OBJECTIVE To study the features of pathogens in children with lower respiratory tract infection. METHODS A total of 108 children who were hospitalized due to lower respiratory tract infection and underwent fiber bronchoscopy between January 2017 and June 2018 were enrolled. Bronchoalveolar lavage fluid samples were collected. Multiple quantitative real-time PCR was performed to detect pathogens. RESULTS Of the108 children, 85 (78.7%) were found to have pathogens, among whom 52 (48.1%) had single pathogen infection and 33 (30.6%) had multiple pathogen infections. Mycoplasma pneumoniae was detected in 38 children (35.2%), and was the most common pathogen. The children aged 36 - <72 months had the highest detection rate of Mycoplasma pneumoniae. Both Streptococcus pneumoniae and Haemophilus influenzae were detected in 29 children (26.9%) and Streptococcus pneumoniae was mainly detected in children aged <24 months. Each of Acinetobacter baumannii, Candida albicans and Klebsiella pneumoniae was detected in 3 children. Among the 31 children with bronchopneumonia, 9 were found to have Haemophilus influenza, with the highest detection rate of 29%. Among the 34 children with lobar pneumonia, 22 were found to have Mycoplasma pneumoniae, with the highest detection rate of 65%. Among the 22 children with bronchial foreign bodies and bronchopneumonia, 10 were found to have Streptococcus pneumoniae, with the highest detection rate of 45%. CONCLUSIONS In children with lower respiratory tract infection, Mycoplasma pneumoniae is the most common pathogen, followed by Streptococcus pneumoniae and Haemophilus influenzae. There are differences in the detection rates of pathogens between children with different ages and different types of lower respiratory tract infection.