Studies have shown that along the female reproductive tract a continuum of a gradually changing and unique microbiome seem to exist of which the microbial abundance decreases from the lower to the upper part of the tract. The reproductive tract harbours different kinds of microbes and include bacteria, viruses and bacteriophages. As the gut microbiome environment regulates homeostasis and metabolism, actively interacts with the local immune system and provides protection against pathogens, such directive roles are also expected from the reproductive microbiome environment. The most dominant reported bacteria of the lower reproductive tract are of the genus Lactobacillus, which is associated with vaginal and reproductive health. The composition of the lower part of the female reproductive system, more importantly, the presence, absence and abundance of specific bacteria, prior to fresh embryo transfer, is associated with and predictive of IVF outcome.