A protected catheter brush introduced by fiberoptic bronchoscopy was used to sample the tracheai and bronchial mucosa in 28 horses with small airway disease. Tracheal and bronchial brushings were examined for the presence of fungi, aerobic and anaerobic bacteria, and a cytoiogical evaluation was also done on fluid collected by the bronchoalveolar lavage (BAL) technique. Microorganisms (bacteria and fungi) were isolated more often in tracheal brushings (53.6%) than in bronchial brushings (10.7%). Anaerobic bacteria were not isolated. Results of this study indicate that fiberoptic bronchoscopy using a protected catheter brush is an easy and practical technique to obtain minimally contaminated samples for isolation of microorganisms from the lower respiratory tract of horses. However, no association was observed between isolation of high numbers of microorganisms from the bronchi and severity of small airway disease.