The aim of the present study was to examine the modification of initial empirical treatment based on the microbiological results of bronchoscopic techniques after comparing the diagnostic yield of protected specimen brush (PSB) and bronchoalveolar lavage (BAL) in the immunocompetent patient with community acquired pneumonia (CAP) with results obtained from conventional sputum cultures. 88 patients with presumptive diagnosis of CAP necessitating hospitalization were prospectively studied. Fibreoptic bronchoscopy with quantitative PSB and BAL cultures for common pathogens, mycobacteria and fungi was performed. Conventional sputum cultures were also obtained. PSB and BAL quantitative cultures added 26.1% and 36.4%, respectively, more microbiological documentation for CAP compared to conventional sputum cultures (p < 0.0001). Gram staining was indicative of the pathogen mostly in cases where Streptococcus pneumoniae was isolated, which was also the most frequently isolated pathogen (19.3%), followed by Haemophilus influenzae (9%). M. tuberculosis was isolated in 6.8% of patients. Modification of treatment ensued in 27.3% of patients because of the application of the cultures of sputum and invasive technique. PSB and BAL added significant information to the aetiological diagnosis of hospitalized immunocompetent patients with CAP.