The BCR-ABL1 oncoprotein is the cause of chronic myeloid leukemia and occurs as a consequence of the translocation t(9;22), a well-defined genetic event that results in the formation of the Philadelphia chromosome. While this genomic aberration is recognized to be the main culprit of the chronic phase of chronic myeloid leukemia, the natural clonal evolution of this myeloproliferative neoplasm involves the accumulation of secondary alterations through genomic instability. Thus, efforts to dissect the frequency and nature of the genomic events at diagnosis and at later stages are producing valuable insights into understanding the mechanisms of blastic transformation and development of resistance in chronic myeloid leukemia. The identification of alternative BCR-ABL1-dependent and BCR-ABL1-independent targets that sustain the survival of leukemic blasts and/or leukemia-initiating cells will facilitate the development of novel viable therapeutic options for patients who become resistant or intolerant to the currently available therapeutic options based on tyrosine kinase inhibitors.