Protein conformation disorders or proteinopathies are a growing family of human diseases that are characterized by the accumulation of proteins in intracellular aggregates (also known as inclusions) in specific tissues/organs. The role of aggregates in these diseases has been a subject of vigorous debate. However, irrespective of the nature(s) of the toxic species, it is desirable for cells to be able to control the levels of these toxic proteins and restrict their accumulation. Here we discuss how the autophagy-lysosome pathway may regulate protein clearance in some of the protein conformation disorders and why this pathway may represent a possible therapeutic target in such conditions.