A real-time quantitative polymerase chain reaction assay was devised to determine the load of human herpesvirus (HHV)-6A and -6B DNA in paired samples of plasma and peripheral blood leukocytes (PBL) of 25 bone marrow transplant patients. The assay detects HHV-6 DNA variants A and B in a linear range of 10(7)-10(1) genome equivalents per assay. Viral DNA was measured in 336 paired DNA PBL samples and in corresponding plasma samples. HHV-6A and/or -6B DNA was detected in PBL of 23 of 25 patients and in plasma of 24 of 25 patients. HHV-6B was the predominant variant found in PBL and also was detected in the corresponding plasma. Surprisingly, only 1 of 25 patients had detectable HHV-6A DNA in PBL, although 23 of 25 patients were positive for HHV-6A DNA in plasma. HHV-6 DNA load in plasma was significantly higher for HHV-6A than for HHV-6B (P=.0066).