A 20-year observation showed that there were significant changes in the species composition and ratio of the sensitive and resistant variants of opportunistic bacteria constituting the main part of the pathogens causing infectious complications in somatic hospitals. However, the taxonomic structure of the pathogens changed slowly, perhaps due to the ever increasing role of the hospital strains in the development of the infections in the inpatients. The higher number of the resistant variants primarily depended on the rate of the drug use, as well as on the biological and physiological properties of the bacteria, the structure of the drugs, the nature of the resistance, etc. Therefore, the following up of the species composition of the pathogens for estimating the role of every taxon in the development of the infections with their particular localization and the determining of the relative number of the strains sensitive to the drugs used in the hospitals are the obligatory conditions for rational antibacterial chemotherapy.