Introduction. Male infertility is a complex condition with many potential causes, including hormonal imbalances, anatomical problems, genetic factors, lifestyle factors and more. But today, there is a fairly large group of infertile men with unknown causes of the disease. Objective. To analyze the taxonomic microbial diversity of testicular tissue and the urogenital tract of infertile men and to identify correlations between the microbiome and mastocytes in the testicular parenchyma. Materials & methods. The study was performed on testicular tissue samples from infertile patients with azoospermia (n = 33). All patients were divided into two groups based on the form of azoospermia: group 1 — infertile patients with non-obstructive azoospermia (NOA) (n=21); and group 2 — infertile with obstructive azoospermia (OA) patients (n=12). The bacterial diversity of testicular tissue was studied by the method of high-performance new generation sequencing (NGS). Immunohistochemical staining with anti-MCT (Anti-Mast Cell Tryptase) was used to determine the IHC expression of mastocyte markers. Results. The microbiome of patients with NOA differs markedly from the microbiome of patients with OA (p < 0.05). In group 1, representatives of the Enterobacteriaceae and Xanthomonadaceae families, the genera Finegoldia, Bifidobacterium, Porphiromonas, Prevotella, Peptoniphilus and Pseudomonas are significantly more often found. A distinctive feature of group 2 is the rare occurrence of the genus Prevotella. Histochemical analysis revealed mastocytosis in the in-between-canalicular stroma approximately in 83% of azoospermia cases. Mastocytes are found in tubule structures in 68% of cases and correlate with the microbiome of testicular tissue. Conclusions. Injuries caused by mastocytes in the stroma and tubular structures are interrelated with the taxonomic diversity of testicular tissue. Moreover, the testicles of NOA-patients have a qualitatively and quantitatively more diverse spectrum both at the level of families and genera, unlike OA-patients. © 2024 Rostovskii Gosudarstvennyi Meditsinskii Universitet. All rights reserved.