OBJECTIVE: To study the value of fluorescence quantitative polymerase chain reaction (FQ-PCR) for detecting Mycoplasma pneumoniae (MP)-DNA in bronchoalveolar lavage fluid (BALF) in the early diagnosis of Mycoplasma pneumoniae pneumonia (MPP). METHODS: FQ-PCR was used to detect MP-DNA in BALF obtained by fiberoptic bronchoscopy from 61 children with MPP, and the sensitivity and the specificity of FQ-PCR were compared with the traditional serological test. RESULTS: The sensitivity and the specificity of BALF FQ-PCR for detecting MP-DNA were 94% and 100% respectively. The accuracy of BALF FQ-PCR assay for detecting MP-DNA was higher than that of the serological test at the early stage of the disease (1-7 days) (P<0.01). In the children with refractory MPP, BALF FQ-PCR assay also showed higher accuracy for detecting MP-DNA than the serological test (P<0.01). The copies of MP-DNA in children with refractory MPP were significant higher than those in children with common MPP (P<0.05). The copies of MP-DNA were positively correlated with CRP values (r=0.845, P<0.01). CONCLUSIONS: FQ-PCR assay of BALF for detecting MP-DNA in BALF is superior to the serological test. It is a reliable method for the early diagnosis of MPP, especially refractory MPP. The copies of MP-DNA can be used as an index for evaluation of the treatment outcome of refractory MPP.