Background: Preschool children with refractory respiratory symptoms often undergo diagnostic bronchoscopy. The objective of this retrospective analysis was to analyze BAL fluid findings regarding bacterial colonization, cytology and following treatment changes. Moreover, we aimed to correlate bacterial colonization of the airways to allergic sensitization status, asthma severity, vaccination titers and comorbidities like gastroesophageal reflux disease (GERD) or eosinophilic esophagitis (EoE). Methods: In a retrospective analysis, the electronic medical records of 355 children aged 1 to 5 years between 2010 and 2019 who underwent bronchoscopy and further diagnostic testing for persistent respiratory symptoms were analyzed. Results: In 214 children (61.7%) a bacterium was found by culture in the BAL fluid. Of these, 105 (49%) received antibiotic treatment. The most common bacteria were Haemophilus influenzae, Streptococcus pneumoniae and Moraxella catarrhalis (34%, 25% and 16%). There was a significant difference between neutrophil counts in bacteria positive vs. bacteria negative BAL (29.2 + 28.1 % vs. 21.2 + 25.4 %, p=0.02). Children lacking sufficient S. pneumoniae antibodies had significantly more often positive S. pneumoniae cultures in BAL (28.3% vs. 12.8%; p=0.0024). GERD was detected in a total of 115 children (32%) and 9 (2.8%) were diagnosed with EoE Conclusion: Bronchoscopy is a valuable diagnostic tool in persistent respiratory symptoms in preschoolers. Bacterial colonization of the airways is common and airway neutrophils were significantly higher in colonized airways. In many bronchoscopies, results were obtained that led to a change in therapy. Moreover, testing for adequate pneumococcal titers is reasonable in children with persistent respiratory symptoms.