Microorganisms which are present in the human urogenital tract may be involved in the development of inflammatory changes negatively affecting the genitals in both men and women. Pathological conditions due to inflammatory alterations may result in complete loss of fertility. Infections of the urogenital tract are responsible for 15% of all cases of infertility in couples. Negative impact on the human reproduction is mainly caused by direct damage to the genital tract mucosa by metabolic products of microorganisms or by induction of pro-inflammatory responses of the body. Another mechanism is indirect impact of microorganisms on the genital function. Moreover, the effect of bacteria on spermatogenesis and semen quality is important in men. Infections mainly caused by Chlamydia trachomatis or Neisseria gonorrhoeae represent the greatest risk in terms of permanent consequences for human reproduction. As for other sexually transmitted disorders, such as infections caused by Gardnerella vaginalis, urogenital mycoplasmas or ureaplasmas, the link between infection and infertility has been intensively researched.