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Human cytomegalovirus (HCMV) is the most common viral cause of intrauterine infection throughout the world. Its distribution patterns in different clinical samples are poorly understood. This study was performed to determine the frequency of CMV DNA positivity in maternal/fetus sera, placentas and amniotic fluid, together with maternal/fetus serology. Clinical specimens were obtained from 92 pregnant women who delivered by cesarean section. 98% of women and their neonates were HCMV IgG positive and 5.4% of these mothers were IgM positive, while no IgM was detected in neonates of IgM positive mothers. Among the IgG positive mothers, IgM was detected in 3.3% of their fetuses. 5.4% and 3.3% of maternal and fetal sera were HCMV DNA positive, respectively. The three neonates who were positive for HCMV DNA in sera were also positive for HCMV IgM and the PCR of their amnions was positive (p < 0.0001). 9.8% of placenta samples and 4.3% of amniotic fluid specimens were positive for HCMV DNA while among these placenta samples, two amnions were PCR positive (p = 0.046). Our results showed that there is not always a correlation between placenta and amnion infections. This may be due to reactivation of HCMV leading to placenta infection, as all affected placentas do not pass infection to fetuses and amniotic fluids. Detection of HCMV DNA in amnion and fetus plasma and the existence of fetus IgM against HCMV can also occur without clinical symptoms.