Introduction: Children with Down syndrome (DS) often present with chronic or recurrent respiratory symptoms. This can be caused by anatomical and/or immunological predisposition. With this study, we aim to evaluate the differences in microbiota in the lower airways of patients with DS versus controls. Methods: All endoscopic procedures under general anesthesia in patients with DS were reviewed retrospectively. We compared the microbiological data from BAL samples (when available) to a cohort of children with chronic respiratory symptoms but without any other relevant medical history. Results: Endoscopic data were available for 65 DS patients, microbiological data for 47 out of 65 patients (72%). The control group consisted of 150 children without significant underlying disease, who were matched for age and sex. Microbiological data were available for 135 out of 150 patients (90%). Microorganisms were categorized and compared in both groups, with no statistical differences. Mostly present were typical bacteria such as H. influenzae, Moraxella catarrhalis, Streptococci and Staphylococci. Conclusion: There were no significant differences in presence of pathogens in the lower airways of children with DS and chronic respiratory symptoms, compared to controls with similar symptomatology.