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The aim of this study was to correlate human herpesvirus (HHV)‐6 viral load with clinical symptoms in allogeneic stem cell transplant (SCT) patients. Seventy‐four patients were monitored during the first 3 months after SCT using a qualitative polymerase chain reaction (PCR) for HHV‐6 DNA. HHV‐6 was detected in 181 out of 494 samples (36%) from 58 (78%) patients. These 181 samples were analysed using a quantitative competitive PCR. DNA could be quantified from 146 out of 181 samples (80·6%). The HHV‐6 viral load was highest at 4 weeks compared with 8 weeks (P < 0·001) and 12 weeks (P = 0·01) after SCT. Three patients had HHV‐6 encephalitis and one patient had hepatitis. The HHV‐6 DNA levels were higher in patients with HHV‐6 than in those without HHV‐6 (P = 0·01). Patients who received grafts from unrelated or HLA‐mismatched family donors had significantly higher HHV‐6 DNA …