Abstract Study question Are there any quantitative associations between endometrial macrophages populations and microorganisms’ diversity? Summary answer The quantities and spatial distribution of endometrial macrophages populations correlated significantly with several microbiome diversity indices. What is known already Numerous studies have linked the relative abundance of Lactobacilli with a receptive endometrium, while the presence of multiple other bacterial species has been implicated in implantation failure. Another determinant of endometrial receptivity is the local immune cell composition and its inflammatory status. Knowing that the microbiome affects the immune system, it is worth studying the potential interplay between bacterial composition and immune cell populations in the endometrium during its receptive state. The present study aimed to investigate associations between the quantity and distribution of endometrial macrophages populations and the local microbiome diversity during the mid-secretory phase of the menstrual cycle. Study design, size, duration This prospective observational study was conducted between April 2021 and January 2023. Endometrial biopsies were collected from 25 female patients of reproductive age on day 7 after luteinising hormone surge. Eligibility criteria included no endometrial pathologies, no history of recent or chronic inflammatory or infectious disease, no recent antibiotic treatment, and no endocrinological, autoimmune or oncological conditions. Participants/materials, setting, methods Half of each biopsy was used for immunohistochemistry with CD11c + (Proteintech) and CD163 + (Quartett) to reveal pro- and anti- inflammatory macrophages, respectively. Their quantities and spatial distribution were analysed by HALO® image analysis software. The remaining endometrial tissue underwent DNA isolation and subsequent 16S rRNA (v4-v5 region) gene sequencing to determine endometrial microbiota composition. Alpha diversity indices - Good’s coverage, Shannon and phylogenic diversity - were evaluated and tested for correlation with the macrophages metrics. Main results and the role of chance The observed median percentage and range of the studied macrophages populations in the endometrial stroma were: 1.16% (2.98) CD11c+ macrophages and 1.96% (4.48) CD163+ macrophages. The evaluated alpha diversity indices were: 0.99±0.01 Good’s coverage, 2.53±1.20 Shannon and 38.56±15.43 phylogenic diversity.The CD11c+ macrophages percentage was not related to the microbial diversity of the studied samples. The percentage of the CD163+ macrophages, however, showed significant correlation with the Good’s coverage alpha diversity index (R = 0.397, p = 0.04). The median distance between CD11c+ and CD163+ cells in the endometrial stroma was 63.7µm (108.36) and it was significantly related to the Shannon alpha diversity index (R=-0.347, p = 0.05) and phylogenic diversity whole tree index (R=-0.367, p = 0.05).In summary, the anti-inflammatory macrophages percentage in the mid-secretory endometrial stroma is positively related to the local microbial diversity. Moreover, the distances between the pro- and anti-inflammatory macrophages populations in the endometrium are negatively associated to Shannon and PD whole tree alpha diversity indices. Limitations, reasons for caution The results of this study should be confirmed in a larger study population. Wider implications of the findings This study’s findings indicate that there is a correlation of the endometrial macrophages quantity and stromal distribution with the endometrial microbiome diversity. The association between these determinants of endometrial receptivity could help in understanding the fine tuning of the endometrium for accepting the embryo. Trial registration number The current research was funded by the National Science Fund, Ministry of Education, Bulgaria, Contract № KP-06-N53/14/16.11.2021.