Stem cell therapy holds the promise to treat degenerative diseases, cancer and repair of damaged tissues for which there are currently no or limited therapeutic options. The potential of stem cell therapies has long been recognised and the creation of induced pluripotent stem cells (iPSC) has boosted the stem cell field leading to increasing development and scientific knowledge. Despite the clinical potential of stem cell based medicinal products there are also potential and unanticipated risks. These risks deserve a thorough discussion within the perspective of current scientific knowledge and experience. Evaluation of potential risks should be a prerequisite step before clinical use of stem cell based medicinal products.The risk profile of stem cell based medicinal products depends on many risk factors, which include the type of stem cells, their differentiation status and proliferation capacity, the route of administration, the intended location, in vitro culture and/or other manipulation steps, irreversibility of treatment, need/possibility for concurrent tissue regeneration in case of irreversible tissue loss, and long-term survival of engrafted cells. Together these factors determine the risk profile associated with a stem cell based medicinal product. The identified risks (i.e. risks identified in clinical experience) or potential/theoretical risks (i.e. risks observed in animal studies) include tumour formation, unwanted immune responses and the transmission of adventitious agents.Currently, there is no clinical experience with pluripotent stem cells (i.e. embryonal stem cells and iPSC). Based on their characteristics of unlimited self-renewal and high proliferation rate the risks associated with a product containing these cells (e.g. risk on tumour formation) are considered high, if not perceived to be unacceptable. In contrast, the vast majority of small-sized clinical trials conducted with mesenchymal stem/stromal cells (MSC) in regenerative medicine applications has not reported major health concerns, suggesting that MSC therapies could be relatively safe. However, in some clinical trials serious adverse events have been reported, which emphasizes the need for additional knowledge, particularly with regard to biological mechanisms and long term safety.