To investigate the diagnostic application of molecular detection of enterovirus type 71 (EV71) infection using post-mortem paraffin-embedded tissue. Two autopsy cases of EV71 infection were studied by histopathological and immunohistochemical methods. Reverse transcription polymerase chain reaction (RT-PCR) was performed to detect the viral RNA in paraffin-embedded tissue samples. Characteristic features of acute encephalitis were seen in the brain, with most prominent lesions found in the brain stem in both cases. Inflammatory cells were largely CD68-positive microglia with a few CD15-positive neutrophils in the areas of neuronal necrosis. The 5'-untranslated region of EV71 was detected in the medulla by RT-PCR using paraffin-embedded tissues of both cases. Sequencing analysis of the RT-PCR products showed 100% homology to the EV71 strain, recently submitted to the GenBank database from Fuyang, Anhui province. Molecular detection of EV71 can be performed on formalin-fixed, paraffin-embedded tissue samples from fatally infected patients. Timely and accurate diagnosis of the infection by such molecular approach is crucial for the proper clinical and public health intervention.