Objective To investigate the application of bronchoalveolar lavage of flexible bronchoscopy in diagnosis and treatment of children with Mycoplasma pneumoniae pneumonia(MPP). Methods Clinical data of 155 pneumonia patients (57 cases of MPP and 98 cases of non-MPP),who had examination in flexible bronchoscopy, MP-DNA of bronchoalveolar larlavage fluid(BALF),and the traditional blood serological test of Mycoplasma pneumoniae,were retrospectively analyzed from Aug.2011 to Apr.2012 in Anhui Provincial Children’s Hospital. Results Mycoplasma pneumoniae pneumonia often occur red in children over the age of 5 or with lobar pneumonia or atelectasis in the left lung. The accuracy of MP-DNA in BALF was higher than that of the blood serological test. After alveolar wash and administration of medicines, 95.7% of the atelectasis cases were cured. Conclusions Flexible bronchoscopy and bronchoalveolar lavage should be applied to MPP and atelectasis cases as soon as possible to promote lung recruitment and improve the outcome.