The early diagnosis of herpes simplex encephalitis (HSE) is essential because early introduction of antiviral therapy can significantly reduce the mortality of this disease. Herpes simplex virus (HSV) DNA detection in cerebrospinal fluid (CSF) samples is a rapid, noninvasive, specific, and highly sensitive method for HSE diagnosis. Neurodiagnostic methods have also been studied for noninvasive diagnosis of HSE. Magnetic resonance imaging (MRI) seems to be the most sensitive of them but it has not been compared to PCR in terms of efficacy for HSE diagnosis. In this study, 17 patients with focal encephalitis were prospectively evaluated by PCR analysis of CSF samples and MRI examination. MRI lesions involving the inferomedial region of one or both temporal lobes were observed in all PCR-positive patients but one. No PCR-negative patient presented with the same pattern of MRI lesions. MRI was also important for the establishment of an alternative diagnosis in three of eight PCR-negative patients. Both methods should be routinely applied in the evaluation of presumed HSE cases.