Lysosomal proteases are abundantly expressed in fetal muscles, but poorly represented in the adult skeletal muscles. The lysosomal proteolytic system is nonetheless stimulated in adult muscles in a variety of pathological conditions. Furthermore, recent investigations describe autophagosomes in muscle fibers in vitro and in vivo, and report myopathies with excessive autophagy. This review presents our current knowledge about the lysosomal proteolytic system and summarizes the evidences pertaining to the role of lysosomes and autophagosomes in muscle physiology and pathology.