BACKGROUND The microbiome is the collection of all micro-organisms and their genes, which naturally live in and on the body. The cervical and endometrial bacterial microbiome has previously been reported to affect fertility and influence the outcomes of assisted reproductive therapy (ART), including embryo transfer. This study aimed to evaluate the cervical and endometrial bacterial microbiome in 177 women treated for infertility before, during, and after embryo implantation, and the outcomes. MATERIAL AND METHODS Cervical and endometrial swabs were collected from 177 women diagnosed with infertility at 3 time points: (1) during the initial examination, (2) during implantation, (3) 10-14 days after implantation. Next-generation sequencing (NGS) was used to analyze the bacterial microbiome. Taxonomic identification was performed with the Usearch algorithm. RESULTS There was a significant change in the number of patients with Escherichia coli depending on the collection time. For the first swab collection, there were significant negative relationships between the percentage of Gardnerella vaginalis and Lactobacillus spp. For the second collection, there was a negative relationship between Lactobacillus helveticus and Lactobacillus jensenii. For the third collection, negative relationships were found between Escherichia coli and Lactobacillus spp. A similar distribution of the bacterial microbiome was observed in all 3 swab collections. CONCLUSIONS Lactobacillus spp. were the main bacteria identified in the cervix and endometrium, present before, during, and after successful embryo transfer. E. coli and G. vaginalis reduced the protective effect of Lactobacilli before, during, and after embryo transfer.