We report a case of a 51-year-old woman with newly diagnosed glioblastoma multiforme (GBM) who was treated with surgery followed by the standard concomitant temozolomide (TMZ) and radiotherapy (RT). Although TMZ is generally safe and well-tolerated, she developed a sudden onset of prolonged and severe thrombocytopenia as the most prominent event of pancytopenia during the combined treatment, leading to discontinuation of the combined therapy. Thrombocytopenia lasted for more than 2 months with intensive, intermittent platelet transfusions. A bone marrow aspiration and biopsy performed after recovery of severe suppression still revealed reduced number of megakaryocytes. O(6)-methylguanine-DNA methyltransferase (MGMT) analyses showed methylated MGMT promoter in GBM, but unmethylated promoters in both peripheral blood leukocytes and bone marrow cells. This is the first report suggesting the irrelevance of MGMT status of normal hematopoietic cells to TMZ-induced severe thrombocytopenia and pancytopenia.