Reactivation of human herpesvirus 6 (HHV-6) is common following allogeneic marrow transplantation, however, little is known about the immune control and pathogenic potential of HHV-6 infection after transplantation. In order to determine whether reactivation of HHV-6 plays an important role in the development of complications in patients undergoing allogeneic bone marrow transplantation or not, we developed a very rapid quantification of viral DNA using a LightCycler. The amount of viral DNA was determined using a supernatant of a chronically infected cell line [TaY(OK)] which contains a known amount of viral DNA. Peripheral blood cells were collected from 5 patients undergoing allogeneic bone marrow transplantation once before transplant and once per week after transplant for 8-24 weeks. The real-time PCR system revealed that there was a linear correlation in the range of 101 to 105 molecules of reference. Using this system, we have found the presence of non-diagnosed HHV-6 reactivation as well as symptomatic infection, indicating the potential for routine implementation of this technology for laboratory diagnosis of HHV-6 infection. Our study shows that this method of rapid quantification of HHV-6 genomes by the real-time PCR using a LightCycler may be useful not only to understand the reconstitution of the immune system following marrow transplantation but also to manage the care of patients.