Cytomegalovirus (CMV), is the most common cause among congenital infections and is the most seen etiology in long-term sensorineural hearing loss (SNHL) and neurological impairment. Congenital CMV infection (CCMV) was reported in 0.15-2.2% of live-borne neonates in studies from different countries. A significant proportion of infected infants are asymptomatic after birth and might only be detected by routine screening methods during the new born period. The aim of this study was to screen the saliva of live-born neonates with areal-time PCR based method for the detection of CCMV in our hospital. Saliva samples collected in half an hour after birth by dry dacron swabs and were evaluated for CMV DNA (Rt-PCR, Abbott Molecular USA) from 1000 babies born in Ege University Faculty of Medicine Hospital Obstetrics Clinic between October 2015-October 2017. For the confirmation of CCMV, saliva positive newborns were evaluated with the same method for CMV DNA from their urine or blood within 21 days. All newborns were screened for sensorineural hearing tests. Subjects were 497 girls (49.7%) and 503 boys (50.3%), with a mean weight of 3116.8 g and mean of 37.61 birth week. CMV DNA was positive in the saliva of 16 newborns (1.6%). Fourteen newborns were weakly positive for CMV DNA in their saliva and were not confirmed for CCMV infection. Congenital CMV was confirmed in only two (0.2%) with the CMV DNA results in urine and/or blood samples. One of the two newborns with CCMV was symptomatic and had a neurosensorial hearing loss. The other one was asymptomatic. Saliva samples, taken immediately after birth with a noninvasive and easy method for the detection of CMV DNA is very important for diagnosis of CCMV. Positive samples should be confirmed with CMV DNA in urine or blood samples of these newborns. In this study, detection of positivity in saliva samples that were confirmed with other samples of our newborn population for CCMV was 0.2%. The specific diagnosis for CCMV in newborns with a noninvasive and easy collecting sample is important to avoid sequelae and for public health concerns.