The aim of this study was to evaluate the correlation between the stage of cystic fibrosis and the intensity of accompanying morphological changes--including transmission electron microscopy--within bronchial mucosa. The stage of the disease was assessed on the basis of clinical status and radiological and endoscopic examination. We focused on morphological changes in epithelial cells, the presence of metaplasia and/or dysplasia, the type of inflammatory infiltrate, and the presence of epithelial ulcerations, thickening of epithelial basement membrane and collagenization of lamina propria. We found two clinically different patients groups. The first one was in a poor clinical condition, advanced inflammatory fiberoptic bronchoscopy and radiological changes, multiple exacerbations, and with chronic inflammation and only focal appearance of ciliated epithelium. Moreover, squamous cell metaplasia and dysplasia was diagnosed in 3 and 4 cases, respectively. The other group, in a better clinical condition, had normal BMI and small changes on chest Xray. In this group the diagnosis of cystic fibrosis was made at later age. Two patients from this group displayed features of acute phase; ciliated epithelium was covering the whole sample. After statistical analysis, we found a correlation between the clinical course and the morphological changes in bronchial mucosa. Bronchial ulcerations, squamous cell metaplasia and dysplasia were found in the group with the more severe clinical course.