Abstract: OBJECTIVE To investigate the performance of fully automated fluorescent polymerase chain reaction(PCR) detection for six pathogens in the lower respiratory tract. METHODS A total of 299 lower respiratory tract secretions samples were collected from patients with lower respiratory tract infections in the respiratory ICU of a three-A hospital in Beijing from Jun. 2024 to Feb. 2025. Pathogenic bacteria were detected through both a fully automated fluorescent PCR and microbial culture method. A comparative analysis was conducted on the positive detection rates,number of positive bacterial species, categories of positive bacterial species, concentrations and consistency rates of detection for six bacteria(Haemophilus influenzae, Klebsiella pneumoniae, Streptococcus pneumoniae, Acinetobacter baumannii, Stenotrophomonas maltophilia and Pseudomonas aeruginosa) between the two methods. RESULTS The positive detection rate of the fully automated fluorescent PCR method(26.64%) was higher than that of the microbial culture method(10.48%) among the 299 lower respiratory tract secretions samples, with a statistically significant difference(P＜0.05). Except for S. pneumoniae, there were statistically significant differences in the positive detection rates between the two methods for the other five bacterial species(P＜0.001), with higher detection rates for K. pneumoniae and A. baumannii by the fully automated fluorescent PCR method, at 48.83% and 39.80%, respectively. The overall consistency rate of positive detection results between the two methods was 82.39%, which was statistically significant(P＜0.001). The median times for microbial culture and fully automated fluorescent PCR detection methods were 96 h and 1.77 h, respectively, with a statistically significant difference(P＜0.05). CONCLUSIONS The fully automated fluorescent PCR detection method can be used for the etiological diagnosis of lower respiratory tract diseases. It exhibits high consistency and sensitivity with the microbial culture method, detects a wide range of bacterial species, has short detection time, is simple to operate, can detect the nucleic acid concentration of samples, and has high clinical application value.