To establish a practical monitoring system of human herpesviruses reactivation in patients undergoing stem cell transplantation, we developed a new, very rapid, highly sensitive, and quantitative PCR assay for accurate measurement of human cytomegalovirus (CMV), human herpesvirus 6 (HHV-6) and Epstein-Barr virus (EBV) DNA using LightCycler. The LightCycler system revealed that there was a linear correlation in the wide range of viral template DNA at the indicated number of PCR cycles. Peripheral blood cells were collected from 16 patients undergoing stem cell transplantation. The cut-off level of CMV and HHV-6 was assessed as 10(2) copies/microg and that of EBV as 10(3). High numbers of CMV genomes were detected in 3/13 patients after transplant, and reactivation of HHV-6 was frequently seen, whereas none of the patient showed an elevation of EBV genome copies until the end of the observation period. In the present study, the reactivation of beta herpesviruses is associated with the occurrence of thrombotic microangiopathy (TMA) in two patients undergoing allogeneic BMT. Therefore, it may contribute in clarifying the pathological potential of human herpesviruses using a large number of clinical samples. Our results suggest that this system may be useful for monitoring viral reactivation.