Objectives: The objective of the study was to investigate the detection rates of Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium, Mycoplasma hominis, Ureaplasma urealyticum, Gardnerella vaginalis, Escherichia coli, Streptococcus agalactiae and Enterococcus faecalis, showing no clinical signs of an ongoing, acute inflammatory state of the vagina and/or the cervix, in fertile and infertile women. Material and methods: The study encompassed 161 women, including 101 women treated for infertility and 60 fertile women who had already given birth to healthy children. The material for the presence of C. trachomatis, N. gonorrhoeae, M. genitalium, M. hominis and U. urealyticum was collected from the cervical canal and analyzed by PCR. Furthermore, BD ProbeTec ET system was used to detect C. trachomatis infection. Vaginal swabs were collected for classification of bacterial vaginosis and aerobic vaginitis and assessed according to the Nugent score, as well as by traditional culture methods. Results: U. urealyticum was identified in 9% of the infertile women and in 8% of controls. Presence of M. hominis was demonstrated only in the former (4%) and C. trachomatis only in latter (3%). N. gonorrhoeae and M. genitalium were not found in any of the examined women. The frequency of aerobic vaginitis in both groups was estimated at 12%. There were 7% bacterial vaginosis cases in the study group, and none in the control group (p=0.0096). Conclusions: Despite having no symptoms of an ongoing acute inflammation of the reproductive tract, many women may experience permanent or periodic shifts of equilibrium of the vaginal and/or cervical microflora. BV develops more frequently in infertile patients when compared to the fertile women.