Protein aggregation trends in neurodegenerative diseases are largely unmapped due to the complex nature of protein-protein interactions and their regulatory machineries such as protein proteolytic systems. Since the protein aggregation process in humans is a slow process, early determination of the patients that will develop neurodegenerative diseases later in life is critical in terms of starting effective treatment, which will reduce the expensive health care. In this chapter, I will discuss the nature of protein aggregation of signature proteins and the status of protein proteolytic systems such as proteasome and autophagosome in Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, frontotemporal lobar degeneration, Huntington's disease, and prion disease under the light of recent studies including our new findings.