Aim. To assess changes in the structure of the small intestine microbial community in the context of the “gut microbiota-immune system-brain axis” in healthy aging, depression and dementia. Materials and methods. 74 elderly people included in the groups: “Healthy ageing”, “Depression”, “Dementia” were investigated. Evaluation of 5 main types of microorganisms of the small intestine (Bacteroidetes, Firmicutes, Actinobacteria, Proteobacteria, Fusobacteria) by method of gas chromatography - mass spectrometry of microbial markers was carried out. For statistics, hierarchical cluster analysis with the construction of a heat map was used. Results. Reconstruction affected 15 out of 30 studied bacterial species of the phylums Firmicutes, Actinobacteria, Proteobacteria in the “Dementia” and “Depression” groups in relation to the “Healthy ageing” group. In depression, the number of all types of bacteria involved in the fermentation of food polysaccharides increased in relation to the “Healthy ageing” group. In dementia, low levels of Clostridium spp., Eubacterium spp., Bifidobacterium spp. was shown, in relation to depression, but number of C. perfringens, С. difficile and facultative anaerobes: Streptococcus spp., Enterococcus spp., Lactobacillus spp., S. aureus, S. epidermidis was increased, compared to “Healthy ageing” group. Conclusions. The indicators of the systems included in the axis “intestinal microbiota - immune system - brain” indicated a pronounced disintegration of the axis in dementia in relation to depression and healthy ageing. The results can be used as biological markers in the differential diagnosis of these pathologies (dementia/depression), which have common risk factors and clinical symptoms.