Encephalomyocarditis virus (EMCV) is widespread and the economic losses caused by an EMCV outbreak in pig holdings and the similarity between a foot-and-mouth disease virus (FMDV) and an EMCV infection in young piglets stress the need for a rapid, specific and broad diagnostic assay. An alternative to the time-consuming seroneutralisation assay, currently used for the characterisation of EMCV, is described. An EMCV specific reverse transcription-polymerase chain reaction (RT-PCR), using primers located in a conserved region of the 3D gene of the viral genome, was developed and tested on 114 different EMCV isolates. The identity of the respective amplicons was confirmed by sequencing. The potential of this assay for future diagnostic purposes was demonstrated by applying the RT-PCR on tissue samples collected from an experimentally infected piglet.