Abstract: Objective To explore the application value of the detection of respiratory tract pathogenic gene for the diagnosis of Streptococcus pneumoniae infection in children. Methods From June, 2016 to June, 2017, 224 cases who were newly diagnosed with bacterial pneumonia hospitalized in the Department of respiration, Capital Institute of Pediatrics were collected. Each case was collected deep sputum or bronchoalveolar lavage specimens, according to the traditional bacterial culture was divided into non Streptococcus pneumoniae group 136 cases and 88 cases of Streptococcus pneumoniae group. The pathogens in the two groups were detected by respiratory tract gene detection kit (loop mediated isothermal amplification). The detection efficiency of the two detection methods was compared by SPSS 17.0 software and Kappa test. Results The detection of respiratory pathogens were detected in Streptococcus pneumoniae gene of Streptococcus pneumoniae in 40 cases, including deep sputum samples were detected in 32 cases, bronchoalveolar lavage fluid were detected in 8 cases. Streptococcus pneumoniae was detected in the detection of respiratory pathogens gene of Streptococcus pneumoniae in 80 cases, including deep sputum samples were detected in 52 cases, bronchoalveolar lavage fluid were detected in 28 cases. Compared with traditional pathogen culture, the sensitivity, specificity, total coincidence rate, positive predictive value and negative predictive value of respiratory tract pathogen gene detection for Streptococcus pneumoniae were 90.9%, 74.4%, 80.3%, 66.7% and 92.3%, respectively. The two detection methods were consistent with the detection rate of Streptococcus pneumoniae (Kappa>0.4). Conclusion Respiratory tract pathogen gene detection has the advantage of fast, specific and sensitive. It has high consistency with traditional pathogen isolation and culture test, and it can provide reliable diagnosis and treatment basis for clinicians.