The major autophagy alterations in human disease and examples of diseases for each class are listed. (A) In diseases with “overactive” autophagy, inhibition of autophagy (via 3-MA or CQ) may provide therapeutic benefit. In diseases that lead to a defect in (B) autophagy induction/initiation or (C) cargo recognition, patients may benefit from drugs such as rapamycin (Rap) that induce autophagy. (D) In diseases that lead to a block in autophagic maturation, Rap treatment may partially restore flux and provide a cytoprotective effect. Alternatively, in diseases with a severe block in autophagic maturation, blocking autophagy at an early step (e.g., via 3-MA) may be therapeutically useful because they mitigate the cytotoxic accumulation of autophagosomes and lysosomes.