Polymerase chain reaction (PCR) assay was used to detect herpes simplex virus (HSV) DNA in mouth, skin, sera, or cerebrospinal fluid (CSF) from seven neonates with HSV infection. In a culture-negative patient, the diagnosis was confirmed by detection of HSV DNA. Serial examinations revealed that HSV DNA remained in the serum and/or CSF from several patients for 1-2 weeks after the beginning of treatment. Next, the results of PCR assay in neonatal HSV infections were compared with those in older children with herpes simplex encephalitis (HSE). HSV DNA was detected in CSF from four neonates with central nervous system involvement and in CSF from all nine children with HSE. Sera were positive for HSV DNA in five of seven neonates, including two cases of localized infections, but in none of the children with HSE. These results suggest that HSV may be spread principally via viremia in neonates. PCR assay could be useful for the confirmative diagnosis of neonatal HSV infections, especially in culture-negative cases.