Human herpesvirus-6 (HHV-6) is known to cause critical encephalitis, as a central nervous system infection, in some hematopoietic stem cell transplantation (HSCT) recipients. Chromosomally integrated human herpesvirus-6 (CIHHV-6) persistently shows HHV-6 DNA in blood, but this does not necessarily suggest active infection. The true clinical significance in HSCT is not clear. The prevalence of CIHHV-6 in Japan is reportedly 0.21%. We herein report two HSCTs: from a CIHHV-6-positive donor to a negative recipient and from a negative donor to a positive recipient. In the CIHHV-6-positive donor case, the recipient's plasma, which had been negative for HHV-6 before HSCT, became positive after transplantation and the level then remained high, although the subject was asymptomatic. In the CIHHV-6-positive recipient case, the patient's plasma viral load was high just after transplantation, although the subject was asymptomatic, and the load gradually decreased after engraftment. Antivirals had no effect on the viral load in either case. We should consider CIHHV-6 when the HHV-6 DNA load in blood persists asymptomatically after HSCT, to avoid misdiagnosis of reactivated HHV-6 infection and overuse of antivirals. It is also useful to monitor HHV-6 DNA in blood before HSCT, to distinguish HHV-6 reactivation from CIHHV-6.