Specific PCR primers were selected for each pestivirus genotype which flanked the 3′-part of the NS5B gene and more than three quarters of the 3′-UTR. PCR products were sequenced in both directions using an automatic sequencing device and analyzed by computer package program DNASTAR. A comparative analysis of the 3′ untranslated region (3′-UTR) of 82 viruses, representing the four genotypes of the Pestivirus genus, provided a similar phylogenetic grouping as other genomic regions. Intertypic recombination was not observed, but Border disease virus (BDV) and Bovine viral diarrhoea virus type 1 (BVDV I) showed great intragenotypic variability. In most pestiviruses the stop codon is TGA, but BDV isolates were found to have either a TAG or a TAA stop codon. Various deletions and insertions were observed in the 3′-UTR region. Viruses of the BVDV Ib group contained a characteristic deletion of 41 nucleotides. Compared to the 5′-UTR, the 3′-UTR was less conserved. The first 50–60 nucleotides were particularly variable, whilst the most conserved part was found at the 3′ end of the studied region. All 82 viruses contained AT-rich stretches, the positions and sizes of which differed between the genotypes.