We determined the frequency of colonization of nasopharynx by Gram-negative rods in 63 patients with lung cancer undergoing thoracic surgery who routinely receive antimicrobial prophylaxis. Throat and nasal specimens were taken from each patient twice: on the day of hospital admission (examination I) followed by thoracic surgery and on the fourth day after thoracic surgery (examination II). The isolated strains were identified using API 20E or API 20NE microtests. Susceptibility to selected antimicrobial agents was detected by the disc diffusion method according to Clinical Laboratory Standards Institute recommendations. A total of 27 strains of Gram-negative rods were cultured from 21 patients. During short-term hospitalization, in patients with lung cancer undergoing thoracic surgery and preoperative prophylaxis, qualitative and quantitative changes in Gram-negative rods colonizing the nasopharynx were observed. A statistically significant increase in the frequency of these bacteria on mucous membranes of nasopharynx in examination II was found (Chi-squared test, p<0.00001). The strains of Enterobacteriaceae were highly susceptible to antimicrobial agents, whereas most of the non-fermenting rods were classified as multi-drug resistant organisms.