Introduction. The endometrium is a complex tissue that meets many functional processes in human reproduction, namely the implantation of the embryo, the formation of the placenta, the normal development of the embryo, and so on. In recent years, thanks to new discoveries in the field of reproductive health and with the development of medicine, knowledge about the structure and functional efficiency of the endometrium has subsequently been refined and expanded. Purpose of the study. The study of microbiological, immunological and morphological aspects of the endometrium in patients with primary infertility. Material and methods. A prospective cohort study was conducted with 96 patients divided into 2 groups. The main group (L1) consisted of 48 patients with an established diagnosis of primary infertility, the control group (L0) consisted of 48 fertile patients. Endometrial sampling was performed using a Pipelle aspiration curette in the proliferative phase of the menstrual cycle. The endometrial microbiome was studied by PCR reaction using the Femoflor-16 reagent kit. Cytokines IL1β , IL8, IL10, IL4 were evaluated from endometrial fluid. For histological examination of endometrial biopsies, hematoxylineosin staining was used. Research Ethics Committee of the State University of Medicine and Pharmacy. Nicolae Testemitanu, (Chisinau, Republic of Moldova) approved the study protocol (No. 79/62 dated April 26, 2017). The patients signed an informed consent to participate in the study. Statistical data was processed in SPSS 20 and Microsoft Excel 2016. Results. The presence of Lactobacillus spp. L1 75%, χ2 = 0.236; p = 0.627; followed by Ureaplasma urealiticum + parvum in L1 37.5% vs L2 6.3%, χ2= 13.714; p <0.001; Atopobium vaginae L1 25% vs L0 14.6%, χ2 = 1.640; p = 0.1; Enterobacteriaceae L1 18.8% vs L0 0%, χ2 = 9.931; p = 0.001, in the main group, which led to inflammatory changes in the endometrium in L1 79.2% vs L0 31.3%, χ2 = 22.238; p<0.001. The level of pro-inflammatory cytokines IL1 β and IL 8 was higher in the endometrium of patients with primary infertility. Conclusion. The study demonstrated the presence of a pathological microbiome in the study group of patients, which led to disruption of local immunological processes, endometrial morphology, and as the final stage in the development of endometrial dysfunction.