Objectives The source of the bacteria involved in silent aspiration remains to be completely defined. This study aimed to obtain reliable evidence on silent aspiration of oral bacteria in elderly patients. Methods After obtaining informed consent, the cough and swallowing reflexes of patients were assessed. Bronchial fluids from patients undergoing lung resections were collected with a micro-sampling probe, and α-amylase activity of bronchial fluids was measured to estimate the degree of silent aspiration. The bronchial fluids were cultured aerobically and anaerobically on blood agar plates, and colonies were identified by 16S rRNA gene sequencing. Additionally, whole saliva bacterial amounts and composition were analyzed. Results Six patients (72.2±5.8 years) exhibited an impaired swallowing reflex and 5 (75.4±7.9 years) had a normal swallowing reflex, while all patients had a normal cough reflex. α-Amylase activity was detected in bronchial fluids of both the impaired and normal reflex groups. The amount of anaerobic bacteria in bronchial fluids in the impaired reflex group [(3.0±3.5)×104] was higher than in the normal reflex group [(2.5±5.3)×104sup], although the difference was not significant. Actinomyces, Gemella, Streptococcus, Rothia, Mogibacterium, and Campylobacter were the predominant bacterial species in bronchial fluids of the impaired reflex group, while Streptococcus, Lactobacillus, Veillonella, and Actinomyces were predominant in the normal reflex group. Conclusions Our results suggest that bacteria in bronchial fluids associated with silent aspiration are derived from saliva, and that the bronchial fluids of elderly patients with an impaired swallowing reflex may have a characteristic microbiota.