Introduction: Most of the newborns’ diseases transfer to them through their mothers. Cytomegalovirus (CMV) is the most prevalence infections which transfer from mother to embryo. CMV is the cause of congenital infection and is known as spontaneous abortion in mothers. This virus can cross the placenta and cause clinical signs in embryo and infant. The aim of this study was to develop a PCR and Real Time PCR for diagnosis of Cytomegalovirus using molecular tests.

Materials & methods: In this study, out of 100 infants with clinical signs (under 3 weeks) who referred to Qom and were suspected to infection with CMV. The urine samples were studied for existence of DNA for using PCR and Real Time PCR methods and using specialized primers and probe.

Findings: Out of 100 newborn, DNA of CMV was excreted through urine. 58 newborns have CMV DNA in their urines. The results with 2 methods have similar PCR and Real Time PCR. The CMV DNA was not found in 19 newborns.

Discussion & conclusions: The results show that the molecular tests are influential for fast diagnosis especially tracking viral DNA using PCR method. Also on the strength of this research, the importance of this study and submitting solutions for fast and accurate diagnosis of this Virus in newborns immediately after delivery is necessary for treatment and preventing this Virus.