Infectious diseases are serious constraints for improving livestock productivity. Bovine viral diarrhoea virus (BVDV) is a virus causing grave economic losses throughout the cattle producing world. Infection is often not apparent, but the virus can also cause respiratory signs, diarrhoea, reproductive problems and immunosuppression. Risk factors for disease transmission include, but are not limited to, herd size, animal trade and grazing on communal pastures. Several prevalence studies have been conducted in southern Africa, but in Botswana the occurrence is largely unknown. In this study, blood samples were obtained from 100 goats from three villages around the capital city, Gaborone. Also, 364 blood samples from cattle around Gaborone, collected as part of another study, were analysed. The detected antibody prevalence was 0% in goats and 53.6% in cattle when using a competitive enzyme-linked immunoassay. Three animals from two different herds were positive for viral nucleic acids on polymerase chain reaction. The two herds with viraemic animals had significantly higher antibody prevalence compared to the other herds. Also, two of the detected viruses were sequenced and found to be most similar to BVDV-1a. To the authors’ knowledge, this is the first time that sequencing has been performed on BVDV isolated in Botswana.