Abstract: Objective　To study the pathogenic etiology between nasopharyngeal aspirates (NPA) and bronchoalveolar lavage fluid (BALF) in children with lower respiratory infection. Methods Multiple pathogen in NPA and BALF from 210 cases with lower respiratory tract infection was detected. Seven common respiratory virus (respiratory syncytial virus, adenovirus, influenza virus A, influenza virus B, parainfluenza 1, parainfluenza 2, parainfluenza 3) were detected by direct immunofluorescence assay. MP, CP and HBoV were detected by fluorescence quantitative PCR.HRV and hMPV were detected by RT-PCR. Aspirates were cultured for bacteria. The results of pathogen detection in secretions of upper and lower respiratory tract were analyzed. Results Total positive detection rate of NPA and BALF in 210 cases was 91.9% (193/210), which is higher than that in NPA 75.2% (158/210) and that in BALF 85.2% (179/210). Bacteria detection rate in NPA was 13.3% (28/210), and 8.6% (18/210) in BALF, without significant difference (P=0.118). Bacteria detection rate in NPA and BALF was of poor consistency (Kappa=0.262). Virus detection rate in NPA was 24.3%, which is higher than that in BALF15.2%. BALF-MP detection rate was 77.6% (163/210), significantly higher than that in NPA 53.3% (112/210). There are 95.5% (107/112) cases with positive results in NPA-MP detectioncan also be detected in the BALF-MP. MP copies in BALF were significantly higher than that in NPA (4.28×106 vs. 1.31×105), and its positive rate in NPA was still higher than that in BALF. MP detection rate in NPA in children with clinical course of longer than two weeks was much lower than those with clinical course of two weeks or less. Conclusions The pathogen detection of virus and MP in NPA can be used as a reference for lower respiratory tract infection. The joint detection of NPA and BALF can improve the detection power. The sensitivity of virus detection in NPA is higher than that in BALF. NPA pathogen detection of virus and MP is of great important evidence-based medicine in the diagnosis of lower respiratory infection. MP detection rate and its copies in BALF are significantly higher than that in NPA. BALF detection is the supplement of pathogen diagnosis in severe or refractory lower respiratory infections.