The gut - brain axis plays a significant role in the pathophysiology of migraine. This interaction can be influenced by multiple factors, such as gut microbiota profiles. The aim of the study was to analyze the gut microbiome state in patients with migraine and healthy individuals, to assess possible correlations between the detected changes in patients with migraine and the frequency, intensity of headaches, their psycho-emotional state, and quality of life. In total, 112 patients-16.3% of men and 83.7% of women. Subjects were divided into 2 groups depending on the presence of migraine: the main - patients with chronic and episodic forms of migraine, the control - healthy individuals. The study of the intestinal microbiome was performed by chromato-mass spectrometry. The following scales were used: Visual Analogue Scale/VAS, Migraine Disability Assessment/MIDAS, Back Depression Inventory/BDI. In patients with migraine compared with healthy individuals, significant changes were noted in the quantitative composition of certain resident microorganisms including Alcaligenes spp (p=0.0061), Clostridium coccoides (p=0.0021), Clostridium propionicum (p=0.0287), Eggerthella lenta (p=0.0138), Pseudonocardia spp (p=0.0210), and Rhodococcus spp (p=0.0164). The number of microscopic fungi such as Candida spp (p=0.0079), Micromycetes spp (p=0.0011) and Micromycetes spp (p=0.0010) were increased in patients with migraine compared to the control group. In the main group, a negative correlation was found between the level of 16 Alcaligenes spp and the score on the BDI score, HARS score (respectively: r= -0.6226, p= 0.007; r= -0.509, p=0.03), the frequency of attacks (r=-0.4879, p=0.046) and the VAS score (r=-0.487, p=0.046). Significant negative correlation was found between elevated level of Clostridium coccoides and MIDAS score (r=-0.5123, p=0.03), BDI score (r=-0.54, p=0.025) in the patients with migraine. At the same time, in the main group a positive correlation was detected between Eggerthella lenta level of and VAS score (r=0.4830, p=0.049). In the main group negative correlations were found between slightly increased content of endotoxin in the main group, the BDI score, HARS score (respectively: r=-0.697, p=0.001; r=-0.557, p=0.02) the frequency of attacks (r=-0.547, p=0.023), on the VAS score (r= -0.531, p=0.028), as well as MIDAS score (r =-0.556, p=0.02). The revealed peculiarities of gut microbiome changes in patients with migraines need further clarification in order to identify the possible role of the gut microbiome in the pathogenesis, clinical picture, and therapy of migraine, and is a promising area of further scientific research.