The diseases of the respiratory system occupy one of the leading positions in the range of morbidities among the Russian population, both in adults and children. Partly, it is due to an increase of patients with primary and secondary immunodeficiencies, with anatomical anomalies of the respiratory tract, and other diseases of the bronchopulmonary system. Classical pathogens, causing the bacterial respiratory diseases, as a rule, are: Streptococcus pneumoniae, Haemophilus influenzae, Klebsiella pneumoniae, Pseudomonas spp., Staphylococcus spp., as well as other representatives of the Enterobacteriacae family. But each year, the scientific literature presents more and more microorganisms - pathogens of infectious diseases of various localization in humans, the clinical significance of which has long remained poorly understood. These pathogens include representatives of large families of Corynebacteriaceae, Mycobacteriaceae, Nocardiaceae. Clinical physicians need to consider possible disorders in the immune system in patients with respiratory impairment, as well as a wide range of pathogens affecting the respiratory tract. To manage such patients effectively, the close interaction of pulmonologists, bacteriologists, and allergologists-immunologists is important.