Allogeneic stem cell transplantation (SCT) had traditionally been the first-line therapy of chronic myeloid leukaemia (CML), but the introduction of tyrosine kinase inhibitors (TKI) has caused a major change to the treatment algorithm. The majority of patients in chronic phase obtain an excellent response to these oral agents with minimal toxicity. SCT is therefore used only in a minority of patients who do not achieve adequate response to first-, second- or even third-generation agents. Patients in accelerated phase are less likely to achieve an optimal response and for patients in blast phase, SCT continues to be the only therapy with curative potential although it is now increasingly used in combination with TKI. This review discusses the place of SCT in the current therapy of CML.