We describe a novel chromosomal aberration acquired in blast crisis (BC) in a patient affected by Philadelphia-positive chronic myeloid leukemia (CML). Conventional cytogenetic studies at onset showed a classic t(9;22)(q34;q11.2) in all bone marrow cells, confirmed by fluorescence in situ hybridization and reverse transcription-polymerase chain reaction (b3a2) analysis. In BC, the malignant clone developed a new additional cytogenetic abnormality consisting of a deletion of chromosome 21. To our knowledge, this is the first case of del(21) reported in literature associated with BC CML. The use of an appropriate set of BAC/PAC clones restricted the breakpoint to an interval of approximately 100 kb. Sequence analysis did not reveal any known gene in this interval. Oncosuppressor genes distal to the breakpoint could be hypothesized to be involved in the progression of disease toward BC. Identification of new chromosome abnormalities in CML may allow further understanding of specific molecular events leading to disease evolution.