Cell-based therapies have taken the emerging field in many clinical directions. Among them, orthopaedic surgery is one of the most promising directions – due to the clinical needs, and because of the availability of the advanced cell-based constructs dedicated to bone and cartilage regeneration. The current practical clinical input is, however, below expectations – because of numerous difficulties which have their source in scientific, practical, finance and legal issues. Regarding legal issues, Advanced Therapy Investigational Medicinal Products (ATIMP) are regulated by three different legal orders. As medicines (according to the EU law, ATIMP is a pharmaceutical) – they are subject to pharmaceutical law; as cell-containing specimens – to cell and tissue banking regulations; as tested by registered clinical trials - they are subject to Good Clinical Practice rules and regulations. Formal requirements coming from these three areas are completely different, sometimes contradictory and incompatible with the specific nature of cell-based products. At the same time they involves the need for huge financial expenditures. We discuss these issues from the perspective of the university laboratory, which currently conducts clinical trials of the ATIMPs for three different clinical indications and, at the same time, has experience in the basic and applied scientific work at the laboratory level – towards improvement of osteogenic capacity of stem cells. With the undoubtful need of well documented scientific results, which is accompanied by complicated and imperfect regulations, we think that the scientific community focused around cellular therapies is now facing challenges that may determine the future of this field.