All cellular components are subjected to continuous surveillance by intracellular quality control systems. The major players involved in this quality control are molecular chaperones, which detect the abnormal components, and proteases, which eliminate them from the cell. Malfunctioning of the cellular surveillance systems inexorably leads to cell toxicity, and often cell death, due to the accumulation of unwanted nonfunctional components inside cells. In this work, we review the contribution of the autophagic system to cellular quality control and the consequences that autophagy malfunction has on cellular function. Special emphasis is made on the recently identified role of this system in maintenance of neuronal homeostasis and in the links currently established between alterations in the autophagic system and major neurodegenerative disorders such as Alzheimer’s disease, Parkinson’s disease, and Huntington’s disease.