CFS, a recently named heterogeneous disorder, is an illness of unknown etiology, The association of CFS with viral infections has been suggested, A common association between CFS and several viruses examined has not been confirmed, Here, we centered on the possible link between CFS and BDV infection, By nested RT-PCR followed by hybridization, BDV RNA was demonstrated as a clear signal in PBMCs in 3 out of 25 CFS patients, The amplified cDNA fragments were cloned and sequenced, A total of 16 clones were studied, Intra-patients divergencies of the p24 were 2-9%, 3-20%, and 3-11% in the deduced amino acids, Inter-patient divergencies among the 16 clones were 3-24%, Antibodies to recombinant BDV p24 protein were detected in 6 CFS patients including one carrying BDV RNA, Overall, these gave the prevalence of 32% (8/25) in Japanese CFS patients, suggesting that Japanese CFS is highly associated with active infection of BDV, or a related agent.