Since very few unusual BCR/ABL fusion transcripts in chronic myeloid leukemia have been reported, no clear evidence exists concerning their clinical and prognostic implications. We describe here a CML case with normal karyotype at standard cytogenetics and an atypical e6a2 BCR/ABL fusion transcript, presenting at diagnosis isolated thrombocytosis and mild leukopenia; the patient, who was tested negative for JAK2 mutation, obtained a complete response to imatinib. The few previous observations from literature are also reviewed.