Paraffin-embedded necropsy material from 6 patients with human cytomegalovirus encephalitis (HCMVE) corroborated by immunocytochemistry and 11 control cases were examined for the presence of human cytomegalovirus (HCMV) DNA by a nested polymerase chain reaction (nPCR). A characteristic 183 base pair (bp) fragment of the HCMV genome could readily be amplified in 4 cases of HCMVE. In 2 cases of HCMVE, viral DNA could be demonstrated only sporadically by PCR, due most likely to inefficient DNA extraction or DNA degradation. All control cases remained negative. The nPCR provides a specific method for detecting HCMV DNA in routinely processed biopsy and necropsy material and may be used in archival tissues for the diagnosis of infection. Fixation of samples and DNA extraction are, however, crucial steps and require careful control if PCR is used for detection of HCMV, to avoid false negative results.