Introduction: In Mongolia, diagnostic tests for the detection of the sexually transmitted congenital virus and human papilloma virus are currently not routinely used in clinical settings and the frequency of these STIs is enigmatic. Goal: The prevalence of this virus were prospectively evaluated among 200 Mongolian pregnant women and their newborns and correlated with pregnancy outcome. Materials and Methods: Taq Man PCRs were used to detect some virus in pre-birth vaginal swabs of the pregnant women and in oral swabs of their newborns. A standardized questionnaire concerning former and present pregnancies was developed and regression analysis was used to correlate virus detection with pregnancy outcome. Result: Cytomegalovirus was the most prevalent of the tested pathogens (46.5% positive women and 10.5% newborns), human papilloma virus (31.5% and 4.5%) and herpes simplex virus-2 (1% and 0%). Statistical analysis: The statistical analysis was conducted using the software program RStudio, version 0.99.896. Multiple regression analysis was used to assess the association between pathogen loads of mothers or newborns and the outcome variables (gestational age, neonatal length, weight, head circumferences and bacterial vaginosis). Conclusions Multiple regression analyses indicate that colonization of the mothers with cytomegalovirus is associated with transmission to newborns and that transmission is associated with reduced neonatal length and gestational age. Thus, diagnostic tests for their detection should be implemented in the clinical settings in Mongolia.