Objective. To study the microbial diversity of the respiratory microbiota in patients with undifferentiated pathological changes in the lungs.Materials and methods. The study of biopsy material obtained during video-assisted thoracoscopic lung resection was conducted in 36 patients with undifferentiated pathological changes in the lungs. The study of the microbial diversity of the lungs was carried out by high-performance sequencing using the MiSeq sequencer (Illumina, USA) using a protocol based on the analysis of variable regions of the 16s rRNA gene.Results. The density and microbial diversity of the pulmonary microbiota of the obtained samples were studied. In all patient samples, the dominant taxa at the Phylum level are Proteobacteria (the median relative representation of the taxon is more than 90%); the Phylums Firmicutes, Bacteroidetes, Actinobacteria are represented in smaller numbers, and the Phylums Fusobacteria and Cyanobacteria – only in some groups. Fusobacteria were found only in patients with lung sarcoidosis, and only in this group the median relative representation of the Phylum Actinobacteria was much higher than in the rest (p<0.05). The Genuses Stenotrophomonas and Delftia are the most widely represented in all samples. A bacterium of the Genus Pseudomonas has been found in patients with lung cancer. Conclusion. Proteobacteria were a significantly predominant Phylum of microbiota in patients with undifferentiated pathological changes in the lungs; Fusobacteria were found only in patients with lung sarcoidosis, and only in this group the median relative representation of the Actinobacteria were much higher than in the other groups. The greatest taxonomic diversity at the Genus level was observed in patients with lung sarcoidosis. Keywords: microbiota, lungs, tuberculosis, sarcoidosis, lung cancer> ˂ 0.05). The Genuses Stenotrophomonas and Delftia are the most widely represented in all samples. A bacterium of the Genus Pseudomonas has been found in patients with lung cancer.Conclusion. Proteobacteria were a significantly predominant Phylum of microbiota in patients with undifferentiated pathological changes in the lungs; Fusobacteria were found only in patients with lung sarcoidosis, and only in this group the median relative representation of the Actinobacteria were much higher than in the other groups. The greatest taxonomic diversity at the Genus level was observed in patients with lung sarcoidosis.