A 52-year-old woman presented with isolated thrombocytosis in 2003. After 5 years of observation under a tentative diagnosis of essential thrombocythemia (ET), she was referred to our hospital because of anemia and leukopenia. Bone marrow biopsy demonstrated increases of megakaryocytes and myelofibrosis, but splenomegaly was absent. A karyotype study of bone marrow detected t(9;22) (q34;q11.2) in 6 of the 20 metaphases studied. Peripheral blood neutrophil BCA-ABL fusion signals (FISH) were not detected. Because RT-PCR assay of bone marrow detected major-BCR-ABL mRNA (b3a2), treatment with imatinib (400 mg/day) was started. After transient thrombocytopenia, normalization of blood cell counts and improvement of myelofibrosis were achieved. JAK2 V617F mutation and M-BCR-ABL mRNA was negative in peripheral blood. Clinical and laboratory data suggest that this case represents a rare and atypical myeloproliferative neoplasm with BCR-ABL translocation restricted mainly to the megakaryocyte lineage.