Introduction. Among chronic prostatitis with chronic pelvic pain syndrome, about 90% are considered abacterial, i.e. unrelated to certain microorganisms, and belong to diseases of unclear etiology. It is chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) that is the focus of modern research due to the fact that it is the most common type of disease with the least satisfactory treatment results. Objectives. To determine the structural composition of the microbiota and the total bacterial load in patients with chronic abacterial prostatitis (CAP) of category III obtained using gas chromatography-mass spectrometry of microbial markers (HCMS). Material and methods. In the period 2018 to 2023, a prospective comparative study was conducted of 220 patients at the SM-Clinic medical center aged 25 to 50 years with prostatitis-like symptoms lasting more than 3 years, meeting the inclusion criteria, and 74 males who applied for screening examination with no complaints, which were subsequently divided into two groups: group 1 - with clinical manifestations of chronic prostatitis (n=220) and group 2 (n=74) – without clinical manifestations of prostatitis / control group. The study of the microbiota of the prostate and urethra was carried out using HCMS using the method of mass spectrometry of microbial markers in the obtained samples. The gas chromatograph of the Maestro mass spectrometer (Interlab LLC, Russia) was used. Results. According to the data obtained, statistical analysis of HCMS indicators in patients with HAP did not reveal significant taxonomic differences in the structure of the urethral microbiota in the main and control groups, with the exception of an increase in plasmalogen indicators. The frequency of detection of microorganisms in the secret of the prostate gland in patients of both groups was comparable. To determine the significance of differences in the occurrence of microorganisms, the indicators of both groups were tested using the test Manna – Whitney. It was found that the level of cocci and bacilli, anaerobes, actinobacteria, fungi and yeast, as well as total viruses in patients with HAP compared with the control group was significantly higher (p = 0.0020; p < 0.0001; p < 0.0001; p = 0.0254; p = 0.0254). Of the three representatives of the enterobacteria group, two were not identified in the control group. The control group lacked a number of so-called opportunistic microorganisms: Enterobacteriaceae spp., Velionella spp., Mycobacterium spp., Helicobacter pylori, Porphyromonas spp., Pseudomonas aeruginosa, Stenotrophomonas maltophilia. In addition, a significant increase in the level of transient opportunistic pathogens (Streptococcus spp., Bacterioidis fragilis, Bifidobacterium spp., Eubacterium spp., Fusobacterium spp. / Haemophilus spp., Peptostreptococcus anaerobius 18623, Peptostreptococcus anaerobius 17642, Prevotella spp., Propionibacterium spp., Velionella spp.) and resident microorganisms (p = 0.0007). The total bacterial load in patients with HAP is significantly higher than in the control group (p < 0.0001). Conclusion. The identification of microbial associations in the prostate gland secretion by the HCMS method and an increase in the total bacterial load in patients with CP/CPPS III compared with the control group suggest an important role of infection in a certain part of patients with CP/CPPS, which dictates the need to change tactics in the diagnosis and treatment of this category of patients.