Jembrana disease virus (JDV) is a lentivirus that causes an acute, severe disease syndrome in infected Bali cattle in Indonesia. An in situ hybridization technique was developed that detected JDV genomic RNA in formalin-fixed paraffin-embedded tissue sections, using a digoxigenin-labelled riboprobe. Large numbers of JDV-infected cells were demonstrated in many tissue sections from experimentally infected animals early in the disease course, which was consistent with the extremely high circulating viraemia previously reported to occur during the febrile phase. The number of infected cells was consistently highest in sections of spleen, followed by many other tissues including lymph nodes, lungs, bone marrow, liver and kidney. Infected cells were also identified in the general circulation and within unusual intravascular lesions in lung sections. The relatively high level of infection found in bone marrow suggested that its involvement may be important in the disease pathogenesis, as it is with other lentiviruses.