Derived from different origins in the human body, stem cells are a source of cells that can be transformed into different types of cell structures. Stem cell studies are increasing in clinical treatments day by day. Mesenchymal stem cells are the most commonly used type of stem cells. Mesenchymal stem cells present applications for treatment in different areas of clinical studies. Some of these studies are cell-based therapies, gene carriers, and in particular the application of tissue-engineering as an up-to-date and popular engineering practice. Clinical studies rapidly continue with regards to the applications of mesenchymal stem cells and tissue-engineering, such as bone tissue-engineering, bone defects and spinal cord injuries. In this review, we explain stem cells, mesenchymal stem cells, clinical studies in relation to their application areas and bone tissue-engineering applications.