Objective: There is no specific antiviral therapy or a vaccine, which could be safely administered to the pregnant women with primary human cytomegalovirus (CMV) infection. Therefore, prenatal diagnosis has a critical role in the management of pregnancy, complicated by this disease. In this study, we investigated the prevalence and clinical consequences of human CMV infection from cervicovaginal smear and amniotic fluid samples of pregnant women by using real-time polymerase chain reaction (RT-PCR) assay, in one of the Obstetrics and Gynecology outpatient clinics of Turkey. The identification of reliable prognostic markers of fetal disease remains the main purpose and a major challenge on this issue. Methods: Two hundred and six samples, of which 135 were cervicovaginal smear and 71 were amniotic fluid, were enrolled in the study. The DNAs of the samples were extracted by using Roche Diagnostic (Roche, Germany) kit and amplifications of these DNAs were studied by using Light-Cycler system (Roche Germany) as being quantitative. Anti-CMV IgM antibodies in the samples were studied by both MEIA (Imx system, Abbot Laboratories, USA) and a commercial ELISA kit (Radim SPA, Italy) while anti-CMV IgG antibodies were studied by MEIA (Axsym system, Abbot Laboratories, USA). Results: Human CMV DNA was found to be positive in 1.5% (2 in 135) of cervicovaginal smear and 1.4% (1 in 71) of amniotic fluid samples by RT-PCR. IgM and IgG were found to be negative in all of the cervicovaginal smear samples by both MEIA and ELISA, while IgG antibody was found to be positive in only one of the amniotic fluid samples by MEIA. Conclusion: With RT-PCR assay, we have found the prevalence of human CMV in pregnant women similar to epidemiologic reports, which have been described earlier. Whereas the fetus with positive amniotic fluid in favor of human CMV had an intrauterine growth restriction resulted in intrauterine exitus, no symptoms were observed in the infants of the other two pregnant women with positive RT-PCR results. The fact that the clinical consequence of the newborn whose amniotic fluid evaluation revealed human CMV infection by RT-PCR made us think that this molecular diagnosis method may be a reliable assay in prenatal diagnosis of this pathogen. © Springer-Verlag 2005.