The clinical specimens received from patients hospitalized in Department of Thoracic Surgery between 1997 and 2001 were microbiologically examined. The main specimen for microbiological examination was pleural fluid (median 34%). The frequency of specimens from bronchial tree increased significantly (from 4% to 26%) with concurrent decrease of sputum (from 29% to 6%). Among isolated pathogens, Gram negative rods were the most frequent (median 48%) and Pseudomonas sp. was the main pathogen among them. Occurrence of staphylococci was median 22% and Staphylococcus aureus, with a little decrease in analyzed period, was still the main Gram positive pathogen. Simultaneously the occurrence of MRSA in the last three years dropped three times. The number of isolations of yeasts have risen from 5.8% to 10.3%.