Autophagy is a tightly regulated pathway for the degradation and recycling of proteins delivered to lysosomes, and is an important process in maintaining cellular homeostasis. Whereas a basal level of autophagy can be detected in skeletal muscles, its perturbation can be seen in a variety of conditions affecting the muscle. In certain muscle diseases, moreover, autophagy seems to be a characteristic feature, although the exact role of autophagy in these disorders is just starting to be understood. As autophagy is not only an index of disease progression but also a potential target for treatment in certain disease conditions, its characterization is indeed of relevance. Thus, in this chapter, methods applicable to both human and murine skeletal muscle preparation for the analysis and monitoring of autophagy are presented.