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Background:The vaginal microbiome plays an important role in maintaining health, and there is evidence that microbial colonization of the upper genital tract can also influence successful embryo transfer. The aim of this study is to determine whether the vaginal and endometrial microbiome in people undergoing assisted reproduction techniques could affect the pregnancy rate.Results:Regarding the microbiome dynamics during the cycle, we observed a decrease in alpha diversity from the follicular to luteal phase in the control group, in contrast to a stable pattern in the repetitive implantation failure group. As for endometrial and vaginal microbiome, alpha diversity was higher in the endometrium (Shannon p = 0.0139, Simpson p = 0.046); differences were also observed in beta diversity (p = 0.001). Compared to the endometrium, the vagina showed a greater relative abundance of Lactobacillus spp. (83.17% vs 84.82%, p Streptococcus spp. (1.59% vs 7.74%, p = 0.014) and Ureaplasma spp. (0% vs. 0.89%, p = 0.006), and a lower abundance of Delftia spp. (0.95% vs 0%, p = 0.0003), Anaerobacillus spp. (1.59% vs 0%, p = 0.0004), and Ralstonia spp. (3.17% vs 0%, p = 0.0006). We also observed differences in both alpha diversity (Shannon p = 0.0206, Simpson p = 0.0206) and beta diversity between groups, along with differences for Ralstonia spp. (0.09% study group and 0.73% control, p = 0.0012). Finally, the relative abundance of Lactobacillus spp. differed between patients that did not versus did achieve pregnancy (91% vs 99%, p = 0.0445 visit 1, 94.63% vs. 97.69%, p = 0.0268 visit 2, 97.73% vs 99.74%, p = 0.0492 visit 3). The relative abundance of L.reuteri was also different between groups (0.39% vs 0.17%, p = 0.0397 visit 1, 0.15% vs 0.30%, p = 0.0491 visit 3).Conclusions:The vaginal and endometrial microbiome pattern correlates with the pregnancy rate, and it is different in patients who do versus do not have repetitive implantation failures. No significant differences in the composition of the microbiome were observed through the different visits. The lack of dynamism in the microbiome pattern of repetitive implantation failure patients might reflect an impaired adaptation to endometrial changes. A greater relative abundance of Lactobacillus spp. and L. reuteri is correlated with higher chances of pregnancy.*MC Díaz Martínez and A Bernabeu García share equal responsibility for authorship.