Seventy three field isolates of bovine viral diarrhoea virus (BVDV), obtained from cattle in Mozambique and South Africa, were characterised by comparative nucleotide sequence analysis of part of the 5' non-coding region (5'NCR) of the viral genome. The target region was amplified by reverse transcription-polymerase chain reaction (RT-PCR). The amplicons were cloned in pUC 19 plasmid and both strands were sequenced by T7 polymerase dideoxynucleotide chain-termination sequencing or directly by cycle sequencing. The 245 base pair (bp) nucleotide sequences, derived from the 5'NCR, were aligned and compared to the corresponding positions of published sequences of BVDV type I and II strains and of pestiviruses of ovine and porcine origin. The phylogenetic trees, generated from those comparisons, allowed the Southern African isolates to be assigned to two main groups within the BVDV I genotype. Group A could be subdivided into three clusters, two of which grouped with BVDV strains of European and American origin. The third cluster did not group with any known BVDV I strains and it was confirmed in a comparison from the NS3 coding region. Group B contained more divergent isolates which differed by 18-23%, from BVDV I reference strains NADL, Osloss and SD-1 and comprised another distinct subset within the BVDV I genotype. This grouping was consistent in a comparison involving the NS2-NS3 region. It was concluded that BVD viruses occurring in Southern Africa are genetically diverse, comprising different variants within the BVDV I genotype. They include viruses similar to BVDVs found in Europe and America and others apparently rare or absent in those continents, termed here as BVDV Ic and Id. The co-existence of BVDV strains of European and American origin in certain areas both in Mozambique and South Africa, indicates a probable introduction of those viruses through imports of cattle or through potentially infectious bovine products. In addition, the detection of isolates apparently rare or absent from Europe and America may indicate the presence of African variants of BVDV I (Pestivirus 1).