The aim of this study was to determine the incidence of viral infections in the central nervous system (CNS) of neonates with seizures of unknown origin. Serum and cerebrospinal fluid (CSF) samples of 50 neonates were studied for antibodies to 13 different microbes by enzyme immunoassay, and CSF samples were investigated for four specific nucleic acids by polymerase chain reaction. For viral cultures throat, stool and CSF samples were obtained. CNS viral infection was suggested in 13 of the 50 neonates (26%). Antibodies to varicella, herpes simplex 1, influenza A or B, parainfluenza 1, adeno or enteroviruses were detected in the CSF of nine children; and herpes simplex 2 specific DNA was found in one child. Cytomegalovirus was cultured from the urine of two children. In one child unspecified, but evident pleocytosis in the CSF was observed. The incidence of CNS viral infections in association with neonatal seizures may be much higher than previously reported.