We report the case of a 42-year-old male who underwent allogeneic bone marrow transplantation (BMT) for acute myelogenous leukemia, and then developed pneumonitis with a bronchiolitis obliterans organizing pneumonia (BOOP)-like shadow. When he came with exertional dyspnea four months after BMT, the chest X-ray and CT findings disclosed bilateral infiltration, and remarkable elevation of his serum KL-6 level, a monitoring marker for disease activity in interstitial lung disease. Although organizing pneumonia (OP) was revealed by a transbronchial lung biopsy, no pathogen was detected in bacterial, fungal and routine viral cultures or by direct cytological examinations using bronchoalveolar lavage (BAL) specimens. Since human herpes virus-6 (HHV-6) was detected in BAL specimens by the polymerase chain reaction (PCR), a diagnosis of a pneumonitis-like BOOP shadow related to HHV-6 was made, and he was treated with methylprednisolone and ganciclovir (GCV). Although there was a relapse of his OP 1.5 months later, with re-elevation of his serum KL-6 level, continuous administration of GCV led to disappearance of HHV-6 in BAL specimens assayed by PCR, in association with normalization of the serum KL-6 level. HHV-6 should be considered as a cause of unexplained pneumonitis in BMT recipients, and KL-6 is useful for monitoring the pneumonitis status in these patients.