Although some modulators of autophagy are emerging as drugs or supplements for anti-cancer therapy, the effects of these compounds on normal tissues must be examined carefully. Here, I review the role of autophagy in skeletal tissues in this context. First, I briefly review preclinical studies indicating the role of autophagy in cancer, as well as related on-going clinical trials. Thereafter, the role of autophagy in the physiology of skeletal tissues is discussed, with a focus on recent genetic preclinical studies. Specifically, I discuss the mTOR-autophagy pathway in relationship to epiphyseal chondrocytes, articular chondrocytes, osteoblasts, osteocytes and osteoclasts and potential side effects of targeting either mTOR pathway or autophagy in general in connection with anti-cancer therapy. Current preclinical findings indicate that inhibiting autophagy will not seriously reduce bone mass and enhance osteoporosis. However, inhibition of autophagy might damage articular cartilage and cause osteoarthritis, whereas treatment with rapalogs might result in relatively beneficial effects on articular cartilage. Modulation of the mTOR pathway or autophagy during childhood may have an undesirable influence on adult height, as well as acquisition of bone mass.