Introduction: Infections caused by multiple drug-resistant pathogens represent an increasingly often encountered challenge in clinical practice. The problem particularly applies to patients with chronic lung diseases resulting in multiple hospitalisations. The aim of this paper was to analyse the incidence of alert pathogens isolated from patients hospitalised in the department of lung diseases, who were divided into three groups: patients qualified for lung transplantation, patients treated for neoplastic diseases and patients with chronic lung diseases. Materials and methods: Analysis involved microbiological test results of 3950 samples obtained from 3521 patients divided into: 200 patients being qualified for lung transplantation, 1292 patients treated for neoplastic diseases and 2029 patients with chronic lung diseases. Results: Infection with alert pathogen was found in 155 of 3521 patients (4.4%). Most often isolated infectious agent was P. aeruginosa, which accounted for 27% of infections. Other pathogens were as follows A. baumanii ESBL(−) (13%), S. pneumoniae (12%), E. cloacae ESBL(+) (10%), K. pneumoniae ESBL(+) (10%), S. aureus MRSA (8%), E. faecalis (7%), E. coli ESBL(+) (6%), S. maltophilia ESBL(+) (5%) and E. kobei ESBL(+) (2%). Alert pathogens were found in 31 (15%) of 200 patients being qualified for lung transplantation, 89 (4.4%) of 2029 patients with chronic lung diseases and 35 (2.7%) of 1292 patients treated for neoplastic diseases. Difference between infection frequency in patients being qualified for lung transplantation and the remaining groups was statistically significant (p < 0.01). P. aeruginosa infection was the most frequent in all groups. It constituted 35% in patients being qualified for lung transplantation, 29% in patients treated for neoplastic diseases and 22% in patients with chronic lung diseases. Conclusions: Infections caused by alert pathogens were found in more than 4% of patients hospitalised in the department of lung diseases between 2007 and 2011. Their frequency was significantly higher in patients being qualified for lung transplantation than in other analysed groups. In all examined groups the most frequently isolated bacteria was P. aeruginosa (27% of all isolates).