Abstract Study question The endometrial microbiome, in addition to other parameters of inflammation (CD138 presence, NK bright fraction presence), may be a complementary marker of ongoing local inflammation. Summary answer Presented results of the microbiome in comparison with the CD 138 marker may indicate inflammation in the endometrium, which is caused by dysbiosis. What is known already The study of the microbiome and the assessment of its impact on female reproductive system on embryo implantation, pregnancy maintenance and the success of the in vitro fertilization (IVF) procedure is an increasingly popular research topic. The protective role of Lactobacillus (other than L.iners) is known, and probably its low number may be related to the impossibility of embryo implantation. Dysfunctional mycobiome may be the cause of chronic inflammation of the endometrium, including endometriosis and recurrent implantation failures. Importantly, the dysbiotic profile of the endometrial microflora often does not cause any clinical symptoms. Study design, size, duration The clinical study included 182 women in child-bearing age, who were patients of the Gyncentrum Clinic (Poland), and who were qualified for the IVF procedure. In this group of patients, 201 samples combined were tested, obtaining 19 negative results due to the low quality of swabs, and the small amount of microbiota impossible to efficiently isolate. In the study, samples were analysed from January to December 2022 collection. Participants/materials, setting, methods To analyze the assumed parameters, patients treated at the Gyncentrum Clinic underwent a routine hysteroscopy procedure, during which endometrial swabs (determination of the molecular microbiome using the Next Generation Sequencing NGS method) and tissue fragments (determination of CD138 immunohistochemically and NK fractions by flow cytometry) were collected. Nucleic acids were isolated from the swabs for the preparation of libraries, based on the Illumina-16S Metagenomic Sequencing Library Preparation. Main results and the role of chance The microbiome study and other inflammation parameters in the group of our patients allowed us to observe some trends. Due to the microbiological endometrium profile, the patients were divided into 3 groups: 1) normal microflora (domination of Lactobacillus other than L.iners and/or Bifidobacterium;n =135), 2) moderate dysbiosis (presence of Lactobacillus and/or Bifidobacterium and/or L. iners-max. 50 % of all sample- and also other potentially harmful species e.g. Enterobacteriaceae group, Streptococcus group, Veilonella;n =28); 3) dysbiosis (with/without low number of Lactobacillus and Bifidobacterium, strong dominance of harmful species listed above or L.iners dominance;n =19). We observed that in the group of endometrial dysbiosis patients, an increased CD138 index ( ⩾1/10 high power fields HPF) is more often noted - in the group of dysbiotic patients with CD138 = 0/10 HPF 7.21 %, in the group of dysbiotic patients with increased CD 138 15.49 %. We didn `t notice any trends comparing the results of CD138 to the NK bright fraction (CD56 + +/CD16-) tested in endometrial specimens, or the relationship of this fraction to the microbiome. Observed trend indicates a certain relationship in the presence of abnormal microflora and inflammation expressed by CD138, but it requires confirmation on a larger study group and obtain information about the success of pregnancy. Limitations, reasons for caution The conducted research require broader analysis on a larger group of patients. It is necessary to obtain full information about the success of pregnancy in all analyzed patients. Identification of taxa using the NGS method is not the same as the identification of microorganisms living in the studied microenvironment. Wider implications of the findings Presented results should be treated as a starting point for further analyses, important in the context of research based on infertility, focusing on relationships between the microbiome and the IVF effectiveness. It seems interesting to extend the molecular study of the microbiome to its other elements - viruses, fungi, protozoa. Trial registration number 161/KBL/OIL/2021 Study funding No Funding source Funding by hospital/clinic(s)