All infants treated with antiviral medication for symptomatic congenital (diagnosis <3 weeks) and probably postnatal (>3 weeks) cytomegalovirus infection were characterized with the help of a survey covering all German Pediatric hospitals between 2012 and 2013. We found that >50% of infants treated for cytomegalovirus were classified as probably postnatal cytomegalovirus infection, which was associated with preterm birth and underlying diseases of the immune system, heart or lung.