Microbiologic analysis of tracheal and gastrostomic discharge was performed in 327 patients with iatrogenic injuries of trachea and esophagus, operated during 2003-2008. Main groups of microorganisms, colonizing the tracheobronchial tree were defined. St. epidermalis was defined in 3,9-13,3%, St. aureus - in 12,4-21,1%, Ps. аeruginosa - in 9,2-17,5% of cases. Increase of Candidae colonization was revealed (7,8-12,2%). The increase of polyresistant strains identification was typical. St. epidermalis and St. aureus demonstrated the preserving high sensitivity to vankomycin and linesolide, whereas Ps. aeruginosa showed the growth of resistance to all groups of antibiotics, but polymyxin. The common decrease of antibiotic activity requires the realization of complex antibacterial and antimycotic treatment.