The Philadelphia chromosome and its corresponding fusion gene, BCR-ABL, is one of the best-known genetic abnormalities in hematological malignancies. Major BCR-ABL translocation is much more common in chronic myelogenous leukemia (CML) and minor BCR-ABL in acute lymphoblastic leukemia. We experienced an extraordinarily rare case of CML with an e8a2 variant. An unusual band, other than the common transcripts, was observed in reverse transcription-polymerase chain reaction (RT-PCR) for the BCR-ABL gene rearrangement. Sequence analysis of the PCR product revealed an 1172-bp e8a2 fusion with a 14-bp insertion of ABL intron Ia. The patient achieved a complete hematological response 3 months after imatinib treatment. It is necessary to keep in mind that an unexpected band revealed with RT-PCR may mean the presence of unusual fusion gene.