mycobacterium chelonei. Results Clarithromycin were given to 21 cases, and replaced by azithromycin 20 cases for its side effects. The cure rate was 100%. The side effects of Clarithromycin were more than that of azithromycin. 5 years follow-up showed that no case recurred. Conclusions The efficacy of clarithromycin and azithromycin to mycobacterium chelonei is good. Azithromycin is much safe in the two medicines.