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Structural abnormalities of the long arm of chromosome 3 (3q) have been associated with elevated platelet count and hyperplasia of megakaryocytes with dysplasia in various hematological malignancies. Some cases of chronic myeloid leukemia (CML) may acquire inv(3) (q21q26) or t(3;3)(q21;q26), and such a finding usually indicates accelerated or blast phase of their disease. We report a case of concomitant inv(3) (q21q26) and cryptic BCR/ABL1 rearrangement in the blast crisis of CML. The patient was 17-year-old male and showed marked leukocytosis and thrombocytosis at admission. Leukocyte differentials showed eosinophilia, basophilia and increased blasts. The bone marrow was hypercellular with granulocytic hyperplasia, and dysmorphic megakaryocytes were frequently observed. Conventional cytogenetic analysis revealed only an inv(3)(q21q26)and no Philadelphia chromosome was observed. FISH and RT-PCR analyses confirmed cryptic BCR/ABL1 rearrangement. The patient responded poorly with imatinib and induction chemotherapy, and expired during the course of 2nd chemotherapy with increased dose of imatinib.