Background: Herpes encephalitis in children entails a significant risk of mortality and morbidity. The diagnosis of herpes simplex virus (HSV) encephalitis has been markedly facilitated by the availability of assays that amplify viral DNA to detectable levels by using polymerase chain reaction (PCR). This study aimed to obtain the incidence of HSV encephalitis in Qena Governorate, Egypt, to highlight the role of different investigation studies in diagnosis and prognosis of herpetic encephalitis and to highlight the role of PCR in detection of HSV. Methods: This study was conducted on 50 patients suspected to have viral encephalitis. All were subjected to complete history and examination, cerebrospinal fluid (CSF) examination, electroencephalogram (EEG), CT brain and PCR amplification for HSV DNA by real-time PCR using SYBR Green I Dye as the detection signal. Results: Encephalitis was more detected in cases less than 1 year (52.2%), males, in rural (61.3%) and in lower socioeconomic state (55%) than others. Seizures (60%) and focal neurological findings (46%) were the most common presentations. HSV DNA was detected by PCR in CSF samples from 28 patients (56%). Conclusions: PCR may be one of the sensitive and specific investigative methods for laboratory diagnosis of HSV encephalitis. The incidence of HSV-induced encephalitis in children in Qena governorate was 56%. Int J Clin Pediatr. 2017;6(1-2):1-7 doi: https://doi.org/10.14740/ijcp274w