Endometriosis is an estrogen-dependent inflammatory condition in women that is characterised by the ectopic growth of endometrial glands and stroma outside of the uterine cavity. Although there exists many theories for the pathogenesis of endometriosis, none has been successively confirmed as a direct cause for disease development. The human body comprises a diverse microflora across all tissues that can have fundamental roles in health and disease. The microbial flora in a healthy individual can vary remarkably between anatomical sites due to the physical and chemical properties of specific tissues. This includes the female reproductive tract, notably the vagina, which harbors a microbiota dominated by Lactobacilli species. In addition, a core unique microbiome has been defined for the endometrium that also includes Lactobacilli spp. In this review we examine the possibility that endometriosis could result from microbial dysbiosis, whereby significant changes to the natural microflora within the endometrium could reduce mucosal immune regulation in this tissue with concomitant expansion of pathogenic bacteria that trigger local tissue inflammation that could perpetuate the development of endometrial disease.