Assisted reproductive technologies (ART) are one of the most effective ways in fighting infertility, but their effectiveness is influenced by various factors. Our study focuses on examining importance of risk factors underlying ART failure related to altered microbiome pattern in the female reproductive system. The case-control study was based on conducting a laboratory examination of 129 infertile couples applied to the Department of Assisted Reproductive Technologies due to failure of in vitro fertilization (IVF), whereas control group consisted of females with successful progressive pregnancy after ART. Chlamydia, herpes virus and cytomegalovirus were assessed by using PCR and ELISA, whereas culture method was used to detect Trichomonas vaginalis in vaginal swabs and ejaculate applying Trichomonas Modified CPLM Medium (HiMedia, India) followed by microscopy. In addition, the qualitative and quantitative composition of the vaginal biocenosis was studied with multiplex RT-PCR by using Femoflor-16 kit (DNA-technologies, Russia). Serological tests were based on measuring IgG and IgA antibodies against Chlamydia trachomatis in ELISA (diagnostic kits purchased from Vektor Best, Russia; NovaTec, Germany; ImmunoComb, Israel) as well as antibodies against immediate early HSV-1/2 proteins (BioService, Russia) and immediate early HHV-5 proteins (Vector Best, Russia). C. trachomatis and herpesvirus DNA was measured by using PCR diagnostic kits Amplisens (Interlabservice, Russia). It was found that sexually transmitted infection agents were highly prevalent in infertile couples applying to the hospital for IVF. Significant factors for non-pregnancy were vaginal dysmicrobiocenosis (OR = 7.5 (95% CI 1.04-54.1), p = 0.02) and detected T. vaginalis (OR = 2.6 (95% CI 1.12-6.4), p = 0.01). Dysbiosis of the reproductive system, including those occurring due to trichomonas infection is associated with lowered ART effectiveness. It is evident to timely detect urogenital infections and dysbiosis while preparing infertile couples for IVF cycles.