Two children, 5 and 10 years of age, received unrelated cord blood transplantation (CBT) for malignant lymphoma. Both of them suffered from pleurisy with and without interstitial pneumonitis after transplantation. By the quantitative real-time polymerase chain reaction, human herpesvirus 6 (HHV-6) variant B DNA was detected in pleural effusion. This is the first report of HHV-6-associated pleurisy after hematopoietic stem cell transplantation. HHV-6-associated pleurisy should be considered as a complication after hematopoietic stem cell transplantation even in the absence of pneumonitis. Quantitative polymerase chain reaction is a useful tool for rapid detection of viral DNA, which may facilitate precise diagnosis and appropriate treatment.