Everyone lives in symbiosis with a whole range of microorganisms. This symbiosis system is called microbiome. The first contact is achieved at birth, when colonization of our organism occures. When talking about the microbiome of the reproductive tract, we refer to the vaginal flora and the upper reproductive tract flora. Although it was previously believed that the upper part of the genital tract was sterile, with great advances in technology it has been discovered that the uterus, placenta, and even the ovarian follicle may have their own microbiome. Lactobacillus sp. was the most frequently detected organism in the vaginal flora while the upper part can also be inhabited, again mostly with Lactobacillus sp.. Lactobacillus sp. maintains the vaginal pH below 4.5, which prevents the development of pathogenic organisms. The imbalance in bacterial composition leads to a predisposition to infections and various reproductive complications. Maintenance of "normal" flora affects on implantation and maintenance of a healthy pregnancy. Ascending vaginal infection in pregnancy can cause premature rupture of the membrane as well as premature labor and birth, which puts both mother and child at risk. Apart from just pregnancy, it has been found that the microbiome and hormones play a major role in the success of in vitro fertilization procedures.