We report a case of chronic myeloid leukemia in chronic stage with 48 chromosomes and four BCR/ABL1 fusion signals on two out of three chromosomes 9 and two signals on the two Philadelphia chromosomes. These abnormalities were detected by both conventional cytogenetic analysis and metaphase and interphase fluorescence in situ hybridization studies in approximately 90% of the cells at diagnosis. Real-time-polymerase chain reaction studies on peripheral blood showed b3a2(p210) and e1a2(p190) BCR/ABL1 fusion transcripts. During treatment with imatinib, the patient was asymptomatic with hematological remission. Cytogenetic and fluorescence in situ hybridization analysis revealed that only 6.6% of cells had the initial majority line karyotype, with disappearance of the p210 but increased p190 transcript, which led to the treatment being changed. We discuss the implication of cytogenetic and molecular alterations in the patient's evolution and treatment.