We studied a patient with hypereosinophilic syndrome (HES) who had myeloproliferative features, was unresponsive to imatinib mesylate, and showed cyclic oscillations in blood cell counts. No rearrangement in PDGFRA, PDGFRB and ETV6 genes was detected. Clonal analysis of hematopoiesis consistently showed skewed X-chromosome inactivation patterns in both granulocytes and T-lymphocytes, indicating a clonal myeloproliferative disorder originating in a pluripotent stem cell.