Comparative analysis of nucleotide sequences in the 5' non-coding region (NCR) of pestivirus RNA detected from live porcine and human virus vaccines indicated that the contaminants are of bovine viral diarrhea virus (BVDV), and that there are at least three genotypes, which are distinct from hog cholera virus, among the BVDV strains. Most of the nucleotide changes in variable regions of the 5' NCR were covariant, with complementary substitutions at other positions for secondary structures. The proposed secondary structure in the 5' NCR was similar to the prokaryotic ρ independent terminator. Short open reading frames in the 5' NCR were well conserved among pestiviruses.