The microbiological profile of the tracheobronchial tree (TBT) was studied in newborn infants after surgery in case of congenital heart diseases. Mechanical ventilation is used for more than 24 hours in all patients. The study included 50 children with respiratory pathology. It was performed dynamic microbiological study of biomaterial from tracheobronchial tree and pharynx. Also it was determined characterization of endogenous intoxication. It was revealed that gram-positive dominated in the microbial profile of tracheobronchial tree in most cases. Cephalosporins 2nd generation was used in the initial therapy. Strains of microorganisms were isolated in every second patient by the end of the first week of staying in the reanimation department. The microorganisms were resistant to initial antibacterial prevention. It was the reason for the antibiotic change. Preference is given to cephalosporins 3 and 4 generations, carbapenems, glycopeptides. In 11 (22%) patients treatment was corrected repeatedly, because a resistance against the appointed antibiotics formed in the future.