Recent data from the human microbiome project show that endometrium, previously considers to be sterile, has its own unique microbiome. Although the uterine cervix serves as barrier for ascending microorganisms from the vagina new wide spread non-culturable techniques show presence of Lactobacillus-dominant environment. Rapidly accumulating data show that this microbiome is qualitatively and quantitatively different from the microbiome in lower genital tract. It plays role in embryo adhesion and development. In some conditions changes in uterine microbiome could cause disturbances in normal physiological processes and subsequent gynecological diseases.