OBJECTIVE: We aimed to compare the cellular composition of bronchoalveolar lavage (BAL) fluids in children with chronic unexplained cough (group 1) and severely neurologically impaired children with chronic or recurrent respiratory problems (group 2) with the BAL cytology of children without pulmonary or systemic diseases (group 3). METHODS: Bronchoscopy with BAL fluid analysis was performed in all subjects. Children with respiratory symptoms underwent 24-hour multichannel intraluminal impedance monitoring. RESULTS: A significant difference was found between the groups in the total number of cells in BAL fluid cytology (191 [range, 24-12,747], 747 [range, 53-13,000], and 105 [range, 41-233] cells/μL, P = .015), in the percentage of neutrophils (21.2 [SD = 32.4], 49.4 [SD = 36.6], and 3.6 [SD = 2.4], P < .001), and in the percentage of lipid-laden macrophages (10.3 [SD = 11.4], 13.7 [SD = 15.8] and 0.44 [SD = 1.0], P < .001). CONCLUSION: The BAL fluid cytology provides useful data for determining the cause of chronic unexplained cough and chronic or recurrent respiratory problems in severely neurologically impaired children.