Viruses have been proposed as etiologic cofactors in the pathogenesis of HIV-related neurological disease. To investigate the etiologic potential of Borna disease virus (BDV) in these disorders, two populations were studied: (1) 27 prospectively identified patients with various neurological disorders were evaluated with BDV RT-PCR (CSF, PBMC), and BDV serology, and (2) a separate group of 25 retrospectively studied patients with AIDS dementia complex was evaluated using BDV serology only. A novel, BDV p40 gene RT-PCR assay was developed: conserved primers were used in a non-nested amplification, detecting less than 100 BDV RNA copies and all of nine wild-type, confirmed animal BDV infections. BDV seroprevalences were 12.5% and 8.0%, respectively, which are similar to the general HIV-infected population. None of the prospectively studied patients had detectable BDV RNA in their CSF or PBMC. Our findings do not support the hypothesis that BDV infections are responsible for HIV-related neurological disorders.