Nucleotide sequence, 1713nt in length, of porcine reproductive and respiratory syndrome virus (PRRSV) isolated in Japan was determined. The sequence encompassed 3 overlapping open reading frames (ORFs), ORF5 to ORF7. These ORFs encodes major structural proteins of PRRSV. The deduced amino acid sequence of each ORF showed higher than 87.5% identity with an American isolate, and lower (54.6 to 80.5%) identity with an European isolate. This result supported a previous report about antigenic characteristics of the EDRD-1 strain. Leader-body junction sequence in subgenomic mRNA of the EDRD-1 strain was determined by sequencing cDNA clones of subgenomic RNAs. A common sequence motif of 5 nucleotide, represented by UA(A/G)CC, was identified as the junction sequence.