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Tendon injuries, bone defects, and cartilage defects are complex clinical conditions leading to pain and dysfunctions. Tendon, bone, and cartilage are highly specialized and organized tissues, and the self-healing may be limited by their histologic features, or impaired by the local conditions. Furthermore, the resultant tissue often shows inferior properties compared with native tissue, leading to high rates of reruptures and revision surgeries. A growing field of research has explored tendon, bone, and cartilage regeneration using mesenchymal stem cells (MSCs), because of their multipotency, and because they are relatively easy to harvest. Great expectations arose from the use of MSCs in regenerative medicine in the last decade, although both the potential and the drawbacks of this method remain under reflection. This is a narrative review of the literature about different strategies to differentiate MSCs into tenocytes, osteoblasts, and chondrocytes. Challenges and limitations on the use of MSCs in vivo and in clinical practice are also discussed.