Ninety children, aged from 7 days to 12 months, with perinatal damage of the central nervous system (CNS) were virologically tested. The persistence of cytomegalovirus (CMV) DNA in the blood, urine and oropharyngeal swabs was identified in 18.9% of children. In 14.4% of children, CMV DNA was found only in oropharyngeal swabs and urine samples. In some cases, the severity of neurologic symptoms and absence of positive changes in the restoration treatment could be caused by the activity of CMV infection, blood CMV DNA and the increase in blood-brain barrier permeability. The authors recommend performance of a comprehensive immunological and molecular-biological survey in patients with suspected CMV infection. In case of positive reactions, a specific antiviral treatment should be started. Tree clinical cases are reported.