Only a handful of cases of chromosomally integrated human herpesvirus 6 (CI-HHV-6) have been reported, suggesting that this phenomenon is rare. We here present a familial case of HHV-6 variant A (HHV-6A) transmission through a generation, which was identified in the setting of allogeneic hematopoietic stem cell transplantation (HSCT). A 31-year-old man with myelodysplastic syndrome underwent allogeneic HSCT from a human leukocyte antigen-identical sibling, and was found to be continuously yielding high copy numbers of HHV-6A DNA in plasma evaluated by real-time polymerase chain reaction (PCR). Antiviral therapy with ganciclovir or foscarnet failed to decrease the copy numbers. HHV-6A DNA was detected in the patient's buccal mucosa and hair follicles, and was also detected in the plasma, whole blood, and buccal mucosa of the patient's father and 2 siblings, but not in his mother. The sequences of HHV-6A DNA isolated from all family members were identical. Since monitoring of HHV-6 by PCR has been widely introduced to the field of HSCT, transplant physicians should be aware of such an alternative form of HHV-6 transmission, particularly when HHV-6A is detected.