Isolation of herpes simplex virus (HSV) from brain tissue after biopsy has been considered the reference standard for the diagnosis of herpes simplex encephalitis (HSE). During the evaluation of antiviral treatment of HSE, cerebrospinal fluid (CSF) was obtained from patients with clinical disease indicative of HSE who underwent diagnostic brain biopsy. HSV DNA was detected by polymerase chain reaction (PCR) in CSF of 53 (98%) of 54 patients with biopsy-proven HSE and was detected in all 18 CSF specimens obtained before brain biopsy from patients with proven HSE. Four of 19 CSF specimens were positive after 2 weeks of antiviral therapy. Positive results were found in 3 (6%) of 47 patients whose brain tissue was culture-negative. Detection of HSV DNA in the CSF correlated significantly with age and focal radiographic findings. Thus, PCR detection of HSV DNA should be the standard for diagnosis of HSE.