The present review examines in the first place various kinds of naturally occurring stem cells, including germ cells and embryonic stem cells (ES cells), as well as haemopoietic stem cells, which are historically the first to be used for medical treatment. Attention is also given to cancer stem cells, as a source of perseverant malignant disease. The main interest is now represented by the variety of somatic cells, which can be re-programmed to different types of differentiated cells, the so-called induced pluripotent stem cells (IPSC’s). Focus is now directed not only to the factors which make such events possible like de-differentiation and reconversion but also to the stages involved in this process. It is actually postulated that the transition from differentiated cells to pluripotent cells follows a definite sequence with evidence of two waves of gene regulations. Main applications of stem cell therapy are reviewed, from the established use of haemopoietic stem cells for clinical transplantation in a variety of haematological disorders to the initial attempts to employ stem cells for the treatment of other disparate conditions. Problems related to stem cell treatment with both ES and IPS cells, like the necessity of a large in vitro expansion to provide sufficient amounts of cells and the related risk of genomic abnormalities are illustrated. The necessity of safe procedures for the development of this venture is also outlined.