Autophagy is a degradation system for intracellular components. One of the roles of autophagy is the prompt removal of damaged organelles. Another unique role is to supply resources that maintain metabolism in response to the cellular nutritional state. Precise management of all the components in the autophagic system is essential for cellular health. Especially important are the selectivity of target cargos for autophagy, and the coordination of autophagy with the lysosomal catabolic process. This review outlines our current understanding of autophagy and discusses potential therapeutic perspectives. Emphasis will be given to lysosomal function as a central controller of metabolism, and to selective autophagy as a key mechanism for the efficient removal of dysfunctional organelles.