To determine the incidence and clinical relevance of active human herpesvirus 6 (HHV-6) infection, 92 consecutive unselected recipients of autologous or allogeneic stem cell grafts were investigated in a prospective longitudinal study. Active infection was assessed by the presence of viral deoxyribonucleic acid (DNA) in 846 peripheral blood mononuclear cell specimens and 115 plasma specimens, by means of a specially developed polymerase chain reaction designed to avoid detection of latent genome. The incidence of HHV-6 infection observed was 42.5%, irrespective of the type or source of graft, and infection was significantly associated with partial (P=.002) or total myelosuppression (P=.01) and fever (P<. 000001). Infusion of bone marrow as the source of graft, reactivation occurring before platelet or neutrophil engraftment, and presence of HHV-6 DNA in plasma were identified as risk factors for symptomatic HHV-6 infection (P<.002).