The aims of this retrospective study were to (i) determine the risk of contamination of lower respiratory tract samples obtained during fiberoscopy in children; (ii) determine the incidence and profile of the bacterial flora of the lower respiratory tract in a selected group of asthmatic children at high risk for bacterial infection; and (iii) identify risk markers for such findings. In 29 asthmatic children, comparison of bacterial cultures of specimens obtained from the upper and, lower respiratory tracts showed that contamination was a possibility in only 3.4% (1/29) of cases. The results from bacterial samples obtained via flexible bronchoscopy in a further 273 consecutively investigated physician-diagnosed asthmatic children were analysed. Patients were selected for bronchoscopy if they had severe chronic asthma or in order to exclude other diseases able to provoke wheezing. Their mean (SD) and median ages were 32.2 (38.3) and 17.5 mo, respectively. The incidence of positive bacterial cultures was 12.1% (33/273 patients). Bacterial flora included H. influenzae (39.5%, 15/38), B. catarrhalis (23.7%, 9/38), Neisseria species (7.9%, 3/38), M. pneumoniae (7.9%, 3/38), P. non-aeruginosa (5.3%, 2/38) and P. aeruginosa (2.6%, 1/38). No clinical or radiological markers were significantly associated with lower respiratory tract bacterial infection. Large quantities of bacteria were present in the lower respiratory tracts of a substantial number of children (1/8) in this selected group of asthmatics. For the moment, however, the clinical implications of this finding remain unclear.