Background: Chronological changes of the incidence of congenital cytomegalovirus (CMV) infection and the longitudinal prognosis in children with asymptomatic congenital infection were investigated. Methods: Congenital CMV infection, as demonstrated by isolation of the virus within the first week of life, was diagnosed in infants born in Sapporo, Japan, during the 26-year period between 1977 and 2002. Results: Congenital infection was diagnosed in 37 (0.31%) of 11,938 infants. Thirty-two infants were (86.5%) asymptomatic and 5 (13.5%) were symptomatic at birth. Conclusions: Although a decrease in the total incidence of congenital CMV infection has been seen in recent years, screening of congenital infection at birth seems to be necessary to detect late-onset neurodevelopmental sequelae.