The rapid loss of muscle mass, which occurs with disuse and systemically with fasting, cancer and many other diseases, results primarily from accelerated breakdown of muscle proteins. In atrophying muscles, the ubiquitin-proteasome pathway catalyzes the accelerated degradation of myofibrillar proteins, but the possible importance of the autophagic/lysosomal pathway in atrophy has received little attention. Our prior studies demonstrate that activation of FoxO transcription factors is essential for muscle atrophy, and that activated FoxO3 by itself causes dramatic atrophy of muscles and cultured myotubes via transcription of a set of atrophy-related genes ("atrogenes") including critical ubiquitin ligases. Using selective inhibitors, we measured isotopically the actual contribution of proteasomes and lysosomes to the FoxO3-induced increase in protein breakdown in myotubes and found that FoxO3 coordinately activates both proteolytic systems, but especially lysosomal proteolysis. Activated FoxO3 stimulates autophagy through a transcription-dependent mechanism and increases the transcription of many autophagy-related genes, which are also induced in mouse muscles atrophying due to denervation or fasting. Thus, in atrophying muscles, decreased IGF1-PI3K-Akt signaling stimulates autophagy, not only through mTOR, but also more slowly by FoxO3-dependent transcription. These findings on muscle provide the first evidence for coordinate regulation of proteasomal and lysosomal systems, although in neuronal and hepatic cells, FoxO3 stimulates the autophagic process selectively.