Cancer stem cells, previously identified in acute leukemias, have now been isolated from several human malignancies, such as breast, brain and gastrointestinal tumors. The origin of these cells is still questionable, but a growing body of evidence supports the idea that they are responsible for tumor growth and maintenance. For this reason, they have become a primary subject of investigation with a view to developing novel therapies that might lead to the eradication of neoplastic diseases. As previously demonstrated, cancer stem cells in haematological diseases have biological properties similar to those of normal adult stem cells. Therefore, better knowledge of the apoptotic machinery in stem cells might help in the development of targeted therapy for treating cancers. In this review, we discuss some concepts relating to stem cell biology, focusing on the apoptotic responses of haematopoietic and neural stem cells to conventional and novel cancer treatment strategies.