Imatinib has revolutionised the management of chronic phase chronic myelogenous leukemia (CML). Unfortunately it has had less of an impact on the management of the advanced phases of CML. These historically difficult-to-treat phases of disease remain largely resistant to therapy. Even when responses are obtained with the tyrosine kinase inhibitors, they are brief, particularly in blast phase (BP) disease. Allogeneic stem cell transplantation is the only curative option for these patients and should be considered early as an integral part of the treatment plan. But transplant outcomes are dependent on cytogenetic and gross disease burden at the time of transplant. This review will compare and contrast the various tyrosine kinase- and non-tyrosine kinase inhibitor-based treatments for accelerated and BP CML before allogeneic transplantation.