Philadelphia (Ph) chromosome as a result of t (9; 22) (q34; q11) is observed in more than 90% of chromic myeloid leukemia (CML) patients. Cases in which the typical Ph chromosome is not visible at the karyotype level comprise 5-10% of CML patients. CML cases with fusion transcripts such as e13a3 in which ABL exon 3 rather than exon 2 has fused to BCR are very rare. Such reported cases with the e13a3 transcript show the Ph chromosome on karyotype analysis. We reported an atypical karyotype CML patient with the e13a3 BCR-ABL transcript caused by complex translocation. Fluorescence in situ hybridization (FISH) analysis of the metaphase led to a precise cytogenetical characterization. The patient showed favorable response to imatinib, and achieved major molecular responses.