Autophagy is a self-protective mechanism of living cells or organisms under various stress conditions. Studies of human genetics and pathophysiology have implicated that alterations in autophagy affect the context of cellular homeostasis and disease-associated phenotypes. The molecular components of autophagy are currently being explored as new pharmacologic targets for drug development and therapeutic intervention of various diseases. Drugs that restore the normal autophagic pathways have the potential for effectively treating human disorders that depend on aberrations of autophagy. Here, we review the role of autophagy and its alterations in the pathogenesis of diverse diseases, and drug discovery strategies for modulating autophagy for therapeutic benefits as well as possible safety concerns and caveats associated with such approaches.