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Knowledge of the prevalence of congenital cytomegalovirus infection is necessary to evaluate the need for prevention. We performed a multicentre one-year study involving 11 neonatology divisions to ascertain the prevalence in Lombardy. Cytomegalovirus was isolated by culturing saliva samples from all babies born (n = 1268) of two 15-day sample periods and from 185 neonates with suspected congenital CMV based on clinical and laboratory findings and the history. The overall prevalence of congenital infection was 0.47% (6/1268) in the sample period group and 5% (9/185) in the second group. Clinical monitoring revealed sequelae in two of three children with symptomatic infection and no asymptomatic child at age two years. In a subgroup of 205 babies including 14 of the infected infants we also evaluated a test to detect cytomegalovirus DNA in the Guthrie cards obtained in neonatal screening for genetic and metabolic disorders. The test's sensitivity was 100% and specificity 98.5%, encouraging its use for early identification of infected neonates and for large epidemiological studies.