We examined 46 samples of human interferons for the presence of pestivirus RNA by the reverse transcription-polymerase chain reaction, and found 30.4% were contaminated with pestivirus RNA. Comparative analysis of nucleotide sequences in the 5' untranslated region (UTR) of the pestivirus RNA detected from the interferons indicated that the contaminants are derived from bovine viral diarrhea virus, and that there are at least three genotypes, I, II and III, among them. The incidence of genotypes I, II and III was 86%, 7% and 7%, respectively. Most of the nucleotide changes at variable regions in the 5' UTR were covariant, with complementary substitutions at other positions of the stem regions in secondary structures.