Borna disease virus (BDV) was previously believed to have a strict tropism for the nervous system. BDV has recently been identified by a reverse transcription-polymerization chain reaction-enzyme immunosorbent assay (RT-PCR-EIA) in bone marrow cells and peripheral blood mononuclear cells (PBMC) in BDV-infected Lewis rats. We now report the identification of BDV RNA and infectious virus in thymus cells from rats infected either as neonates (PTI-NB) or as adults (4 weeks of age). Based on in vitro studies, we determined that the BDV-infected cells in bone marrow and thymus tissue are fibroblastic stromal cells. Bone marrow stromal cells are nonhematopoietic, fixed-tissue elements that support hematopoiesis, and, thus, it was not surprising that BDV infection altered the recovery from granulocytopenia and leukocytopenia after myelosuppressive treatment. Notably, unlike other immunotropic and neurotropic viruses, BDV does not appear to infect cells of myeloid or lymphoid lineages. We also report the association between BDV in the thymus with the lack, or loss, of encephalitis in neonatally inoculated rats or adult-inoculated rats during the chronic stage of disease.