Three alpacas (Vicugna pacos) aged two to 22 months with a history of illthrift and diarrhoea were examined postmortem, and tissues were collected for histology, including immunohistochemical labelling for pestivirus antigen, virus isolation and TaqMan reverse transcriptase-pcr assay. Blood samples from two clinical cases and the remaining herd members were tested for bovine viral diarrhoea virus (bvdv) antibody by serum neutralisation, antigen detection and pcr assay. The three affected alpacas were positive for bvdv by pcr of splenic tissue and/or heparinised blood. Non-cytopathic bvdv was isolated from several tissues and plasma of two of the alpacas. dna sequencing and phylogenetic analysis of the viral genome from the pcr product showed that the bvdv was of subgenotype 1b. Immunohistochemical examination of brain tissue was positive in two cases, consistent with a persistent infection. bvdv antibodies were detected in 16 of 25 clinically unaffected alpacas. There was no evidence of persistent infection in the in-contact animals. The source of the infection was not determined.