Decades of research have shown that many, if not all, fully developed and differentiated organs and tissues contain a subpopulation of undifferentiated stem cells or progenitors of stem cells, which under natural or experimental conditions can self-renew and differentiate into specialised cells. These findings have opened countless possibilities of novel therapeutic applications for the treatment of adult and child diseases. The main sources of stem cells used in paediatric therapies are umbilical cord and umbilical cord blood, amniotic fluid, placenta, bone marrow, adipose tissue, urine, and induced pluripotent stem cells derived from the patient's cells. Here, we describe some of the paediatrically applicable stem cell therapies. We focus our attention on the therapeutic applications of mesenchymal stem cells in paediatric diseases. An important but negative effect of stem cell therapies is the risk of oncogenic potential of therapeutically applied stem cells. Under certain circumstances, these stem cells can lead to tumour development. In addition, the majority of adult and paediatric tumours contain a subpopulation of cancer stem cells which are privileged therapeutic targets for numerous paediatric cancers. In this article, we review these two opposite properties ("double face") of stem cells in general and paediatric medicine.