Malignancies in the haematopoietic system seem to depend on a small subset of so-called cancer stem cells (CSC) for their continued growth and progression - this was first described as the "sleeper-feeder theory" for leukaemia. The leukaemia stem cell was the first of such subsets to be described although the origins of these cells have been difficult to dissect. Consequently, their biology is not fully elucidated, which also holds true for the normal-tissue counterparts. The stem cell concept describes stem cells to be of low frequency, self renewing and with multilineage potential based on phenomenology - a definition which may not hold strictly true for CSCs when studied in animals and humans in vivo and in vitro. Several studies have analysed the cellular hierarchy of the haematopoietic system by cell sorting of few and even single cells, tracking acquired genetic changes and performing transplantation model studies to document subsets within the differentiating hierarchy as potential CSC compartments. In leukaemia the CSC has been described in the bone marrow compartment of haematopoietic stem cells (HSC); however, in other bone marrow disorders like multiple myeloma it is likely that the cell of origin is a more differentiated cell, like post-germinal memory B cells or plasmablasts. Studies performed so far have even indicated that the genetic events may occur in different B cell subsets in accordance with the stepwise oncogenesis of the disease. Although our understanding of the nature and biology of these initiating cells remains unknown, the obvious existence of such cells has implications for understanding initial malignant transformation and disease metastasis or progression and, most important, the selection of individualised therapeutic strategies targeting the subsets harbouring the CSC function. In the present review on stem cells in haematological malignancies we have focused on two topics, first, describing the stem cell concept in health and disease, and its "phenomenology", and second, describing the CSC compartments in leukaemia and multiple myeloma.