Amplification/duplication of the BCR-ABL gene has been found to be one of the key factors leading to drug resistance to imatinib mesylate (IM). In the present study, we used G-banding to identify the presence of de novo identical isodicentric chromosomes in IM-resistant patients. Fluorescence in situ hybridization (FISH) analysis on interphase nuclei confirmed the heterogeneity and amplification of the fused BCR-ABL gene. FISH analysis superimposed on G-banding confirmed the presence of isodicentric Philadelphia chromosomes. The impact of the isodicentric Philadelphia chromosomes on genomic instability, heterogeneity, and amplification of the Philadelphia chromosomes in IM-resistant patients is discussed.