Based on the deletion information of high virulent PRRSV genome, 3 oligonucleotide primer were designed and synthesized. Specific and sensitive reverse transcription-PCR (RT-PCR) assays were developed for the detection of high virulent PRRSV. The sensitivity and specificity of RT-PCR assays were evaluated, the results showing that the detection limit of the assay was found to be 0.265 pg of tissue total RNA, and the protocol have no cross-reaction with classical swine fever virus, porcine circovirus type 2, pseudorabies virus, streptococcus, haemophilus parasuis and Escherichia coli. Then 36 cell cultures, two PRRSV live vaccine strains and 184 clinical specimens from 52 farms were tested. Five PRRSV field isolates were the high virulent PRRSV; two PRRSV live vaccine strains from normal PRRSV, and 123 specimens from 42 farmer were positive (only 1 specimen was normal PRRSV). This RT-PCR method proved to be accurate differential diagnosis of the high virulent PRRSV and normal PRRSV with the characteristics of rapidity, sensitivity and specificity, and has a strong clinical relevance.